Patent Application
20220011320
The ASCII file, entitled 88450SequenceListing.txt, created on Jul. 12, 2021, comprising 58,567 bytes, submitted concurrently with the filing of this application is incorporated herein by reference.
The present invention, in some embodiments thereof, relates to the identification of signatures and determinants associated with bacterial and viral infections. More specifically it was discovered that certain protein determinants are differentially expressed in a statistically significant manner in subjects with bacterial and viral infections.
Antibiotics are the world's most prescribed class of drugs with a 25-30 billion $US global market. Antibiotics are also the world's most misused drug with a significant fraction of all drugs (40-70%) being wrongly prescribed.
One type of antibiotics misuse is when the drug is administered in case of a non-bacterial disease, such as a viral infection, for which antibiotics is ineffective. For example, according to the USA center for disease control and prevention CDC, over 60 Million wrong antibiotics prescriptions are given annually to treat flu in the US. The health-care and economic consequences of the antibiotics over-prescription include: (i) the cost of antibiotics that are unnecessarily prescribed globally, estimated at >$10 billion annually; (ii) side effects resulting from unnecessary antibiotics treatment are reducing quality of healthcare, causing complications and prolonged hospitalization (e.g. allergic reactions, Antibiotics-associated diarrhea, intestinal yeast etc.) and (iii) the emergence of resistant strains of bacteria as a result of the overuse.
Resistance of microbial pathogens to antibiotics is increasing world-wide at an accelerating rate (“CDC—Get Smart: Fast Facts About Antibiotic Resistance” 2013; “European Surveillance of Antimicrobial Consumption Network (ESAC-Net)” 2014; “CDC—About Antimicrobial Resistance” 2013; “Threat Report 2013 I Antimicrobial Resistance|CDC” 2013), with a concomitant increase in morbidity and mortality associated with infections caused by antibiotic resistant pathogens (“Threat Report 2013|Antimicrobial Resistance|CDC” 2013). At least 2 million people are infected with antibiotic resistant bacteria each year in the US alone, and at least 23,000 people die as a direct result of these infections (“Threat Report 2013|Antimicrobial Resistance I CDC” 2013). In the European Union, an estimated 400,000 patients present with resistant bacterial strains each year, of which 25,000 patients die (“WHO Europe-Data and Statistics” 2014). Consequently, the World Health Organization has warned that therapeutic coverage will be insufficient within 10 years, putting the world at risk of entering a “post-antibiotic era”, in which antibiotics will no longer be effective against infectious diseases (“WHO I Antimicrobial Resistance” 2013). The CDC considers this phenomenon “one of the world's most pressing health problems in the 21st century” (“CDC—About Antimicrobial Resistance” 2013).
Antibiotics under-prescription is not uncommon either. For example up to 15% of adult bacterial pneumonia hospitalized patients in the US receive delayed or no Abx treatment, even though in these instances early treatment can save lives and reduce complications.
Technologies for infectious disease diagnostics have the potential to reduce the associated health and financial burden associated with antibiotics misuse. Ideally, such a technology should: (i) accurately differentiate between a bacterial and viral infections; (ii) be rapid (within minutes); (iii) be able to differentiate between pathogenic and non-pathogenic bacteria that are part of the body's natural flora; (iv) differentiate between mixed co-infections and pure viral infections and (v) be applicable in cases where the pathogen is inaccessible (e.g. sinusitis, pneumonia, otitis-media, bronchitis, etc).
Circulating host-proteins are routinely used to support diagnosis of infection (for example IL-6, PCT and CRP). However, these markers are sensitive to inter-patient variability, including time from symptom onset, clinical syndrome, and pathogen species [1-6]. For example, multiple studies found that procalcitonin is valuable for guiding antimicrobial therapy duration and for predicting disease severity [7-9], however its diagnostic accuracy for detecting bacterial etiology in cases such as sepsis and pneumonia has been challenged [1,10-13]. Elevated CRP levels are suggestive of a bacterial infection [14], but similar levels may be observed in patients with some viral strains (e.g., adenovirus and influenza) [15], and inflammatory diseases. Combinations of these proteins resulted in limited-to-moderate diagnostic improvement over individual proteins, presumably since they share biological pathways, and are thus inherently sensitive to the same factors.
To overcome this the present inventors have previously developed a multi-protein signature for distinguishing between bacterial and viral infections [16]. The signature includes both viral- and bacterial-induced proteins (TRAIL [TNF-related apoptosis-inducing ligand], CRP [C-reactive protein], IP-10 [Interferon gamma-induced protein-10]—TCP signature). When tested in a heterogeneous group of patients, in a clinical study that included 1002 subjects presenting with various acute infection conditions, the TCP signature demonstrated sensitivity of 92%±4 and specificity of 89%±3 [16].
Correct identification of bacterial patients is of high importance as these patients require antibiotic treatment and in some cases more aggressive management (hospitalization, additional diagnostic tests etc). Misclassification of bacterial patients increases the chance of morbidity and mortality. Therefore, increasing the sensitivity of a diagnostic test that distinguishes between bacterial and viral infections is desired, even at a cost of reduced specificity.
Additional background art includes US Patent Application No. 20080171323, WO2011/132086 and WO2013/117746.
According to an aspect of some embodiments of the present invention there is provided a method of distinguishing between an infective exacerbation state and a non-infective exacerbation state of chronic obstructive pulmonary disease (COPD) in a subject, the method comprising measuring the amount of at least two polypeptides selected from the group consisting of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP), Interferon gamma-induced protein 10 (IP10), Interleukin 6 (IL-6) and Procalcitonin (PCT) in a sample derived from the subject, wherein the amount is indicative of the exacerbation state of COPD.
According to an aspect of some embodiments of the present invention there is provided a method of distinguishing between sepsis and non-infective systemic inflammatory response syndrome (SIRS) comprising measuring the amount of at least two polypeptides selected from the group consisting of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP), Interferon gamma-induced protein 10 (IP10), Interleukin 6 (IL-6) and Procalcitonin (PCT) in a sample derived from the subject, wherein the amount is indicative of sepsis or non-infective SIRS.
According to an aspect of some embodiments of the present invention there is provided a method of ruling in sepsis in a subject suspected of having in infection comprising:
(a) measuring the amount of at least two polypeptides selected from the group consisting of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP), Interferon gamma-induced protein 10 (IP10), Interleukin 6 (IL-6) and Procalcitonin (PCT) in a sample derived from the subject;
(b) measuring the respiratory rate of the subject;
(c) analyzing the mental state of the subject; and
(d) measuring the blood pressure of the subject;
wherein when each of steps provide a result which is indicative of sepsis, sepsis is ruled in.
According to an aspect of some embodiments of the present invention there is provided a method of analyzing biological data, the method comprising:
obtaining biological data containing at least expression levels of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP), Interferon gamma-induced protein-10 (IP-10) and Interleukin 6 (IL-6) in the blood of a subject;
applying a non-linear multinomial logistic regression to expression levels of the TRAIL, the CRP, the IP-10 to provide a calculated score;
calculating a distance between a segment of a curved line and an axis defined by a direction, the distance being calculated at a point over the curved line defined by a coordinate δ along the direction; and correlating the distance to the presence of, absence of, or likelihood that the subject has, a bacterial infection;
wherein at least 90% of the segment is between a lower bound line f(δ)-ε0 and an upper bound line f(δ)+ε1, wherein the f(δ) equals 1/(1+exp(−δ)), wherein the coordinate δ, once calculated, equals a0+a1X+a2Y, wherein the X is a value of the calculated score, and the Y is a value of the IL-6 in pg/ml, wherein each of the ε0 and the ε1 is less than 0.5, and wherein a0 is from about 2.75 to about 3.40, a1 is from about 4.5 to about 5.5, and a2 is from about 0.0044 to about 0.0055.
According to an aspect of some embodiments of the present invention there is provided a method of analyzing biological data, the method comprising:
obtaining biological data containing at least expression levels of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP), Interferon gamma-induced protein-10 (IP-10) and Procalcitonin (PCT) in the blood of a subject;
applying a non-linear multinomial logistic regression to expression levels of the TRAIL, the CRP, the IP-10 to provide a calculated score;
calculating a distance between a segment of a curved line and an axis defined by a direction, the distance being calculated at a point over the curved line defined by a coordinate δ along the direction; and
correlating the distance to the presence of, absence of, or likelihood that the subject has, a bacterial infection;
wherein at least 90% of the segment is between a lower bound line f(δ)-ε0 and an upper bound line f(δ)+ε1, wherein the f(δ) equals 1/(1+exp(−δ)), wherein the coordinate δ, once calculated, equals a0+a1X+a2Y, wherein the X is a value of the calculated score, and the Y is a value of the PCT in μg/L, wherein each of the ε0 and the ε1 is less than 0.5, and wherein a0 is from about 2.70 to about 3.30, a1 is from about 4.55 to about 5.60, and a2 is from about 0.176 to about 0.215.
According to an aspect of some embodiments of the present invention there is provided a method of analyzing biological data, the method comprising:
obtaining biological data containing expression levels of C-reactive protein (CRP), Interleukin 6 (IL-6), and TNF-related apoptosis-inducing ligand (TRAIL) in the blood of a subject;
calculating a distance between a segment of a curved line and an axis defined by a direction, the distance being calculated at a point over the curved line defined by a coordinate δ along the direction; and
correlating the distance to the presence of, absence of, or likelihood that the subject has, a bacterial infection;
wherein at least 90% of the segment is between a lower bound line f(δ)-ε0 and an upper bound line f(δ)+ε1, wherein the f(δ) equals 1/(1+exp(−δ)), wherein the coordinate δ, once calculated, equals a0+a1X+a2Y+a3Z, wherein the X is a value of the CRP in μg/ml, the Y is a value of the IL-6 in pg/ml and the Z is a value of the TRAIL in pg/ml, wherein each of the ε0 and the ε1 is less than 0.5, and wherein a0 is from about −1.05 to about −0.85, a1 is from about 0.025 to about 0.032, a2 is from about 0.004 to about 0.006, and a3 is from about −0.022 to about −0.017.
According to an aspect of some embodiments of the present invention there is provided a method of analyzing biological data, the method comprising:
obtaining biological data containing expression levels of C-reactive protein (CRP), Procalcitonin (PCT), and TNF-related apoptosis-inducing ligand (TRAIL) in the blood of a subject;
calculating a distance between a segment of a curved line and an axis defined by a direction, the distance being calculated at a point over the curved line defined by a coordinate δ along the direction; and
correlating the distance to the presence of, absence of, or likelihood that the subject has, a bacterial infection;
wherein at least 90% of the segment is between a lower bound line f(δ)-ε0 and an upper bound line f(δ)+ε1, wherein the f(δ) equals 1/(1+exp(−δ)), wherein the coordinate δ, once calculated, equals a0+a1X+a2Y+a3Z, wherein the X is a value of the CRP in μg/ml, the Y is a value of the PCT in μg/L and the Z is a value of the TRAIL in pg/ml, wherein each of the ε0 and the ε1 is less than 0.5, and wherein a0 is from about −0.60 to about −0.48, a1 is from about 0.024 to about 0.31, a2 is from about 0.13 to about 0.16, and a3 is from about −0.025 to about −0.019.
According to an aspect of some embodiments of the present invention there is provided a method of analyzing biological data, the method comprising:
obtaining biological data containing expression levels of Interferon gamma-induced protein 10 (IP-10), Procalcitonin (PCT), and TNF-related apoptosis-inducing ligand (TRAIL) in the blood of a subject;
calculating a distance between a segment of a curved line and an axis defined by a direction, the distance being calculated at a point over the curved line defined by a coordinate δ along the direction; and
correlating the distance to the presence of, absence of, or likelihood that the subject has, a bacterial infection;
wherein at least 90% of the segment is between a lower bound line f(δ)-ε0 and an upper bound line f(δ)+ε1, wherein the f(δ) equals 1/(1+exp(−δ)), wherein the coordinate δ, once calculated, equals a0+a1X+a2Y+a3Z, wherein the X is a value of the IP-10 in μg/ml, the Y is a value of the PCT in μg/L and the Z is a value of the TRAIL in pg/ml, wherein each of the ε0 and the ε1 is less than 0.5, and wherein a0 is from about 1.42 to about 1.75, a1 is from about 0.00024 to about 0.00031, a2 is from about 0.23 to about 0.29, and a3 is from about −0.038 to about −0.030.
According to an aspect of some embodiments of the present invention there is provided a method of analyzing biological data, the method comprising:
obtaining biological data containing at least expression levels of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP), Interferon gamma-induced protein-10 (IP-10), Interleukin 6 (IL-6) and Procalcitonin (PCT) in the blood of a subject;
applying a non-linear multinomial logistic regression to expression levels of the TRAIL, the CRP, the IP-10 to provide a calculated score;
calculating a distance between a segment of a curved line and an axis defined by a direction, the distance being calculated at a point over the curved line defined by a coordinate δ along the direction; and
correlating the distance to the presence of, absence of, or likelihood that the subject has, a bacterial infection;
wherein at least 90% of the segment is between a lower bound line f(δ)-ε0 and an upper bound line f(δ)+ε1, wherein the f(δ) equals 1/(1+exp(−δ)), wherein the coordinate δ, once calculated, equals a0+a1X+a2Y+a3Z, wherein the X is a value of the calculated score, the Y is a value of the IL-6 in pg/L and the Z is a value of the PCT in μg/ml, wherein each of the ε0 and the ε1 is less than 0.5, and wherein a0 is from about −3.48 to about −2.84, a1 is from about 4.40 to about 5.39, a2 is from about 0.0041 to about 0.0051, and a3 is from about 0.14 to about 0.18.
According to an aspect of some embodiments of the present invention there is provided a method of analyzing biological data, the method comprising:
obtaining biological data containing expression levels of C-reactive protein (CRP), Interleukin 6 (IL-6), Procalcitonin (PCT), and TNF-related apoptosis-inducing ligand (TRAIL) in the blood of a subject;
calculating a distance between a segment of a curved line and an axis defined by a direction, the distance being calculated at a point over the curved line defined by a coordinate δ along the direction; and
correlating the distance to the presence of, absence of, or likelihood that the subject has, a bacterial infection;
wherein at least 90% of the segment is between a lower bound line f(δ)-ε0 and an upper bound line f(δ)+ε1, wherein the f(δ) equals 1/(1+exp(−δ)), wherein the coordinate δ, once calculated, equals a0+a1X+a2Y+a3Z+a4T, wherein the X is a value of the CRP in μg/ml, the Y is a value of the IL-6 in pg/ml, the Z is a value of the PCT in μg/L and the T is a value of the TRAIL in pg/ml, wherein each of the ε0 and the ε1 is less than 0.5, and wherein a0 is from about −1.13 to about −0.92, a1 is from about 0.025 to about 0.031, a2 is from about 0.0045 to about 0.0055, a3 is from about 0.098 to about 0.13 and a4 is from about −0.021 to about −0.016.
According to an aspect of some embodiments of the present invention there is provided a method of analyzing biological data, the method comprising:
obtaining biological data containing expression levels of Interleukin 6 (IL-6), Interferon gamma-induced protein-10 (IP-10), Procalcitonin (PCT), and TNF-related apoptosis-inducing ligand (TRAIL) in the blood of a subject;
calculating a distance between a segment of a curved line and an axis defined by a direction, the distance being calculated at a point over the curved line defined by a coordinate δ along the direction; and
correlating the distance to the presence of, absence of, or likelihood that the subject has, a bacterial infection;
wherein at least 90% of the segment is between a lower bound line f(δ)-ε0 and an upper bound line f(δ)+ε1, wherein the f(δ) equals 1/(1+exp(−δ)), wherein the coordinate δ, once calculated, equals a0+a1X+a2Y+a3Z+a4T, wherein the X is a value of the IL-6 in pg/ml, the Y is a value of the IP-10 in pg/ml, the Z is a value of the PCT in μg/L and the T is a value of the TRAIL in pg/ml, wherein each of the ε0 and the ε1 is less than 0.5, and wherein a0 is from about 1.029 to about 1.258, a1 is from about 0.0049 to about 0.0060, a2 is from about 0.00013 to about 0.00017, a3 is from about 0.19 to about 0.24 and a4 is from about −0.033 to about −0.027.
According to an aspect of some embodiments of the present invention there is provided a method of analyzing biological data, the method comprising:
obtaining biological data containing expression levels of C-reactive protein (CRP), Interleukin 6 (IL-6), Interferon gamma-induced protein-10 (IP-10), Procalcitonin (PCT), and TNF-related apoptosis-inducing ligand (TRAIL) in the blood of a subject;
calculating a distance between a segment of a curved line and an axis defined by a direction, the distance being calculated at a point over the curved line defined by a coordinate δ along the direction; and
correlating the distance to the presence of, absence of, or likelihood that the subject has, a bacterial infection;
wherein at least 90% of the segment is between a lower bound line f(δ)-ε0 and an upper bound line f(δ)+ε1, wherein the f(δ) equals 1/(1+exp(−δ)), wherein the coordinate δ, once calculated, equals a0+a1X+a2Y+a3Z+a4T+a5W, wherein the X is a value of the CRP in pg/ml, wherein the Y is a value of the IL-6 in pg/ml, the Z is a value of the IP-10 in pg/ml, the T is a value of the PCT in μg/L and the W is a value of the TRAIL in pg/ml, wherein each of the ε0 and the ε1 is less than 0.5, and wherein a0 is from about −3.08 to about −2.52, a1 is from about 0.10 to about 0.13, a2 is from about 0.038 to about 0.047, a3 is from about 0.008 to about 0.010, a4 is from about −0.17 to about −0.13 and as is from about 0.0044 to about 0.0054.
According to an aspect of some embodiments of the present invention there is provided a method of diagnosing an infection type in a subject comprising measuring the amount of at least two polypeptides selected from the group consisting of TRAIL, CRP, IP10, IL-6 and PCT in a sample derived from the subject, wherein the sample is derived from the subject no more than two days following symptom onset, wherein the amount is indicative of the infection type.
According to an aspect of some embodiments of the present invention there is provided a method of diagnosing an infection in a subject comprising measuring the amount of each of the polypeptides TRAIL, CRP, IP10 and at least one additional polypeptide selected from the group consisting of IL-6 and PCT in a sample derived from the subject, wherein the amount is indicative of the infection.
According to an aspect of some embodiments of the present invention there is provided a method of diagnosing an infection in a subject comprising measuring the amount of each of the polypeptides TRAIL, CRP and IL-6 in a sample derived from the subject, wherein the amount is indicative of the infection.
According to an aspect of some embodiments of the present invention there is provided a kit for diagnosing an infection comprising:
(i) an antibody which specifically detects TRAIL;
(ii) an antibody which specifically detects IP10:
(iii) an antibody which specifically detects CRP; and
(iv) at least one additional antibody which specifically detects IL-6 or PCT.
According to an aspect of some embodiments of the present invention there is provided a kit for diagnosing an infection comprising:
(i) an antibody which specifically detects TRAIL;
(ii) an antibody which specifically detects IL-6:
(iii) an antibody which specifically detects CRP; and
(iv) at least one additional antibody which specifically detects IP10 or PCT.
According to some embodiments of the invention, step (a) is effected prior to steps (b), (c) and (d).
According to some embodiments of the invention, step (a) is effected following steps (b), (c) and (d).
According to some embodiments of the invention, the at least two polypeptides comprises each of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP) and Interferon gamma-induced protein 10 (IP10).
According to some embodiments of the invention, the at least two polypeptides comprises each of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP), Interferon gamma-induced protein 10 (IP10), Interleukin 6 (IL-6) and Procalcitonin (PCT).
According to some embodiments of the invention, when the amount of TRAIL is below a predetermined level, the amount of CRP is above a predetermined level, the amount of IP-10 is below a predetermined level, the amount of PCT is above a predetermined level and the amount of IL-6 is above a predetermined level, the subject is diagnosed as having sepsis.
According to some embodiments of the invention, the at least two polypeptides comprises each of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP) and Interferon gamma-induced protein 10 (IP10).
According to some embodiments of the invention, the at least two polypeptides comprises each of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP), Interferon gamma-induced protein 10 (IP10), Interleukin 6 (IL-6) and Procalcitonin (PCT).
According to some embodiments of the invention, the sample is derived from the subject no more than one day following symptom onset.
According to some embodiments of the invention, the at least two polypeptides comprises each of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP) and Interferon gamma-induced protein 10 (IP10).
According to some embodiments of the invention, the at least two polypeptides comprises each of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP) and Procalcitonin (PCT).
According to some embodiments of the invention, the at least two polypeptides comprises each of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP), Interferon gamma-induced protein 10 (IP10), Interleukin 6 (IL-6) and Procalcitonin (PCT).
According to some embodiments of the invention, the level of the IL-6 and the PCT are taken into account when their concentration passes a threshold level, and are not taken into account otherwise.
According to some embodiments of the invention, the diagnosing is effected using an algorithm in which the weight of the IL-6 and the PCT increase as their concentration increases.
According to some embodiments of the invention, the method comprises measuring the amount of each of the polypeptides TRAIL, CRP, IP10, IL-6 and PCT in the sample.
According to some embodiments of the invention, when the amount of TRAIL is below a predetermined level, the amount of CRP is above a predetermined level, the amount of IP-10 is below a predetermined level and the amount of IL-6 is above a predetermined level, the infection is a bacterial infection or when the amount of TRAIL is below a predetermined level, the amount of CRP is above a predetermined level, the amount of IP-10 is below a predetermined level and the amount of PCT is above a predetermined level, the infection is a bacterial infection.
According to some embodiments of the invention, the amount of TRAIL is below a predetermined level, the amount of CRP is above a predetermined level, the amount of IP-10 is below a predetermined level, the amount of PCT is above a predetermined level and the amount of IL-6 is above a predetermined level, the infection is a bacterial infection.
According to some embodiments of the invention, the sample is derived from the subject no more than two days following symptom onset.
According to some embodiments of the invention, when the amount of TRAIL is below a predetermined level, the amount of CRP is above a predetermined level and the amount of IL-6 is above a predetermined level, the infection is a bacterial infection.
According to some embodiments of the invention, when the amount of TRAIL is above a predetermined level, the amount of CRP is below a predetermined level and the amount of IL-6 is below a predetermined level, the infection is a viral infection.
According to some embodiments of the invention, the method further comprises measuring the amount of IP10 or PCT.
According to some embodiments of the invention, the method further comprises measuring the amount of IP10 and PCT.
According to some embodiments of the invention, the method further comprises measuring the amount of at least one polypeptide set forth in Table 2.
According to some embodiments of the invention, the infection is a viral infection, a bacterial infection or a mixed infection.
According to some embodiments of the invention, the infection is sepsis.
According to some embodiments of the invention, no more than 20 polypeptides are measured.
According to some embodiments of the invention, the no more than 5 polypeptides which are differentially expressed in a statistically significant manner in subjects with a bacterial infection compared to subjects with a viral infection are measured.
According to some embodiments of the invention, the sample is whole blood or a fraction thereof.
According to some embodiments of the invention, the blood fraction sample comprises cells selected from the group consisting of lymphocytes, monocytes and granulocytes.
According to some embodiments of the invention, the blood fraction sample comprises serum or plasma.
According to some embodiments of the invention, the kit comprises antibodies which specifically detect the TRAIL, the IP10, the CRP, the IL-6 and the PCT.
According to some embodiments of the invention, the antibodies are attached to a detectable moiety.
According to some embodiments of the invention, the antibodies are attached to a solid support.
According to some embodiments of the invention, the kit comprises antibodies that specifically detect no more than 10 polypeptides.
According to some embodiments of the invention, the kit comprises antibodies that specifically detect no more than 5 polypeptides.
According to some embodiments of the invention, each of the additional antibodies comprise a detectable label selected from the group consisting of a radioactive label, a fluorescent label, a chemiluminescent label, a colorimetric label and an enzyme.
According to some embodiments of the invention, the enzyme is horseradish peroxidase or alkaline phosphatase.
According to some embodiments of the invention, the each of the antibodies are monoclonal antibodies.
According to some embodiments of the invention, the applying the non-linear multinomial logistic regression comprises calculating a value of probabilistic classification function which, once calculated, equals about exp(ξ)/(1+exp(ξ)+exp(η)), wherein ξ=b0+b1P+b2P0.5+b3P2+b4Q+b5R+b6R0.5 and i=c0+c1P+c2P0.5+c3P2+c4Q+c5R+c6R0.5, wherein the P is a value of the CRP, the Q is a value of the IP-10, and the R is a value of the TRAIL, and wherein b0 is from about 4.96 to about 6.1, b1 is from about −0.07 to about −0.05, b2 is from about 1.33 to about 1.64, b3 is from about 0.000031 to about 0.000039, b4 is from about 0.007 to about 0.010, b5 is from about 0.055 to about 0.071, b6 is from about 1.62 to about 1.98, co is from about −0.93 to about −0.75, ci is from about −0.054 to about −0.044, c2 is from about 1.02 to about 1.25, c3 is from about −0.000057 to about −0.000046, c4 is from about 0.0080 to about 0.0098, c5 is from about 0.036 to about 0.045 and c6 is from about 0.054 to about 0.066.
Unless otherwise defined, all technical and/or scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the invention, exemplary methods and/or materials are described below. In case of conflict, the patent specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be necessarily limiting.
Some embodiments of the invention are herein described, by way of example only, with reference to the accompanying drawings. With specific reference now to the drawings in detail, it is stressed that the particulars shown are by way of example and for purposes of illustrative discussion of embodiments of the invention. In this regard, the description taken with the drawings makes apparent to those skilled in the art how embodiments of the invention may be practiced.
In the drawings:
TRAIL and PCT levels of 378 bacterial (grey), 570 viral (black) patients are presented. Diagnostic labels were determined by panel of experts as described in the Examples section. The cutoff for separating between bacterial and viral patients is represented by the bold line that equals PCT/TRAIL=0.05. This classifier will label a patient as bacterial in case PCT/TRAIL>0.05 and as viral in case PCT/TRAIL<0.05. (F) A classifier for distinguishing between bacterial and viral patients based on the PCT/TRAIL ratio. TRAIL and PCT levels of 378 bacterial (grey), 570 viral (black) patients are presented. Diagnostic labels were determined by panel of experts as described in the Examples section. The cutoff for separating between bacterial and viral patients is represented by the bold line that equals PCT/TRAIL=0.02. This classifier will label a patient as bacterial in case PCT/TRAIL>0.02 and as viral in case PCT/TRAIL<0.02. (G) A classifier for distinguishing between bacterial and viral patients based on the PCT/TRAIL ratio. TRAIL and PCT levels of 378 bacterial (grey), 570 viral (black) patients are presented. Diagnostic labels were determined by panel of experts as described in the Examples section. The cutoff for separating between bacterial and viral patients is represented by the bold line that equals PCT/TRAIL=0.01. This classifier will label a patient as bacterial in case PCT/TRAIL>0.01 and as viral in case PCT/TRAIL<0.01.
The present invention, in some embodiments thereof, relates to the identification of signatures and determinants associated with infections. The signatures may be used to distinguish between bacterial and viral infections and also to distinguish between sepsis and non-infectious systemic inflammatory response syndrome (SIRS) and to distinguish between an infective exacerbation state and a non-infective exacerbation state in patients with chronic obstructive pulmonary disease (COPD).
Before explaining at least one embodiment of the invention in detail, it is to be understood that the invention is not necessarily limited in its application to the details set forth in the following description or exemplified by the Examples. The invention is capable of other embodiments or of being practiced or carried out in various ways.
Methods of distinguishing between bacterial and viral infections by analyzing protein determinants have been disclosed in International Patent Application WO2013/117746, to the present inventors. Seeking to expand the number and type of determinants that can aid in accurate diagnosis, the present inventors have now carried out additional experiments and have identified other determinants that can be used for this aim.
Correct identification of bacterial patients is of high importance as these patients require antibiotic treatment and in some cases more aggressive management (hospitalization, additional diagnostic tests etc). Misclassification of bacterial patients increases the chance of morbidity and mortality. Therefore, increasing the sensitivity of a biomarker or diagnostic test that distinguishes between bacterial and viral infections may be desired, even though specificity may be reduced.
Whilst reducing the present invention to practice, the present inventors noted that the markers PCT and IL-6 increase the sensitivity of a previously disclosed signature—TRAIL, CRP and IP-10 (referred to herein as the TCP signature). More specifically, the present inventors have shown that PCT and IL-6 provide a temporal dynamic pattern that complements the TCP signature which is particularly useful in diagnosing infections at a very early stage.
In some embodiments, the TCP signature is calculated as one or more probabilistic classification functions which receive the values of the expression of the TRAIL, CRP and IP-10, and output a score. Based on the type of the respective probabilistic classification function, the score can represent the likelihood that the subject has, a viral infection, a bacterial infection or has no infection. A probabilistic classification function that returns a score that represents the likelihood that the subject has a viral infection can be calculated as exp(ξ)/(1+exp(ξ)+exp(η)), a probabilistic classification function that returns a score that represents the likelihood that the subject has a bacterial infection can be calculated as exp(ξ)/(1+exp(ξ)+exp(η)), and a probabilistic classification function that returns a score that represents the likelihood that the subject has no infection can be calculated as 1/(1+exp(ξ)+exp(η)), where ξ=b0+b1P+b2P0.5+b3P2+b4Q+b5R+b6R0.5 and 1=c0+c1P+c2P0.5+c3P2+c4Q+c5R+c6R0.5, where P is a value of CRP, Q is a value of IP-10, and R is a value of TRAIL, and where b0 is from about 4.96 to about 6.1, b1 is from about −0.07 to about −0.05, b2 is from about 1.33 to about 1.64, b3 is from about 0.000031 to about 0.000039, b4 is from about 0.007 to about 0.010, b5 is from about 0.055 to about 0.071, b6 is from about 1.62 to about 1.98, c0 is from about −0.93 to about −0.75, c1 is from about −0.054 to about −0.044, c2 is from about 1.02 to about 1.25, c3 is from about −0.000057 to about −0.000046, c4 is from about 0.0080 to about 0.0098, c5 is from about 0.036 to about 0.045 and c6 is from about 0.054 to about 0.066. More preferred values for the parameters b0, . . . , b6 and c0, . . . , c6 are provided in Table 3, below.
Furthermore, the present inventors predict that the TCP signature together with PCT and/or IL-6 is useful for distinguishing between additional diseases states such as between a non-infective exacerbation state and an infective exacerbation state in chronic obstructive pulmonary disease (COPD) patients and between sepsis and non-infective systemic inflammatory response syndrome (SIRS).
Thus, according to a first aspect of the present invention there is provided a method of diagnosing an infection in a subject comprising measuring the amount of each of the polypeptides TRAIL, CRP, IP10 and at least one additional polypeptide selected from the group consisting of IL-6 and PCT in a sample derived from the subject, wherein the amount is indicative of the infection type.
According to another aspect of the present invention there is provided a method of diagnosing an infection in a subject comprising measuring the amount of each of the polypeptides TRAIL, CRP and IL-6 in a sample derived from the subject, wherein the amount is indicative of the infection.
The methods disclosed herein are used to identify subjects with an infection or a specific infection type. By type of infection it is meant to include bacterial infections, viral infections, mixed infections, no infection (i.e., non-infectious). More specifically, some methods of the invention are used to distinguish subjects having a bacterial infection, a viral infection, a mixed infection (i.e., bacterial and viral co-infection), patients with a non-infectious disease and healthy individuals. Some methods of the present invention can also be used to monitor or select a treatment regimen for a subject who has a an infection, and to screen subjects who have not been previously diagnosed as having an infection, such as subjects who exhibit risk factors developing an infection. Some methods of the present invention are used to identify and/or diagnose subjects who are asymptomatic for an infection. “Asymptomatic” means not exhibiting the traditional signs and symptoms.
Thus, the infection type may be a bacterial infection, a viral infection or a mixed infection.
In various aspects the method distinguishes a virally infected subject from either a subject with non-infectious disease or a healthy subject; a bacterially infected subject, from either a subject with non-infectious disease or a healthy subject; a subject with an infectious disease from either a subject with an non-infectious disease or a healthy subject; a bacterially infected subject from a virally infected subject; a mixed infected subject from a virally infected subject; a mixed infected subject from a bacterially infected subject and a bacterially or mixed infected and subject from a virally infected subject.
A mixed infected subject refers to a subject having a bacterial and viral co-infection.
The infection may be an acute or chronic infection.
A chronic infection is an infection that develops slowly and lasts a long time. Viruses that may cause a chronic infection include Hepatitis C and HIV. One difference between acute and chronic infection is that during acute infection the immune system often produces IgM+ antibodies against the infectious agent, whereas the chronic phase of the infection is usually characteristic of IgM−/IgG+ antibodies. In addition, acute infections cause immune mediated necrotic processes while chronic infections often cause inflammatory mediated fibrotic processes and scaring (e.g. Hepatitis C in the liver). Thus, acute and chronic infections may elicit different underlying immunological mechanisms.
As used herein, the term “infection” refers to a state caused by an infectious agent of viral or bacterial origin. The bacterial infection may be the result of gram-positive, gram-negative bacteria or atypical bacteria.
The term “Gram-positive bacteria” are bacteria that are stained dark blue by Gram staining. Gram-positive organisms are able to retain the crystal violet stain because of the high amount of peptidoglycan in the cell wall.
The term “Gram-negative bacteria” are bacteria that do not retain the crystal violet dye in the Gram staining protocol.
The term “Atypical bacteria” are bacteria that do not fall into one of the classical “Gram” groups. They are usually, though not always, intracellular bacterial pathogens. They include, without limitations, Mycoplasmas spp., Legionella spp. Rickettsiae spp., and Chlamydiae spp.
In one embodiment, the level of the determinant may be used to rule in an infection type. In another embodiment, the level of the determinant may be used to rule out an infection type.
By “ruling in” an infection it is meant that the subject has that type of infection.
By “ruling out” an infection it is meant that the subject does not have that type of infection.
The subjects of this aspect of the present invention may present with a variety of pathogens including, but not limited to Adenovirus, Coronavirus, Parainfluenza virus, Influenza A virus, Influenza B virus, Respiratory syncytial virus A/B, Chlamydophila pneumoniae, Mycoplasma pneumoniae, Legionella pneumophila, Rota Virus, Staphylococcus aureus, Streptococcus pneumoniae, Astrovirus, Enteric Adenovirus, Norovirus G I and G II, Bocavirus 1/2/3/4, Enterovirus, CMV virus, EBV virus, Group A Strep, or Escherichia coli.
In one embodiment, the method is used to distinguish between non-infective Systemic inflammatory response syndrome (SIRS) and sepsis.
SIRS is a serious condition related to systemic inflammation, organ dysfunction, and organ failure. It is defined as 2 or more of the following variables: fever of more than 38° C. (100.4° F.) or less than 36° C. (96.8° F.); heart rate of more than 90 beats per minute; respiratory rate of more than 20 breaths per minute or arterial carbon dioxide tension (PaCO2) of less than 32 mm Hg; abnormal white blood cell count (>12,000/μL or <4,000/μL or >10% immature [band] forms). SIRS is nonspecific and can be caused by ischemia, inflammation, trauma, infection, or several insults combined. Thus, SIRS is not always related to infection.
Sepsis is a life-threatening condition that is caused by inflammatory response to an infection. The early diagnosis of sepsis is essential for clinical intervention before the disease rapidly progresses beyond initial stages to the more severe stages, such as severe sepsis or septic shock, which are associated with high mortality. Current diagnostics are limited in their ability to distinguish between non-infective SIRS and sepsis. Therefore, there is a need for new biomarkers or combinations of biomarkers that can provide added value in the accurate and timely diagnosis of sepsis.
According to this embodiment, sepsis may be diagnosed as the presence of SIRS criteria in the presence of a known infection.
Thus, according to one aspect, there is provided a method of distinguishing between sepsis and non-infective systemic inflammatory response syndrome (SIRS) comprising measuring the amount of at least two polypeptides selected from the group consisting of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP), Interferon gamma-induced protein 10 (IP10), Interleukin 6 (IL-6) and Procalcitonin (PCT) in a sample derived from the subject, wherein said amount is indicative of sepsis or non-infective SIRS.
Particular combinations of polypeptides are described herein below.
According to this aspect the subject that is tested has been diagnosed with SIRS. The method that is carried out is used to determine if the SIRS is infective (i.e. sepsis) or non-infective.
In another embodiment, sepsis is diagnosed in a subject suspected of having an infection and which fulfils each of the three criteria:
Respiratory rate greater or equal to_22/min
Altered mentation (e.g. a Glasgow coma score of less than 15)
Systolic blood pressure lower than or equal to 100 mmHg.
Further criteria for diagnosing sepsis are disclosed in Singer et al. 2016, 315(8):801-810 JAMA.
Thus, according to another aspect of the present invention there is provided a method of ruling in sepsis in a subject suspected of having in infection comprising:
(a) measuring the amount of at least two polypeptides selected from the group consisting of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP), Interferon gamma-induced protein 10 (IP10), Interleukin 6 (IL-6) and Procalcitonin (PCT) in a sample derived from the subject;
(b) measuring the respiratory rate of the subject;
(c) analyzing the mental state of the subject; and
(d) measuring the blood pressure of the subject;
wherein when each of steps are indicative of sepsis, sepsis is ruled in.
Particular combinations of polypeptides are described herein below.
It will be appreciated that steps (b), (c) and (d) may be carried out as part of determining the SOFA score (originally the Sepsis-related Organ Failure Assessment; Vincent J. L et al Intensive Care Med. 1996; 22(7):707-710) of a subject.
In one embodiment, step (a) is carried out in order to confirm the subject has an infection. Only when subjects have a confirmed infection are steps (b), (c) and (d) carried out to confirm sepsis.
In another embodiment, the subject has a suspected infection, steps (b), (c) ad (d) are carried out to rule in sepsis; and step (a) is carried out to corroborate the diagnosis.
The present inventors contemplate analyzing the amount of at least two polypeptides selected from the group consisting of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP), Interferon gamma-induced protein 10 (IP10), Interleukin 6 (IL-6) and Procalcitonin (PCT) in a sample derived from the subject in order to confirm that the subject has an infection.
In another aspect, sepsis is ruled in a subject suspected of having an infection when his SOFA score is above 2.
In one embodiment, analyzing the amount of at least two polypeptides selected from the group consisting of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP), Interferon gamma-induced protein 10 (IP10), Interleukin 6 (IL-6) and Procalcitonin (PCT) in a sample derived from the subject is carried out in order to confirm the subject has an infection. Only when subjects have a confirmed infection is the SOFA analysis carried out to diagnose sepsis (when the subject has a SOFA score of more than or equal to 2, the subject is diagnosed with sepsis).
Alternatively, a SOFA analysis is carried out to diagnose sepsis. Analyzing the amount of at least two polypeptides selected from the group consisting of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP), Interferon gamma-induced protein 10 (IP10), Interleukin 6 (IL-6) and Procalcitonin (PCT) in a sample derived from the subject is carried out in order to confirm the subject has the sepsis.
In another embodiment, the method is used to discriminate between bacterial and viral etiologies in patients with chronic obstructive pulmonary disease (COPD) exacerbation.
In still another embodiment, the method is used to distinguish between an infective exacerbation state and a non-infective exacerbation state of chronic obstructive pulmonary disease (COPD) in a subject.
Chronic obstructive pulmonary disease (COPD) is an obstructive, inflammatory lung disease characterized by long-term poor airflow. The main symptoms include shortness of breath and cough with sputum production. COPD is a progressive disease, worsening over time.
An exacerbation of COPD may be defined as an event in the natural course of the disease characterized by a change in the patient's baseline dyspnea, cough, and/or sputum that is beyond normal day-to-day variations. The exacerbation is typically acute. It may present with signs of increased work of breathing such as fast breathing, a fast heart rate, sweating, active use of muscles in the neck, a bluish tinge to the skin, and confusion or combative behavior in very severe exacerbations. Crackles may also be heard over the lungs on examination with a stethoscope.
Particular combinations of polypeptides are described herein below.
The subjects (e.g. children) may present with a particular clinical syndrome—for example, low respiratory tract infection (LRTI) infection, upper respiratory tract infection (URTI) or a serious bacterial infection (SBI) such as UTI (urinary tract infections), septic shock, bacteremia, pneumonia or meningitis.
“Measuring” or “measurement,” or alternatively “detecting” or “detection,” means assessing the presence, absence, quantity or amount (which can be an effective amount) of the determinant within a clinical or subject-derived sample, including the derivation of qualitative or quantitative concentration levels of such determinants.
A “sample” in the context of the present invention is a biological sample isolated from a subject and can include, by way of example and not limitation, whole blood, serum, plasma, saliva, mucus, breath, urine, CSF, sputum, sweat, stool, hair, seminal fluid, biopsy, rhinorrhea, tissue biopsy, cytological sample, platelets, reticulocytes, leukocytes, epithelial cells, or whole blood cells.
In a particular embodiment, the sample is a blood sample—e.g. serum or a sample comprising blood cells. In a particular embodiment, the sample is depleted of red blood cells.
In one embodiment, the sample is derived from the subject no more ten days following symptom onset, no more than five days following symptom onset, no more than four days following symptom onset, no more than three days following symptom onset, no more than two days following symptom onset or preferably no more than one day following symptom onset.
The sample may be fresh or frozen.
A “subject” in the context of the present invention may be a mammal (e.g. a human, dog, cat, horse, cow, sheep, pig or goat). According to another embodiment, the subject is a bird (e.g. chicken, turkey, duck or goose). According to a particular embodiment, the subject is a human. The subject can be male or female. The subject may be an adult (e.g. older than 18, 21, or 22 years or a child (e.g. younger than 18, 21 or 22 years). In another embodiment, the subject is an adolescent (between 12 and 21 years), an infant (29 days to less than 2 years of age) or a neonate (birth through the first 28 days of life).
The subject can be one who has been previously diagnosed or identified as having an infection, and optionally has already undergone, or is undergoing, a therapeutic intervention for the infection. Alternatively, a subject can also be one who has not been previously diagnosed as having an infection. For example, a subject can be one who exhibits one or more risk factors for having an infection.
According to a particular embodiment, the subject does not show signs of having had a heart attack (e.g. has a normal level of creatine kinase, troponin or serum myoglobin, and/or has a normal ECG or EKG).
In one embodiment, the subject is one which has undergone a trauma (e.g. car accident or combat related trauma) and/or has undergone a surgical procedure.
As mentioned, in order to determine the type of infection, the amount of each of the following polypeptides are determined: TRAIL, CRP, IP10, together with either IL-6 and/or PCT.
Alternatively, in order to determine the type of infection, the amount of TRAIL, CRP and IL-6 are measured in a sample derived from the subject, wherein the amount is indicative of the infection type.
Other contemplated combinations are provided herein below:
TRAIL, CRP, IP-10 and PCT;
TRAIL, IP-10 and PCT;
TRAIL, CRP, IP-10 and IL-6;
TRAIL, CRP, IP-10, PCT and IL-6;
TRAIL, CRP and PCT;
TRAIL, CRP and IL-6;
TRAIL, CRP, PCT and IL-6
Information regarding the above mentioned polypeptides is provided in Table 1, herein below.
Exemplary ranges of the mentioned polypeptides in bacterial and viral patients include without limitation:
CRP—CRP levels of 0-40 μg/ml are usually indicative of a viral infection, while 40-400 μg/ml are usually indicative of a bacterial infection. Bacterial infection can usually be ruled in if CRP levels are higher than 50, 60, 70 or more preferably 80 μg/ml, and ruled out if CRP levels are lower than 30 and more preferably 20 μg/ml.
TRAIL—TRAIL levels of 100-1000 pg/ml are usually indicative of a viral infection, while 0-85 pg/ml are usually indicative of a bacterial infection. Bacterial infection can usually be ruled in if TRAIL levels are lower than 85 pg/ml, 70 pg/ml, 60 pg/ml or more preferably 50 pg/ml, and ruled out if TRAIL levels are higher than 100 pg/ml.
IP-10—IP-10 levels of 300-2000 pg/ml are usually indicative of a viral infection, while 160-860 pg/ml are usually indicative of a bacterial infection. Viral infection can usually be ruled in if IP10 levels are higher than 800 pg/ml, and ruled out if IP10 levels are lower than 300 pg/ml.
PCT—PCT levels higher than 0.5 μg/L are usually indicative of a bacterial infection.
IL-6—IL-6 levels higher than 100 pg/ml are usually indicative of a bacterial infection.
CRP: C-reactive protein; additional aliases of CRP include without limitation RP11-419N10.4 and PTX1.
An exemplary amino acid sequence of human CRP is set forth below in SEQ ID NO: 1.
The level of CRP typically increases in infections (as compared to non-infectious diseases), with the level of CRP being higher in bacterial infections as opposed to viral infections.
Thus, when the level of CRP is above a predetermined level, it is indicative that the infection is a bacterial infection and a bacterial infection may be ruled in (or a viral infection may be ruled out).
When the level of CRP is below a predetermined level, it is indicative that the infection is a viral infection and a viral infection may be ruled in (or a bacterial infection may be ruled out).
TRAIL: The protein encoded by this gene is a cytokine that belongs to the tumor necrosis factor (TNF) ligand family. The present invention contemplates measuring either the soluble and/or the membrane form of this protein. In one embodiment, only the soluble form of this protein is measured. Additional names of the gene include without limitations APO2L, TNF-related apoptosis-inducing ligand, TNFSF10 and CD253. This protein binds to several members of the TNF receptor superfamily such as TNFRSF10A/TRAILR1, TNFRSF10B/TRAILR2, TNFRSF10C/TRAILR3, TNFRSF10D/TRAILR4, and possibly also to TNFRSF11B/OPG
Exemplary amino acid sequences of TRAIL are set forth in SEQ ID NOs: 4-8.
In a particular embodiment, TRAIL is the protein that is recognized by the antibody of the kit R&D systems, Human TRAIL/TNFSF10 Quantikine ELISA Kit catalog #DTRL00.
The level of TRAIL increases in viral infections (as compared to non-infectious diseases), and decreases in bacterial infections (as compared to non-infectious diseases).
Thus, when the level of TRAIL is above a predetermined level, it is indicative that the infection is a viral infection and a viral infection may be ruled in (or a bacterial infection may be ruled out).
When the level of TRAIL is below a predetermined level, it is indicative that the infection is a bacterial infection and a bacterial infection may be ruled in (or a viral infection may be ruled out).
For example, a bacterial infection may be ruled out if the polypeptide concentration of TRAIL determined is higher than a pre-determined first threshold value. Optionally, the method further includes determining if a subject has a viral infection (i.e., ruling in a viral infection). A viral infection is ruled in if the polypeptide concentration of TRAIL is higher than a pre-determined second threshold value.
In another specific embodiment the invention includes determining if a subject does not have a viral infection (i.e. ruling out a viral infection). A viral infection is ruled out if the polypeptide concentration of TRAIL determined is lower than a pre-determined first threshold value. Optionally, the method further includes determining if a subject has a bacterial infection (i.e., ruling in a bacterial infection). A bacterial infection is ruled in if the polypeptide concentration of TRAIL is lower than a pre-determined second threshold value.
IP10: This gene encodes a chemokine of the CXC subfamily and ligand for the receptor CXCR3. Additional names of the gene include without limitations: CXCL10, Gamma-IP10, INP10 and chemokine (C—X—C motif) ligand 10.
An exemplary amino acid sequence of human IP10 is set forth in SEQ ID NO: 16.
In a particular embodiment, IP10 is the protein that is recognized by the antibody of the kit (R&D systems, Human CXCL10/IP-10 Quantikine ELISA Kit catalog #DIP100).
The level of IP10 increases in infections (as compared to non-infectious diseases), with the level of IP10 being higher in viral infections as opposed to bacterial infections.
Thus, when the level of IP10 is above a predetermined level, it is indicative that the infection is a viral infection and a viral infection may be ruled in (or a bacterial infection may be ruled out).
When the level of IP10 is below a predetermined level, it is indicative that the infection is a bacterial infection and a bacterial infection may be ruled in (or a viral infection may be ruled out).
IL-6: This gene encodes a cytokine that functions in inflammation and the maturation of B cells. In addition, the encoded protein has been shown to be an endogenous pyrogen capable of inducing fever in people with autoimmune diseases or infections. The protein is primarily produced at sites of acute and chronic inflammation, where it is secreted into the serum and induces a transcriptional inflammatory response through interleukin 6 receptor, alpha. The functioning of this gene is implicated in a wide variety of inflammation-associated disease states, including susceptibility to diabetes mellitus and systemic juvenile rheumatoid arthritis.
Exemplary amino acid sequences of human IL-6 is set forth in SEQ ID NOs: 23 and 24.
The data presented herein shows that the level of IL-6 increases in infections (as compared to non-infectious diseases), with the level of IL-6 being higher in bacterial infections as opposed to viral infections.
Thus, when the level of IL-6 is above a predetermined level, it is indicative that the infection is a bacterial infection and a bacterial infection may be ruled in (or a viral infection may be ruled out).
When the level of IL-6 is below a predetermined level, it is indicative that the infection is a viral infection and a viral infection may be ruled in (or a bacterial infection may be ruled out).
PCT: Procalcitonin (PCT) is a peptide precursor of the hormone calcitonin, the latter being involved with calcium homeostasis.
Exemplary amino acid sequences of human PCT are set forth in SEQ ID NOs: 19-22.
The level of PCT typically increases in infections (as compared to non-infectious diseases), with the level of PCT being higher in bacterial infections as opposed to viral infections.
Thus, when the level of PCT is above a predetermined level, it is indicative that the infection is a bacterial infection and a bacterial infection may be ruled in (or a viral infection may be ruled out).
When the level of PCT is below a predetermined level, it is indicative that the infection is a viral infection and a viral infection may be ruled in (or a bacterial infection may be ruled out).
The concentrations of each of the above identified polypeptides may be combined (e.g. by way of a pre-determined mathematical function) to compute a score and the score may be compared to a predetermined reference value as further described herein below.
Further information on generating pre-determined mathematical functions in general and for CRP, IP10 and TRAIL in particular are provided in International Patent Application IL2015/050823, the contents of which are incorporated herein by reference.
Statistical classification algorithms which may be used to calculate the score include, but are not limited to Support Vector Machine (SVM), Logistic Regression (LogReg), Neural Network, Bayesian Network, and a Hidden Markov Model. Alternatively, the integration of the different proteins into a single predictive score could be achieved by applying “Fuzzy OR model” analysis, as shown in the Examples section herein below.
In one embodiment, the level of PCT and/or IL-6 is taken into account in the statistical classification together with the TRAIL, CRP, IP-10 signature (TCP signature) only when concentrations reaches a threshold level. Thus, for example only when the level of PCT is above 1, 1.5, 2, 2.5, 5, or 7.5 μg/L, is PCT included in the algorithm together with the TCP signature. Similarly, only when the level of IL-6 is above 100, 200, 240, 250, 280, 320, or 350 pg/ml is IL-6 included in the algorithm together with the TCP signature. It will be appreciated that the weight of PCT and IL-6 in the algorithm may vary according to its concentration. For example, if the level of PCT is above 5 μg/L, then its relative weight may be higher with respect to the TCP signature that if the level of PCT is below 5 μg/L.
A reference value can be relative to a number or value derived from population studies, including without limitation, such subjects having the same infection, subject having the same or similar age range, subjects in the same or similar ethnic group, or relative to the starting sample of a subject undergoing treatment for an infection. Such reference values can be derived from statistical analyses and/or risk prediction data of populations obtained from mathematical algorithms and computed indices of infection. Reference determinant indices can also be constructed and used using algorithms and other methods of statistical and structural classification.
In one embodiment of the present invention, the reference value is the amount (i.e. level) of determinants in a control sample derived from one or more subjects who do not have an infection (i.e., healthy, and or non-infectious individuals). In a further embodiment, such subjects are monitored and/or periodically retested for a diagnostically relevant period of time (“longitudinal studies”) following such test to verify continued absence of infection. Such period of time may be one day, two days, two to five days, five days, five to ten days, ten days, or ten or more days from the initial testing date for determination of the reference value. Furthermore, retrospective measurement of determinants in properly banked historical subject samples may be used in establishing these reference values, thus shortening the study time required.
A reference value can also comprise the amounts of determinants derived from subjects who show an improvement as a result of treatments and/or therapies for the infection. A reference value can also comprise the amounts of determinants derived from subjects who have confirmed infection by known techniques.
An example of a bacterially infected reference value index value is the mean or median concentrations of that determinant in a statistically significant number of subjects having been diagnosed as having a bacterial infection.
An example of a virally infected reference value is the mean or median concentrations of that determinant in a statistically significant number of subjects having been diagnosed as having a viral infection.
In another embodiment, the reference value is an index value or a baseline value. An index value or baseline value is a composite sample of an effective amount of determinants from one or more subjects who do not have an infection. A baseline value can also comprise the amounts of determinants in a sample derived from a subject who has shown an improvement in treatments or therapies for the infection. In this embodiment, to make comparisons to the subject-derived sample, the amounts of determinants are similarly calculated and compared to the index value. Optionally, subjects identified as having an infection, are chosen to receive a therapeutic regimen to slow the progression or eliminate the infection.
Additionally, the amount of the determinant can be measured in a test sample and compared to the “normal control level,” utilizing techniques such as reference limits, discrimination limits, or risk defining thresholds to define cutoff points and abnormal values. The “normal control level” means the level of one or more determinants or combined determinant indices typically found in a subject not suffering from an infection. Such normal control level and cutoff points may vary based on whether a determinant is used alone or in a formula combining with other determinants into an index. Alternatively, the normal control level can be a database of determinant patterns from previously tested subjects.
The effectiveness of a treatment regimen can be monitored by detecting a determinant in an effective amount (which may be one or more) of samples obtained from a subject over time and comparing the amount of determinants detected. For example, a first sample can be obtained prior to the subject receiving treatment and one or more subsequent samples are taken after or during treatment of the subject.
For example, the methods of the invention can be used to discriminate between bacterial, viral and mixed infections (i.e. bacterial and viral co-infections.) This will allow patients to be stratified and treated accordingly.
In a specific embodiment of the invention a treatment recommendation (i.e., selecting a treatment regimen) for a subject is provided by identifying the type infection (i.e., bacterial, viral, mixed infection or no infection) in the subject according to the method of any of the disclosed methods and recommending that the subject receive an antibiotic treatment if the subject is identified as having bacterial infection or a mixed infection; or an anti-viral treatment is if the subject is identified as having a viral infection.
In another embodiment, the methods of the invention can be used to prompt additional targeted diagnosis such as pathogen specific PCRs, chest-X-ray, cultures etc. For example, a diagnosis that indicates a viral infection according to embodiments of this invention, may prompt the usage of additional viral specific multiplex-PCRs, whereas a diagnosis that indicates a bacterial infection according to embodiments of this invention may prompt the usage of a bacterial specific multiplex-PCR. Thus, one can reduce the costs of unwarranted expensive diagnostics.
In a specific embodiment, a diagnostic test recommendation for a subject is provided by identifying the infection type (i.e., bacterial, viral, mixed infection or no infection) in the subject according to any of the disclosed methods and recommending a test to determine the source of the bacterial infection if the subject is identified as having a bacterial infection or a mixed infection; or a test to determine the source of the viral infection if the subject is identified as having a viral infection.
As well as measuring the polypeptide determinants mentioned herein above, the present inventors contemplate measuring at least one, two, three, four, five, six, seven, eight, nine, ten or more additional (non-identical) determinants (polypeptide, RNA or other), wherein the at least one additional determinant is set forth in US Patent Application No. 20080171323, WO2011/132086 and WO2013/117746 and PCT Application IL 2015/051024 and PCT Application IL 2015/051201 and Provisional Application No. 62/302,849 the contents of each are incorporated herein by reference. Other polypeptide determinants contemplated by the present inventors are the polypeptide counterparts of the RNA determinants described therein.
In one embodiment, at least of the additional determinants is set forth in Table 2 herein below.
According to this aspect of the present invention, in order to distinguish between the different infection types, no more than 30 determinants (e.g. proteins that are differentially expressed in a statistically significant manner in subjects with a bacterial infection compared to subjects with a viral infection) are measured, no more than 25 determinants are measured, no more than 20 determinants are measured, no more than 15 determinants are measured, no more than 10 determinants are measured, no more than 9 determinants are measured, no more than 8 determinants are measured, no more than 7 determinants are measured, no more than 6 determinants are measured, no more than 5 determinants are measured or even no more than 4 determinants are measured.
Other determinants that may be measured according to aspects of the present invention include pathogen (bacterial or viral) specific RNA or polypeptide determinants. This may be carried out in order to aid in identification of a specific pathogen. The measurements may be effected simultaneously with the above described measurements or consecutively.
Methods of measuring the levels of polypeptides are well known in the art and include, e.g., immunoassays based on antibodies to proteins, aptamers or molecular imprints.
The polypeptide determinants can be detected in any suitable manner, but are typically detected by contacting a sample from the subject with an antibody, which binds the determinant and then detecting the presence or absence of a reaction product. The antibody may be monoclonal, polyclonal, chimeric, or a fragment of the foregoing, as discussed in detail above, and the step of detecting the reaction product may be carried out with any suitable immunoassay. The sample from the subject is typically a biological sample as described above, and may be the same sample of biological sample used to conduct the method described above.
In one embodiment, the antibody which specifically binds the determinant is attached (either directly or indirectly) to a signal producing label, including but not limited to a radioactive label, an enzymatic label, a hapten, a reporter dye or a fluorescent label.
Immunoassays carried out in accordance with some embodiments of the present invention may be homogeneous assays or heterogeneous assays. In a homogeneous assay the immunological reaction usually involves the specific antibody (e.g., anti-determinant antibody), a labeled analyte, and the sample of interest. The signal arising from the label is modified, directly or indirectly, upon the binding of the antibody to the labeled analyte. Both the immunological reaction and detection of the extent thereof can be carried out in a homogeneous solution. Immunochemical labels, which may be employed, include free radicals, radioisotopes, fluorescent dyes, enzymes, bacteriophages, or coenzymes.
In a heterogeneous assay approach, the reagents are usually the sample, the antibody, and means for producing a detectable signal. Samples as described above may be used. The antibody can be immobilized on a support, such as a bead (such as protein A and protein G agarose beads), plate or slide, and contacted with the specimen suspected of containing the antigen in a liquid phase. The support is then separated from the liquid phase and either the support phase or the liquid phase is examined for a detectable signal employing means for producing such signal. The signal is related to the presence of the analyte in the sample.
Means for producing a detectable signal include the use of radioactive labels, fluorescent labels, or enzyme labels. For example, if the antigen to be detected contains a second binding site, an antibody which binds to that site can be conjugated to a detectable group and added to the liquid phase reaction solution before the separation step. The presence of the detectable group on the solid support indicates the presence of the antigen in the test sample. Examples of suitable immunoassays are oligonucleotides, immunoblotting, immunofluorescence methods, immunoprecipitation, chemiluminescence methods, electrochemiluminescence (ECL) or enzyme-linked immunoassays.
Those skilled in the art will be familiar with numerous specific immunoassay formats and variations thereof which may be useful for carrying out the method disclosed herein. See generally E. Maggio, Enzyme-Immunoassay, (1980) (CRC Press, Inc., Boca Raton, Fla.); see also U.S. Pat. No. 4,727,022 to Skold et al., titled “Methods for Modulating Ligand-Receptor Interactions and their Application,” U.S. Pat. No. 4,659,678 to Forrest et al., titled “Immunoassay of Antigens,” U.S. Pat. No. 4,376,110 to David et al., titled “Immunometric Assays Using Monoclonal Antibodies,” U.S. Pat. No. 4,275,149 to Litman et al., titled “Macromolecular Environment Control in Specific Receptor Assays,” U.S. Pat. No. 4,233,402 to Maggio et al., titled “Reagents and Method Employing Channeling,” and U.S. Pat. No. 4,230,767 to Boguslaski et al., titled “Heterogeneous Specific Binding Assay Employing a Coenzyme as Label.” The determinant can also be detected with antibodies using flow cytometry. Those skilled in the art will be familiar with flow cytometric techniques which may be useful in carrying out the methods disclosed herein(Shapiro 2005). These include, without limitation, Cytokine Bead Array (Becton Dickinson) and Luminex technology.
Antibodies can be conjugated to a solid support suitable for a diagnostic assay (e.g., beads such as protein A or protein G agarose, microspheres, plates, slides or wells formed from materials such as latex or polystyrene) in accordance with known techniques, such as passive binding. Antibodies as described herein may likewise be conjugated to detectable labels or groups such as radiolabels (e.g., 35S, 125I, 131I), enzyme labels (e.g., horseradish peroxidase, alkaline phosphatase), and fluorescent labels (e.g., fluorescein, Alexa, green fluorescent protein, rhodamine) in accordance with known techniques.
Antibodies can also be useful for detecting post-translational modifications of determinant proteins, polypeptides, mutations, and polymorphisms, such as tyrosine phosphorylation, threonine phosphorylation, serine phosphorylation, glycosylation (e.g., O-GlcNAc). Such antibodies specifically detect the phosphorylated amino acids in a protein or proteins of interest, and can be used in immunoblotting, immunofluorescence, and ELISA assays described herein. These antibodies are well-known to those skilled in the art, and commercially available. Post-translational modifications can also be determined using metastable ions in reflector matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF) (Wirth U. and Muller D. 2002).
For determinant-proteins, polypeptides, mutations, and polymorphisms known to have enzymatic activity, the activities can be determined in vitro using enzyme assays known in the art. Such assays include, without limitation, kinase assays, phosphatase assays, reductase assays, among many others. Modulation of the kinetics of enzyme activities can be determined by measuring the rate constant KM using known algorithms, such as the Hill plot, Michaelis-Menten equation, linear regression plots such as Lineweaver-Burk analysis, and Scatchard plot.
In particular embodiments, the antibodies of the present invention are monoclonal antibodies.
Suitable sources for antibodies for the detection of determinants include commercially available sources such as, for example, Abazyme, Abnova, AssayPro, Affinity Biologicals, AntibodyShop, Aviva bioscience, Biogenesis, Biosense Laboratories, Calbiochem, Cell Sciences, Chemicon International, Chemokine, Clontech, Cytolab, DAKO, Diagnostic BioSystems, eBioscience, Endocrine Technologies, Enzo Biochem, Eurogentec, Fusion Antibodies, Genesis Biotech, GloboZymes, Haematologic Technologies, Immunodetect, Immunodiagnostik, Immunometrics, Immunostar, Immunovision, Biogenex, Invitrogen, Jackson ImmunoResearch Laboratory, KMI Diagnostics, Koma Biotech, LabFrontier Life Science Institute, Lee Laboratories, Lifescreen, Maine Biotechnology Services, Mediclone, MicroPharm Ltd., ModiQuest, Molecular Innovations, Molecular Probes, Neoclone, Neuromics, New England Biolabs, Novocastra, Novus Biologicals, Oncogene Research Products, Orbigen, Oxford Biotechnology, Panvera, PerkinElmer Life Sciences, Pharmingen, Phoenix Pharmaceuticals, Pierce Chemical Company, Polymun Scientific, Polysiences, Inc., Promega Corporation, Proteogenix, Protos Immunoresearch, QED Biosciences, Inc., R&D Systems, Repligen, Research Diagnostics, Roboscreen, Santa Cruz Biotechnology, Seikagaku America, Serological Corporation, Serotec, SigmaAldrich, StemCell Technologies, Synaptic Systems GmbH, Technopharm, Terra Nova Biotechnology, TiterMax, Trillium Diagnostics, Upstate Biotechnology, US Biological, Vector Laboratories, Wako Pure Chemical Industries, and Zeptometrix. However, the skilled artisan can routinely make antibodies, against any of the polypeptide determinants described herein.
The presence of a label can be detected by inspection, or a detector which monitors a particular probe or probe combination is used to detect the detection reagent label. Typical detectors include spectrophotometers, phototubes and photodiodes, microscopes, scintillation counters, cameras, film and the like, as well as combinations thereof. Those skilled in the art will be familiar with numerous suitable detectors that widely available from a variety of commercial sources and may be useful for carrying out the method disclosed herein. Commonly, an optical image of a substrate comprising bound labeling moieties is digitized for subsequent computer analysis. See generally The Immunoassay Handbook [The Immunoassay Handbook. Third Edition. 2005].
Traditional laboratory risk factors and additional clinical parameters may also be measured together with the above described polypeptides to further increase the accuracy of the signatures.
“Traditional laboratory risk factors” encompass biomarkers isolated or derived from subject samples and which are currently evaluated in the clinical laboratory and used in traditional global risk assessment algorithms, such as absolute neutrophil count (abbreviated ANC), absolute lymphocyte count (abbreviated ALC), white blood count (abbreviated WBC), neutrophil % (defined as the fraction of white blood cells that are neutrophils and abbreviated Neu (%)), lymphocyte % (defined as the fraction of white blood cells that are lymphocytes and abbreviated Lym (%)), monocyte % (defined as the fraction of white blood cells that are monocytes and abbreviated Mon (%)), Sodium (abbreviated Na), Potassium (abbreviated K), Bilirubin (abbreviated Bili).
“Clinical parameters” encompass all non-sample or non-analyte biomarkers of subject health status or other characteristics, such as, without limitation, age (Age), ethnicity (RACE), gender (Sex), core body temperature (abbreviated “temperature”), maximal core body temperature since initial appearance of symptoms (abbreviated “maximal temperature”), time from initial appearance of symptoms (abbreviated “time from symptoms”) or family history (abbreviated FamHX).
The patient medical background conditions such as chronic lung diseases and diabetes may affect its immune response to infection that is reflected by changes in diagnostic accuracy of immune-based diagnostics (see Example 1, herein below). Thus, information regarding the patient background clinical conditions could potentially be integrated with protein biomarker classifiers predicted outcome in order to improve patient diagnosis.
As mentioned, the signature polypeptides described herein are particularly useful at classifying early infections.
Thus, according to another aspect of the present invention there is provided a method of diagnosing an infection in a subject comprising measuring the amount of at least two polypeptides selected from the group consisting of TRAIL, CRP, IP10, IL-6 and PCT in a sample derived from the subject, wherein the sample is derived from the subject no more than two days following symptom onset, wherein the amount is indicative of the infection.
In one embodiment, the sample is derived from the subject no more than one day following symptom onset.
Exemplary symptoms include but are not limited to fever, nausea, headache, rash and/or muscle soreness.
Exemplary pairs of polypeptides that may be analyzed for any of the aspects described herein include:
TRAIL and CRP;
TRAIL and IP10;
TRAIL and IL-6;
TRAIL and PCT;
CRP and IP10;
CRP and IL-6;
CRP and PCT;
IP10 and IL-6;
IP10 and PCT;
IL-6 and PCT;
MX1 and PCT or
MX1 and IL-6.
Exemplary triplets of polypeptides that may be analyzed include:
TRAIL, CRP and IP10;
TRAIL, CRP and IL6;
TRAIL, IP10 and PCT; or
TRAIL, CRP and PCT.
Exemplary quadruplets of polypeptides that may be analyzed include:
TRAIL, CRP, IP-10, PCT;
TRAIL, CRP, IP-10, IL-6; or
TRAIL, CRP, PCT, IL-6.
In another embodiment, each of the polypeptides are measured: TRAIL, CRP,
IP 10, PCT and IL-6.
For particular embodiments, when the amount of TRAIL is below a predetermined level, the amount of CRP is above a predetermined level, the amount of IP-10 is below a predetermined level and the amount of IL-6 is above a predetermined level, the subject is diagnosed as having sepsis. Alternatively, when the amount of TRAIL is below a predetermined level, the amount of CRP is above a predetermined level, the amount of IP-10 is below a predetermined level and the amount of PCT is above a predetermined level, the subject is diagnosed as having sepsis. Alternatively, when the amount of TRAIL is below a predetermined level, the amount of CRP is above a predetermined level, the amount of IP-10 is below a predetermined level, the amount of PCT is above a predetermined level and the amount of IL-6 is above a predetermined level, the subject is diagnosed as having sepsis.
In other embodiments, when the amount of TRAIL is below a predetermined level, the amount of CRP is above a predetermined level, and the amount of IL-6 is above a predetermined level, the subject is diagnosed as having sepsis. Alternatively, when the amount of TRAIL is below a predetermined level, the amount of CRP is above a predetermined level, and the amount of PCT is above a predetermined level, the subject is diagnosed as having sepsis. Alternatively, when the amount of TRAIL is below a predetermined level, the amount of CRP is above a predetermined level, the amount of PCT is above a predetermined level and the amount of IL-6 is above a predetermined level, the subject is diagnosed as having sepsis.
As mentioned, the markers and combinations thereof may be measured to distinguish between a non-infectious exacerbation state and an infectious exacerbation state of chronic obstructive pulmonary disease (COPD) in a subject. The method comprises measuring the amount of at least two polypeptides selected from the group consisting of TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP), Interferon gamma-induced protein 10 (IP10), Interleukin 6 (IL-6) and Procalcitonin (PCT) in a sample derived from the subject, wherein the amount is indicative of the exacerbation state of COPD.
It will be appreciated that if the exacerbation is due to an infection, the levels of the markers will change according to the infection type (viral/bacterial) as described herein above. If the exacerbation is not due to an infection type, the levels of the markers will be similar to a non-infectious subject.
According to a further aspect of the present invention there is provided a method of determining an infection type in subjects with trauma-induced or combat-related wounds comprising measuring the amount of each of the polypeptides TNF-related apoptosis-inducing ligand (TRAIL), C-reactive protein (CRP), Interferon gamma-induced protein 10 (IP10) and at least one additional polypeptide selected from the group consisting of Interleukin 6 (IL-6) and Procalcitonin (PCT) in a sample derived from the subject, wherein the amount is indicative of the infection type. In yet another embodiment, these signatures are specifically used to monitor post-surgery patients.
Kits
Some aspects of the invention also include a determinant-detection reagent such as antibodies packaged together in the form of a kit. The kit may contain in separate containers antibodies (either already bound to a solid matrix or packaged separately with reagents for binding them to the matrix), control formulations (positive and/or negative), and/or a detectable label such as fluorescein, green fluorescent protein, rhodamine, cyanine dyes, Alexa dyes, luciferase, radiolabels, among others. The detectable label may be attached to a secondary antibody which binds to the Fc portion of the antibody which recognizes the determinant. Instructions (e.g., written, tape, VCR, CD-ROM, etc.) for carrying out the assay may be included in the kit.
The kits of this aspect of the present invention may comprise additional components that aid in the detection of the determinants such as enzymes, salts, buffers etc. necessary to carry out the detection reactions.
Thus, according to another aspect of the present invention, there is provided a kit for diagnosing an infection type comprising:
(i) an antibody which specifically detects TRAIL;
(ii) an antibody which specifically detects IP10:
(iii) an antibody which specifically detects CRP; and
(iv) at least one additional antibody which specifically detects IL-6 or PCT.
According to still another aspect of the present invention there is provided a kit for diagnosing an infection type comprising:
(i) an antibody which specifically detects TRAIL;
(ii) an antibody which specifically detects IL-6:
(iii) an antibody which specifically detects CRP; and
(iv) at least one additional antibody which specifically detects IP10 or PCT.
For example, determinant detection reagents (e.g. antibodies) can be immobilized on a solid matrix such as a porous strip or an array to form at least one determinant detection site. The measurement or detection region of the porous strip may include a plurality of sites. A test strip may also contain sites for negative and/or positive controls. Alternatively, control sites can be located on a separate strip from the test strip. Optionally, the different detection sites may contain different amounts of immobilized detection reagents, e.g., a higher amount in the first detection site and lesser amounts in subsequent sites. Upon the addition of test sample, the number of sites displaying a detectable signal provides a quantitative indication of the amount of determinants present in the sample. The detection sites may be configured in any suitably detectable shape and are typically in the shape of a bar or dot spanning the width of a test strip.
Examples of “Monoclonal antibodies for measuring TRAIL”, include without limitation: Mouse, Monoclonal (55B709-3) IgG; Mouse, Monoclonal (2E5) IgG1; Mouse, Monoclonal (2E05) IgG1; Mouse, Monoclonal (M912292) IgG1 kappa; Mouse, Monoclonal (IIIF6) IgG2b; Mouse, Monoclonal (2E1-1B9) IgG1; Mouse, Monoclonal (RIK-2) IgG1, kappa; Mouse, Monoclonal M181 IgG1; Mouse, Monoclonal VI10E IgG2b; Mouse, Monoclonal MAB375 IgG1; Mouse, Monoclonal MAB687 IgG1; Mouse, Monoclonal HS501 IgG1; Mouse, Monoclonal clone 75411.11 Mouse IgG1; Mouse, Monoclonal T8175-50 IgG; Mouse, Monoclonal 2B2.108 IgG1; Mouse, Monoclonal B-T24 IgG1; Mouse, Monoclonal 55B709.3 IgG1; Mouse, Monoclonal D3 IgG1; Goat, Monoclonal C19 IgG; Rabbit, Monoclonal H257 IgG; Mouse, Monoclonal 500-M49 IgG; Mouse, Monoclonal 05-607 IgG; Mouse, Monoclonal B-T24 IgG1; Rat, Monoclonal (N2B2), IgG2a, kappa; Mouse, Monoclonal (1A7-2B7), IgG1; Mouse, Monoclonal (55B709.3), IgG and Mouse, Monoclonal B-S23*IgG1.
Soluble TRAIL and membrane TRAIL can be distinguished by using different measuring techniques and samples. For example, Soluble TRAL can be measured without limitation in cell free samples such as serum or plasma, using without limitation lateral flow immunoassay (LFIA), as further described herein below. Membrane TRAIL can be measured in samples that contain cells using cell based assays including without limitation flow cytometry, ELISA, and other immunoassays.
Lateral Flow Immunoassays (LFIA): This is a technology which allows rapid measurement of analytes at the point of care (POC) and its underlying principles are described below. According to one embodiment, LFIA is used in the context of a hand-held device.
The technology is based on a series of capillary beds, such as pieces of porous paper or sintered polymer. Each of these elements has the capacity to transport fluid (e.g., urine) spontaneously. The first element (the sample pad) acts as a sponge and holds an excess of sample fluid. Once soaked, the fluid migrates to the second element (conjugate pad) in which the manufacturer has stored the so-called conjugate, a dried format of bio-active particles (see below) in a salt-sugar matrix that contains everything to guarantee an optimized chemical reaction between the target molecule (e.g., an antigen) and its chemical partner (e.g., antibody) that has been immobilized on the particle's surface. While the sample fluid dissolves the salt-sugar matrix, it also dissolves the particles and in one combined transport action the sample and conjugate mix while flowing through the porous structure. In this way, the analyte binds to the particles while migrating further through the third capillary bed. This material has one or more areas (often called stripes) where a third molecule has been immobilized by the manufacturer. By the time the sample-conjugate mix reaches these strips, analyte has been bound on the particle and the third ‘capture’ molecule binds the complex.
After a while, when more and more fluid has passed the stripes, particles accumulate and the stripe-area changes color. Typically there are at least two stripes: one (the control) that captures any particle and thereby shows that reaction conditions and technology worked fine, the second contains a specific capture molecule and only captures those particles onto which an analyte molecule has been immobilized. After passing these reaction zones the fluid enters the final porous material, the wick, that simply acts as a waste container. Lateral Flow Tests can operate as either competitive or sandwich assays.
Different formats may be adopted in LFIA. Strips used for LFIA contain four main components. A brief description of each is given before describing format types.
Sample application pad: It is made of cellulose and/or glass fiber and sample is applied on this pad to start assay. Its function is to transport the sample to other components of lateral flow test strip (LFTS). Sample pad should be capable of transportation of the sample in a smooth, continuous and homogenous manner. Sample application pads are sometimes designed to pretreat the sample before its transportation. This pretreatment may include separation of sample components, removal of interferences, adjustment of pH, etc.
Conjugate pad: It is the place where labeled biorecognition molecules are dispensed. Material of conjugate pad should immediately release labeled conjugate upon contact with moving liquid sample. Labeled conjugate should stay stable over entire life span of lateral flow strip. Any variations in dispensing, drying or release of conjugate can change results of assay significantly. Poor preparation of labeled conjugate can adversely affect sensitivity of assay. Glass fiber, cellulose, polyesters and some other materials are used to make conjugate pad for LFIA. Nature of conjugate pad material has an effect on release of labeled conjugate and sensitivity of assay.
Nitrocellulose membrane: It is highly critical in determining sensitivity of LFIA. Nitrocellulose membranes are available in different grades. Test and control lines are drawn over this piece of membrane. So an ideal membrane should provide support and good binding to capture probes (antibodies, aptamers etc.). Nonspecific adsorption over test and control lines may affect results of assay significantly, thus a good membrane will be characterized by lesser non-specific adsorption in the regions of test and control lines. Wicking rate of nitrocellulose membrane can influence assay sensitivity. These membranes are easy to use, inexpensive, and offer high affinity for proteins and other biomolecules. Proper dispensing of bioreagents, drying and blocking play a role in improving sensitivity of assay.
Adsorbent pad: It works as sink at the end of the strip. It also helps in maintaining flow rate of the liquid over the membrane and stops back flow of the sample. Adsorbent capacity to hold liquid can play an important role in results of assay.
All these components are fixed or mounted over a backing card. Materials for backing card are highly flexible because they have nothing to do with LFIA except providing a platform for proper assembling of all the components. Thus backing card serves as a support and it makes easy to handle the strip.
Major steps in LFIA are (i) preparation of antibody against target analyte (ii) preparation of label (iii) labeling of biorecognition molecules (iv) assembling of all components onto a backing card after dispensing of reagents at their proper pads (v) application of sample and obtaining results.
Sandwich format: In a typical format, label (Enzymes or nanoparticles or fluorescence dyes) coated antibody or aptamer is immobilized at conjugate pad. This is a temporary adsorption which can be flushed away by flow of any buffer solution. A primary antibody or aptamer against target analyte is immobilized over test line. A secondary antibody or probe against labeled conjugate antibody/aptamer is immobilized at control zone.
Sample containing the analyte is applied to the sample application pad and it subsequently migrates to the other parts of strip. At conjugate pad, target analyte is captured by the immobilized labeled antibody or aptamer conjugate and results in the formation of labeled antibody conjugate/analyte complex. This complex now reaches at nitrocellulose membrane and moves under capillary action. At test line, label antibody conjugate/analyte complex is captured by another antibody which is primary to the analyte. Analyte becomes sandwiched between labeled and primary antibodies forming labeled antibody conjugate/analyte/primary antibody complex. Excess labeled antibody conjugate will be captured at control zone by secondary antibody. Buffer or excess solution goes to absorption pad. Intensity of color at test line corresponds to the amount of target analyte and is measured with an optical strip reader or visually inspected. Appearance of color at control line ensures that a strip is functioning properly.
Competitive format: Such a format suits best for low molecular weight compounds which cannot bind two antibodies simultaneously. Absence of color at test line is an indication for the presence of analyte while appearance of color both at test and control lines indicates a negative result. Competitive format has two layouts. In the first layout, solution containing target analyte is applied onto the sample application pad and prefixed labeled biomolecule (antibody/aptamer) conjugate gets hydrated and starts flowing with moving liquid. Test line contains pre-immobilized antigen (same analyte to be detected) which binds specifically to label conjugate. Control line contains pre-immobilized secondary antibody which has the ability to bind with labeled antibody conjugate. When liquid sample reaches at the test line, pre-immobilized antigen will bind to the labeled conjugate in case target analyte in sample solution is absent or present in such a low quantity that some sites of labeled antibody conjugate were vacant. Antigen in the sample solution and the one which is immobilized at test line of strip compete to bind with labeled conjugate. In another layout, labeled analyte conjugate is dispensed at conjugate pad while a primary antibody to analyte is dispensed at test line. After application of analyte solution a competition takes place between analyte and labeled analyte to bind with primary antibody at test line.
Multiplex detection format: Multiplex detection format is used for detection of more than one target species and assay is performed over the strip containing test lines equal to number of target species to be analyzed. It is highly desirable to analyze multiple analytes simultaneously under same set of conditions. Multiplex detection format is very useful in clinical diagnosis where multiple analytes which are inter-dependent in deciding about the stage of a disease are to be detected. Lateral flow strips for this purpose can be built in various ways i.e. by increasing length and test lines on conventional strip, making other structures like stars or T-shapes. Shape of strip for LFIA will be dictated by number of target analytes. Miniaturized versions of LFIA based on microarrays for multiplex detection of DNA sequences have been reported to have several advantages such as less consumption of test reagents, requirement of lesser sample volume and better sensitivity.
Labels: Any material that is used as a label should be detectable at very low concentrations and it should retain its properties upon conjugation with biorecognition molecules. This conjugation is also expected not to change features of biorecognition probes. Ease in conjugation with biomolecules and stability over longer period of time are desirable features for a good label. Concentrations of labels down to 10−9 M are optically detectable. After the completion of assay, some labels generate direct signal (as color from gold colloidal) while others require additional steps to produce analytical signal (as enzymes produce detectable product upon reaction with suitable substrate). Hence the labels which give direct signal are preferable in LFA because of less time consumption and reduced procedure.
Gold nanoparticles: Colloidal gold nanoparticles are the most commonly used labels in LFA. Colloidal gold is inert and gives very perfect spherical particles. These particles have very high affinity toward biomolecules and can be easily functionalized. Optical properties of gold nanoparticles are dependent on size and shape. Size of particles can be tuned by use of suitable chemical additives. Their unique features include environment friendly preparation, high affinity toward proteins and biomolecules, enhanced stability, exceptionally higher values for charge transfer and good optical signaling. Optical signal of gold nanoparticles in colorimetric LFA can be amplified by deposition of silver, gold nanoparticles and enzymes.
Magnetic particles and aggregates: Colored magnetic particles produce color at the test line which is measured by an optical strip reader but magnetic signals coming from magnetic particles can also be used as detection signals and recorded by a magnetic assay reader. Magnetic signals are stable for longer time compared to optical signals and they enhance sensitivity of LFA by 10 to 1000 folds.
Fluorescent and luminescent materials: Fluorescent molecules are widely used in LFA as labels and the amount of fluorescence is used to quantitate the concentration of analyte in the sample. Detection of proteins is accomplished by using organic fluorophores such as rhodamine as labels in LFA.
Current developments in nanomaterial have headed to manufacture of quantum dots which display very unique electrical and optical properties. These semiconducting particles are not only water soluble but can also be easily combined with biomolecules because of closeness in dimensions. Owing to their unique optical properties, quantum dots have come up as a substitute to organic fluorescent dyes. Like gold nanoparticles QDs show size dependent optical properties and a broad spectrum of wavelengths can be monitored. Single light source is sufficient to excite quantum dots of all different sizes. QDs have high photo stability and absorption coefficients.
Upconverting phosphors (UCP) are characterized by their excitation in infra-red region and emission in high energy visible region. Compared to other fluorescent materials, they have a unique advantage of not showing any auto fluorescence. Because of their excitation in IR regions, they do not photo degrade biomolecules. A major advantage lies in their production from easily available bulk materials. Although difference in batch to batch preparation of UCP reporters can affect sensitivity of analysis in LFA, it was observed that they can enhance sensitivity of analytical signal by 10 to 100 folds compared to gold nanoparticles or colored latex beads, when analysis is carried out under same set of biological conditions.
Enzymes: Enzymes are also employed as labels in LFA. But they increase one step in LFA which is application of suitable substrate after complete assay. This substrate will produce color at test and control lines as a result of enzymatic reaction. In case of enzymes, selection of suitable enzyme substrate combination is one necessary requirement in order to get a colored product for strip reader or electroactive product for electrochemical detection. In other words, sensitivity of detection is dependent on enzyme substrate combination.
Colloidal carbon: Colloidal carbon is comparatively inexpensive label and its production can be easily scaled up. Because of their black color, carbon NPs can be easily detected with high sensitivity. Colloidal carbon can be functionalized with a large variety of biomolecules for detection of low and high molecular weight analytes.
Detection systems: In case of gold nanoparticles or other color producing labels, qualitative or semi-quantitative analysis can be done by visual inspection of colors at test and control lines. The major advantage of visual inspection is rapid qualitative answer in “Yes” or “NO”. Such quick replies about presence of an analyte in clinical analysis have very high importance. Such tests help doctors to make an immediate decision near the patients in hospitals in situations where test results from central labs cannot be waited for because of huge time consumption. But for quantification, optical strip readers are employed for measurement of the intensity of colors produced at test and control lines of strip. This is achieved by inserting the strips into a strip reader and intensities are recorded simultaneously by imaging softwares.
Optical images of the strips can also be recorded with a camera and then processed by using a suitable software. Procedure includes proper placement of strip under the camera and a controlled amount of light is thrown on the areas to be observed. Such systems use monochromatic light and wavelength of light can be adjusted to get a good contrast among test and control lines and background. In order to provide good quantitative and reproducible results, detection system should be sensitive to different intensities of colors. Optical standards can be used to calibrate an optical reader device. Automated systems have advantages over manual imaging and processing in terms of time consumption, interpretation of results and adjustment of variables.
In case of fluorescent labels, a fluorescence strip reader is used to record fluorescence intensity of test and control lines. Fluorescence brightness of test line increased with an increase in nitrated seruloplasmin concentration in human serum when it was detected with a fluorescence strip reader. A photoelectric sensor was also used for detection in LFIA where colloidal gold is exposed to light emitting diode and resulting photoelectrons are recorded. Chemiluminescence which results from reaction of enzyme and substrate is measured as a response to amount of target analyte. Magnetic strip readers and electrochemical detectors are also reported as detection systems in LFTS but they are not very common. Selection of detector is mainly determined by the label employed in analysis.
Examples of “Monoclonal antibodies for measuring CRP”, include without limitation: Mouse, Monoclonal (108-2A2); Mouse, Monoclonal (108-7G41D2); Mouse, Monoclonal (12D-2C-36), IgG1; Mouse, Monoclonal (1G1), IgG1; Mouse, Monoclonal (5A9), IgG2a kappa; Mouse, Monoclonal (63F4), IgG1; Mouse, Monoclonal (67A1), IgG1; Mouse, Monoclonal (8B-5E), IgG1; Mouse, Monoclonal (B893M), IgG2b, lambda; Mouse, Monoclonal (C1), IgG2b; Mouse, Monoclonal (C11F2), IgG; Mouse, Monoclonal (C2), IgG1; Mouse, Monoclonal (C3), IgG1; Mouse, Monoclonal (C4), IgG1; Mouse, Monoclonal (C5), IgG2a; Mouse, Monoclonal (C6), IgG2a; Mouse, Monoclonal (C7), IgG1; Mouse, Monoclonal (CRP103), IgG2b; Mouse, Monoclonal (CRP11), IgG1; Mouse, Monoclonal (CRP135), IgG1; Mouse, Monoclonal (CRP169), IgG2a; Mouse, Monoclonal (CRP30), IgG1; Mouse, Monoclonal (CRP36), IgG2a; Rabbit, Monoclonal (EPR283Y), IgG; Mouse, Monoclonal (KT39), IgG2b; Mouse, Monoclonal (N-a), IgG1; Mouse, Monoclonal (N1G1), IgG1; Monoclonal (P5A9AT); Mouse, Monoclonal (S5G1), IgG1; Mouse, Monoclonal (SB78c), IgG1; Mouse, Monoclonal (SB78d), IgG1 and Rabbit, Monoclonal (Y284), IgG.
Polyclonal antibodies for measuring determinants include without limitation antibodies that were produced from sera by active immunization of one or more of the following: Rabbit, Goat, Sheep, Chicken, Duck, Guinea Pig, Mouse, Donkey, Camel, Rat and Horse.
Examples of detection agents, include without limitation: scFv, dsFv, Fab, sVH, F(ab′)2, Cyclic peptides, Haptamers, A single-domain antibody, Fab fragments, Single-chain variable fragments, Affibody molecules, Affilins, Nanofitins, Anticalins, Avimers, DARPins, Kunitz domains, Fynomers and Monobody.
In particular embodiments, the kit does not comprise a number of antibodies that specifically recognize more than 50, 20 15, 10, 9, 8, 7, 6, 5 or 4 polypeptides.
In other embodiments, the array of the present invention does not comprise a number of antibodies that specifically recognize more than 50, 20 15, 10, 9, 8, 7, 6, 5 or 4 polypeptides.
Some aspects of the present invention can also be used to screen patient or subject populations in any number of settings. For example, a health maintenance organization, public health entity or school health program can screen a group of subjects to identify those requiring interventions, as described above, or for the collection of epidemiological data. Insurance companies (e.g., health, life or disability) may screen applicants in the process of determining coverage or pricing, or existing clients for possible intervention. Data collected in such population screens, particularly when tied to any clinical progression to conditions like infection, will be of value in the operations of, for example, health maintenance organizations, public health programs and insurance companies. Such data arrays or collections can be stored in machine-readable media and used in any number of health-related data management systems to provide improved healthcare services, cost effective healthcare, improved insurance operation, etc. See, for example, U.S. Patent Application No. 2002/0038227; U.S. Patent Application No. US 2004/0122296; U.S. Patent Application No. US 2004/0122297; and U.S. Pat. No. 5,018,067. Such systems can access the data directly from internal data storage or remotely from one or more data storage sites as further detailed herein.
A machine-readable storage medium can comprise a data storage material encoded with machine readable data or data arrays which, when using a machine programmed with instructions for using the data, is capable of use for a variety of purposes. Measurements of effective amounts of the biomarkers of the invention and/or the resulting evaluation of risk from those biomarkers can be implemented in computer programs executing on programmable computers, comprising, inter alia, a processor, a data storage system (including volatile and non-volatile memory and/or storage elements), at least one input device, and at least one output device. Program code can be applied to input data to perform the functions described above and generate output information. The output information can be applied to one or more output devices, according to methods known in the art. The computer may be, for example, a personal computer, microcomputer, or workstation of conventional design.
Each program can be implemented in a high level procedural or object oriented programming language to communicate with a computer system. However, the programs can be implemented in assembly or machine language, if desired. The language can be a compiled or interpreted language. Each such computer program can be stored on a storage media or device (e.g., ROM or magnetic diskette or others as defined elsewhere in this disclosure) readable by a general or special purpose programmable computer, for configuring and operating the computer when the storage media or device is read by the computer to perform the procedures described herein. The health-related data management system used in some aspects of the invention may also be considered to be implemented as a computer-readable storage medium, configured with a computer program, where the storage medium so configured causes a computer to operate in a specific and predefined manner to perform various functions described herein.
The polypeptide determinants of the present invention, in some embodiments thereof, can be used to generate a “reference determinant profile” of those subjects who do not have an infection. The determinants disclosed herein can also be used to generate a “subject determinant profile” taken from subjects who have an infection. The subject determinant profiles can be compared to a reference determinant profile to diagnose or identify subjects with an infection. The subject determinant profile of different infection types can be compared to diagnose or identify the type of infection. The reference and subject determinant profiles of the present invention, in some embodiments thereof, can be contained in a machine-readable medium, such as but not limited to, analog tapes like those readable by a VCR, CD-ROM, DVD-ROM, USB flash media, among others. Such machine-readable media can also contain additional test results, such as, without limitation, measurements of clinical parameters and traditional laboratory risk factors. Alternatively or additionally, the machine-readable media can also comprise subject information such as medical history and any relevant family history. The machine-readable media can also contain information relating to other disease-risk algorithms and computed indices such as those described herein.
The effectiveness of a treatment regimen can be monitored by detecting a determinant in an effective amount (which may be one or more) of samples obtained from a subject over time and comparing the amount of determinants detected. For example, a first sample can be obtained prior to the subject receiving treatment and one or more subsequent samples are taken after or during treatment of the subject.
For example, the methods of the invention can be used to discriminate between bacterial, viral and mixed infections (i.e. bacterial and viral co-infections). This will allow patients to be stratified and treated accordingly.
In a specific embodiment of the invention a treatment recommendation (i.e., selecting a treatment regimen) for a subject is provided by identifying the type infection (i.e., bacterial, viral, mixed infection or no infection) in the subject according to the method of any of the disclosed methods and recommending that the subject receive an antibiotic treatment if the subject is identified as having bacterial infection or a mixed infection; or an anti-viral treatment is if the subject is identified as having a viral infection.
Examples of antibiotic agents include, but are not limited to Daptomycin; Gemifloxacin; Telavancin; Ceftaroline; Fidaxomicin; Amoxicillin; Ampicillin; Bacampicillin; Carbenicillin; Cloxacillin; Dicloxacillin; Flucloxacillin; Mezlocillin; Nafcillin; Oxacillin; Penicillin G; Penicillin V; Piperacillin; Pivampicillin; Pivmecillinam; Ticarcillin; Aztreonam; Imipenem; Doripenem; Meropenem; Ertapenem; Clindamycin; Lincomycin; Pristinamycin; Quinupristin; Cefacetrile (cephacetrile); Cefadroxil (cefadroxyl); Cefalexin (cephalexin); Cefaloglycin (cephaloglycin); Cefalonium (cephalonium); Cefaloridine (cephaloridine); Cefalotin (cephalothin); Cefapirin (cephapirin); Cefatrizine; Cefazaflur; Cefazedone; Cefazolin (cephazolin); Cefradine (cephradine); Cefroxadine; Ceftezole; Cefaclor; Cefamandole; Cefmetazole; Cefonicid; Cefotetan; Cefoxitin; Cefprozil (cefproxil); Cefuroxime; Cefuzonam; Cefcapene; Cefdaloxime; Cefdinir; Cefditoren; Cefetamet; Cefixime; Cefmenoxime; Cefodizime; Cefotaxime; Cefpimizole; Cefpodoxime; Cefteram; Ceftibuten; Ceftiofur; Ceftiolene; Ceftizoxime; Ceftriaxone; Cefoperazone; Ceftazidime; Cefclidine; Cefepime; Cefluprenam; Cefoselis; Cefozopran; Cefpirome; Cefquinome; Fifth Generation; Ceftobiprole; Ceftaroline; Not Classified; Cefaclomezine; Cefaloram; Cefaparole; Cefcanel; Cefedrolor; Cefempidone; Cefetrizole; Cefivitril; Cefmatilen; Cefmepidium; Cefovecin; Cefoxazole; Cefrotil; Cefsumide; Cefuracetime; Ceftioxide; Azithromycin; Erythromycin; Clarithromycin; Dirithromycin; Roxithromycin; Telithromycin; Amikacin; Gentamicin; Kanamycin; Neomycin; Netilmicin; Paromomycin; Streptomycin; Tobramycin; Flumequine; Nalidixic acid; Oxolinic acid; Piromidic acid; Pipemidic acid; Rosoxacin; Ciprofloxacin; Enoxacin; Lomefloxacin; Nadifloxacin; Norfloxacin; Ofloxacin; Pefloxacin; Rufloxacin; Balofloxacin; Gatifloxacin; Grepafloxacin; Levofloxacin; Moxifloxacin; Pazufloxacin; Sparfloxacin; Temafloxacin; Tosufloxacin; Besifloxacin; Clinafloxacin; Gemifloxacin; Sitafloxacin; Trovafloxacin; Prulifloxacin; Sulfamethizole; Sulfamethoxazole; Sulfisoxazole; Trimethoprim-Sulfamethoxazole; Demeclocycline; Doxycycline; Minocycline; Oxytetracycline; Tetracycline; Tigecycline; Chloramphenicol; Metronidazole; Tinidazole; Nitrofurantoin; Vancomycin; Teicoplanin; Telavancin; Linezolid; Cycloserine 2; Rifampin; Rifabutin; Rifapentine; Bacitracin; Polymyxin B; Viomycin; Capreomycin.
If a viral infection is ruled in, the subject may be treated with an antiviral agent. Examples of antiviral agents include, but are not limited to Abacavir; Aciclovir; Acyclovir; Adefovir; Amantadine; Amprenavir; Ampligen; Arbidol; Atazanavir; Atripla; Balavir; Boceprevirertet; Cidofovir; Combivir; Dolutegravir; Darunavir; Delavirdine; Didanosine; Docosanol; Edoxudine; Efavirenz; Emtricitabine; Enfuvirtide; Entecavir; Ecoliever; Famciclovir; Fomivirsen; Fosamprenavir; Foscarnet; Fosfonet; Fusion inhibitor; Ganciclovir; Ibacitabine; Imunovir; Idoxuridine; Imiquimod; Indinavir; Inosine; Integrase inhibitor; Interferon type III; Interferon type II; Interferon type I; Interferon; Lamivudine; Lopinavir; Loviride; Maraviroc; Moroxydine; Methisazone; Nelfinavir; Nevirapine; Nexavir; Oseltamivir; Peginterferon alfa-2a; Penciclovir; Peramivir; Pleconaril; Podophyllotoxin; Raltegravir; Reverse transcriptase inhibitor; Ribavirin; Rimantadine; Ritonavir; Pyramidine; Saquinavir; Sofosbuvir; StavudineTelaprevir; Tenofovir; Tenofovir disoproxil; Tipranavir; Trifluridine; Trizivir; Tromantadine; Truvada; traporved; Valaciclovir; Valganciclovir; Vicriviroc; Vidarabine; Viramidine; Zalcitabine; Zanamivir; Zidovudine; RNAi antivirals; inhaled rhibovirons; monoclonal antibody respigams; neuriminidase blocking agents.
In another embodiment, the methods of the invention can be used to prompt additional targeted diagnosis such as pathogen specific PCRs, chest-X-ray, cultures etc. For example, a diagnosis that indicates a viral infection according to embodiments of this invention, may prompt the usage of additional viral specific multiplex-PCRs, whereas a diagnosis that indicates a bacterial infection according to embodiments of this invention may prompt the usage of a bacterial specific multiplex-PCR. Thus, one can reduce the costs of unwarranted expensive diagnostics.
In a specific embodiment, a diagnostic test recommendation for a subject is provided by identifying the infection type (i.e., bacterial, viral, mixed infection or no infection) in the subject according to any of the disclosed methods and recommending a test to determine the source of the bacterial infection if the subject is identified as having a bacterial infection or a mixed infection; or a test to determine the source of the viral infection if the subject is identified as having a viral infection.
Performance and Accuracy Measures of the Invention.
The performance and thus absolute and relative clinical usefulness of the invention may be assessed in multiple ways as noted above. Amongst the various assessments of performance, some aspects of the invention are intended to provide accuracy in clinical diagnosis and prognosis. The accuracy of a diagnostic or prognostic test, assay, or method concerns the ability of the test, assay, or method to distinguish between subjects having an infection is based on whether the subjects have, a “significant alteration” (e.g., clinically significant and diagnostically significant) in the levels of a determinant. By “effective amount” it is meant that the measurement of an appropriate number of determinants (which may be one or more) to produce a “significant alteration” (e.g. level of expression or activity of a determinant) that is different than the predetermined cut-off point (or threshold value) for that determinant (s) and therefore indicates that the subject has an infection for which the determinant (s) is an indication. The difference in the level of determinant is preferably statistically significant. As noted below, and without any limitation of the invention, achieving statistical significance, and thus the preferred analytical, diagnostic, and clinical accuracy, may require that combinations of several determinants be used together in panels and combined with mathematical algorithms in order to achieve a statistically significant determinant index.
In the categorical diagnosis of a disease state, changing the cut point or threshold value of a test (or assay) usually changes the sensitivity and specificity, but in a qualitatively inverse relationship. Therefore, in assessing the accuracy and usefulness of a proposed medical test, assay, or method for assessing a subject's condition, one should always take both sensitivity and specificity into account and be mindful of what the cut point is at which the sensitivity and specificity are being reported because sensitivity and specificity may vary significantly over the range of cut points. One way to achieve this is by using the Matthews correlation coefficient (MCC) metric, which depends upon both sensitivity and specificity. Use of statistics such as area under the ROC curve (AUC), encompassing all potential cut point values, is preferred for most categorical risk measures when using some aspects of the invention, while for continuous risk measures, statistics of goodness-of-fit and calibration to observed results or other gold standards, are preferred.
By predetermined level of predictability it is meant that the method provides an acceptable level of clinical or diagnostic accuracy. Using such statistics, an “acceptable degree of diagnostic accuracy”, is herein defined as a test or assay (such as the test used in some aspects of the invention for determining the clinically significant presence of determinants, which thereby indicates the presence an infection type) in which the AUC (area under the ROC curve for the test or assay) is at least 0.60, desirably at least 0.65, more desirably at least 0.70, preferably at least 0.75, more preferably at least 0.80, and most preferably at least 0.85.
By a “very high degree of diagnostic accuracy”, it is meant a test or assay in which the AUC (area under the ROC curve for the test or assay) is at least 0.75, 0.80, desirably at least 0.85, more desirably at least 0.875, preferably at least 0.90, more preferably at least 0.925, and most preferably at least 0.95.
Alternatively, the methods predict the presence or absence of an infection or response to therapy with at least 75% total accuracy, more preferably 80%, 85%, 90%, 95%, 97%, 98%, 99% or greater total accuracy.
Alternatively, the methods predict the presence of a bacterial infection or response to therapy with at least 75% sensitivity, more preferably 80%, 85%, 90%, 95%, 97%, 98%, 99% or greater sensitivity.
Alternatively, the methods predict the presence of a viral infection or response to viral therapy with at least 75% specificity, more preferably 80%, 85%, 90%, 95%, 97%, 98%, 99% or greater specificity.
Alternatively, the methods rule out the presence of a bacterial infection or rule in a viral infection with at least 75% NPV, more preferably 80%, 85%, 90%, 95%, 97%, 98%, 99% or greater NPV. Alternatively, the methods rule in the presence of a bacterial infection or rule out a viral infection with at least 75% PPV, more preferably 80%, 85%, 90%, 95%, 97%, 98%, 99% or greater PPV.
Alternatively, the methods predict the presence of a viral infection or response to therapy with at least 75% specificity, more preferably 80%, 85%, 90%, 95%, 97%, 98%, 99% or greater specificity. Alternatively, the methods predict the presence or absence of an infection or response to therapy with an MCC larger than 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9 or 1.0.
In general, alternative methods of determining diagnostic accuracy are commonly used for continuous measures, when a disease category has not yet been clearly defined by the relevant medical societies and practice of medicine, where thresholds for therapeutic use are not yet established, or where there is no existing gold standard for diagnosis of the pre-disease. For continuous measures of risk, measures of diagnostic accuracy for a calculated index are typically based on curve fit and calibration between the predicted continuous value and the actual observed values (or a historical index calculated value) and utilize measures such as R squared, Hosmer-Lemeshow P-value statistics and confidence intervals. It is not unusual for predicted values using such algorithms to be reported including a confidence interval (usually 90% or 95% CI) based on a historical observed cohort's predictions, as in the test for risk of future breast cancer recurrence commercialized by Genomic Health, Inc. (Redwood City, Calif.).
In general, by defining the degree of diagnostic accuracy, i.e., cut points on a ROC curve, defining an acceptable AUC value, and determining the acceptable ranges in relative concentration of what constitutes an effective amount of the determinants of the invention allows for one of skill in the art to use the determinants to identify, diagnose, or prognose subjects with a pre-determined level of predictability and performance.
Furthermore, other unlisted biomarkers will be very highly correlated with the determinants (for the purpose of this application, any two variables will be considered to be “very highly correlated” when they have a Coefficient of Determination (R2) of 0.5 or greater). Some aspects of the present invention encompass such functional and statistical equivalents to the aforementioned determinants. Furthermore, the statistical utility of such additional determinants is substantially dependent on the cross-correlation between multiple biomarkers and any new biomarkers will often be required to operate within a panel in order to elaborate the meaning of the underlying biology.
One or more of the listed determinants can be detected in the practice of the present invention, in some embodiments thereof. For example, two (2), three (3), four (4), five (5), ten (10), fifteen (15), twenty (20), forty (40), or more determinants can be detected.
In some aspects, all determinants listed herein can be detected. Preferred ranges from which the number of determinants can be detected include ranges bounded by any minimum selected from between one and, particularly two, three, four, five, six, seven, eight, nine ten, twenty, or forty. Particularly preferred ranges include two to five (2-5), two to ten (2-10), two to twenty (2-20), or two to forty (2-40).
Construction of Determinant Panels
Groupings of determinants can be included in “panels”, also called “determinant-signatures”, “determinant signatures”, or “multi-determinant signatures.” A “panel” within the context of the present invention means a group of biomarkers (whether they are determinants, clinical parameters, or traditional laboratory risk factors) that includes one or more determinants. A panel can also comprise additional biomarkers, e.g., clinical parameters, traditional laboratory risk factors, known to be present or associated with infection, in combination with a selected group of the determinants listed herein.
As noted above, many of the individual determinants, clinical parameters, and traditional laboratory risk factors listed, when used alone and not as a member of a multi-biomarker panel of determinants, have little or no clinical use in reliably distinguishing individual normal subjects, subjects at risk for having an infection (e.g., bacterial, viral or co-infection), and thus cannot reliably be used alone in classifying any subject between those three states. Even where there are statistically significant differences in their mean measurements in each of these populations, as commonly occurs in studies which are sufficiently powered, such biomarkers may remain limited in their applicability to an individual subject, and contribute little to diagnostic or prognostic predictions for that subject. A common measure of statistical significance is the p-value, which indicates the probability that an observation has arisen by chance alone; preferably, such p-values are 0.05 or less, representing a 5% or less chance that the observation of interest arose by chance. Such p-values depend significantly on the power of the study performed.
Despite this individual determinant performance, and the general performance of formulas combining only the traditional clinical parameters and few traditional laboratory risk factors, the present inventors have noted that certain specific combinations of two or more determinants can also be used as multi-biomarker panels comprising combinations of determinants that are known to be involved in one or more physiological or biological pathways, and that such information can be combined and made clinically useful through the use of various formulae, including statistical classification algorithms and others, combining and in many cases extending the performance characteristics of the combination beyond that of the individual determinants. These specific combinations show an acceptable level of diagnostic accuracy, and, when sufficient information from multiple determinants is combined in a trained formula, they often reliably achieve a high level of diagnostic accuracy transportable from one population to another.
The general concept of how two less specific or lower performing determinants are combined into novel and more useful combinations for the intended indications, is a key aspect of some embodiments of the invention. Multiple biomarkers can yield significant improvement in performance compared to the individual components when proper mathematical and clinical algorithms are used; this is often evident in both sensitivity and specificity, and results in a greater AUC or MCC. Significant improvement in performance could mean an increase of 1%, 2%, 3%, 4%, 5%, 8%, 10% or higher than 10% in different measures of accuracy such as total accuracy, AUC, MCC, sensitivity, specificity, PPV or NPV. Secondly, there is often novel unperceived information in the existing biomarkers, as such was necessary in order to achieve through the new formula an improved level of sensitivity or specificity. This hidden information may hold true even for biomarkers which are generally regarded to have suboptimal clinical performance on their own. In fact, the suboptimal performance in terms of high false positive rates on a single biomarker measured alone may very well be an indicator that some important additional information is contained within the biomarker results—information which would not be elucidated absent the combination with a second biomarker and a mathematical formula.
On the other hand, it is often useful to restrict the number of measured diagnostic determinants (e.g., protein biomarkers), as this allows significant cost reduction and reduces required sample volume and assay complexity. Accordingly, even when two signatures have similar diagnostic performance (e.g., similar AUC or sensitivity), one which incorporates fewer proteins could have significant utility and ability to reduce to practice. For example, a signature that includes 5 proteins compared to 10 proteins and performs similarly has many advantages in real world clinical setting and thus is desirable. Therefore, there is value and invention in being able to reduce the number of genes incorporated in a signature while retaining similar levels of accuracy. In this context similar levels of accuracy could mean plus or minus 1%, 2%, 3%, 4%, 5%, 8%, or 10% in different measures of accuracy such as total accuracy, AUC, MCC, sensitivity, specificity, PPV or NPV; a significant reduction in the number of genes of a signature includes reducing the number of genes by 2, 3, 4, 5, 6, 7, 8, 9, 10 or more than 10 genes.
Several statistical and modeling algorithms known in the art can be used to both assist in determinant selection choices and optimize the algorithms combining these choices. Statistical tools such as factor and cross-biomarker correlation/covariance analyses allow more rationale approaches to panel construction. Mathematical clustering and classification tree showing the Euclidean standardized distance between the determinants can be advantageously used. Pathway informed seeding of such statistical classification techniques also may be employed, as may rational approaches based on the selection of individual determinants based on their participation across in particular pathways or physiological functions.
Ultimately, formula such as statistical classification algorithms can be directly used to both select determinants and to generate and train the optimal formula necessary to combine the results from multiple determinants into a single index. Often, techniques such as forward (from zero potential explanatory parameters) and backwards selection (from all available potential explanatory parameters) are used, and information criteria, such as AIC or BIC, are used to quantify the tradeoff between the performance and diagnostic accuracy of the panel and the number of determinants used. The position of the individual determinant on a forward or backwards selected panel can be closely related to its provision of incremental information content for the algorithm, so the order of contribution is highly dependent on the other constituent determinants in the panel.
Construction of Clinical Algorithms
Any formula may be used to combine determinant results into indices useful in the practice of the invention. As indicated above, and without limitation, such indices may indicate, among the various other indications, the probability, likelihood, absolute or relative risk, time to or rate of conversion from one to another disease states, or make predictions of future biomarker measurements of infection. This may be for a specific time period or horizon, or for remaining lifetime risk, or simply be provided as an index relative to another reference subject population.
Although various preferred formula are described here, several other model and formula types beyond those mentioned herein and in the definitions above are well known to one skilled in the art. The actual model type or formula used may itself be selected from the field of potential models based on the performance and diagnostic accuracy characteristics of its results in a training population. The specifics of the formula itself may commonly be derived from determinant results in the relevant training population. Amongst other uses, such formula may be intended to map the feature space derived from one or more determinant inputs to a set of subject classes (e.g. useful in predicting class membership of subjects as normal, having an infection), to derive an estimation of a probability function of risk using a Bayesian approach, or to estimate the class-conditional probabilities, then use Bayes' rule to produce the class probability function as in the previous case.
Preferred formulas include the broad class of statistical classification algorithms, and in particular the use of discriminant analysis. The goal of discriminant analysis is to predict class membership from a previously identified set of features. In the case of linear discriminant analysis (LDA), the linear combination of features is identified that maximizes the separation among groups by some criteria. Features can be identified for LDA using an eigengene based approach with different thresholds (ELDA) or a stepping algorithm based on a multivariate analysis of variance (MANOVA). Forward, backward, and stepwise algorithms can be performed that minimize the probability of no separation based on the Hotelling-Lawley statistic.
Eigengene-based Linear Discriminant Analysis (ELDA) is a feature selection technique developed by Shen et al. (2006). The formula selects features (e.g. biomarkers) in a multivariate framework using a modified eigen analysis to identify features associated with the most important eigenvectors. “Important” is defined as those eigenvectors that explain the most variance in the differences among samples that are trying to be classified relative to some threshold.
A support vector machine (SVM) is a classification formula that attempts to find a hyperplane that separates two classes. This hyperplane contains support vectors, data points that are exactly the margin distance away from the hyperplane. In the likely event that no separating hyperplane exists in the current dimensions of the data, the dimensionality is expanded greatly by projecting the data into larger dimensions by taking non-linear functions of the original variables (Venables and Ripley, 2002). Although not required, filtering of features for SVM often improves prediction. Features (e.g., biomarkers) can be identified for a support vector machine using a non-parametric Kruskal-Wallis (KW) test to select the best univariate features. A random forest (RF, Breiman, 2001) or recursive partitioning (RPART, Breiman et al., 1984) can also be used separately or in combination to identify biomarker combinations that are most important. Both KW and RF require that a number of features be selected from the total. RPART creates a single classification tree using a subset of available biomarkers.
Other formula may be used in order to pre-process the results of individual determinant measurements into more valuable forms of information, prior to their presentation to the predictive formula. Most notably, normalization of biomarker results, using either common mathematical transformations such as logarithmic or logistic functions, as normal or other distribution positions, in reference to a population's mean values, etc. are all well known to those skilled in the art. Of particular interest are a set of normalizations based on clinical-determinants such as time from symptoms, gender, race, or sex, where specific formula are used solely on subjects within a class or continuously combining a clinical-determinants as an input. In other cases, analyte-based biomarkers can be combined into calculated variables which are subsequently presented to a formula.
In addition to the individual parameter values of one subject potentially being normalized, an overall predictive formula for all subjects, or any known class of subjects, may itself be recalibrated or otherwise adjusted based on adjustment for a population's expected prevalence and mean biomarker parameter values, according to the technique outlined in D'Agostino et al., (2001) JAMA 286:180-187, or other similar normalization and recalibration techniques. Such epidemiological adjustment statistics may be captured, confirmed, improved and updated continuously through a registry of past data presented to the model, which may be machine readable or otherwise, or occasionally through the retrospective query of stored samples or reference to historical studies of such parameters and statistics. Additional examples that may be the subject of formula recalibration or other adjustments include statistics used in studies by Pepe, M. S. et al., 2004 on the limitations of odds ratios; Cook, N. R., 2007 relating to ROC curves. Finally, the numeric result of a classifier formula itself may be transformed post-processing by its reference to an actual clinical population and study results and observed endpoints, in order to calibrate to absolute risk and provide confidence intervals for varying numeric results of the classifier or risk formula.
There are various ways (and formulations) to combine two biomarkers into one predictive score. For example, using dual cutoffs—one for each biomarker, generates a quadrary separation pattern that can separate between bacterial, viral and mixed (bacterial-viral co-infection) patients. For some biomarkers, adding another cutoff also enables the identification of healthy patients by generating a separation pattern composed of six units. Alternatively, the separation between bacterial and viral patients could be based on the ratio between the two biomarkers. Using a defined cutoff for the ratio between the two biomarkers generates a line that separates between bacterial and viral zones.
Another way to combine two biomarkers is using statistical classification algorithms that can generate various unique separation hyperplanes that distinguish between two groups of patients with high levels of accuracy in a cutoff independent manner. Importantly, cutoff independent models (generated for example using statistical classification algorithms) can provide a likelihood score (e.g., 90% chance for bacterial infection) compared to a binary result (bacterial or viral result only) obtained using defined cutoffs and a quadrary/six units separation patterns. Thus, it can provide additional clinical information that can guide correct patient management. Examples for statistical classification algorithms include Artificial Neural Networks (ANN), Support Vector Machines (SVM), Bayesian Networks (BN), K-Nearest Neighbor (KNN) and Logistic Regression.
Thus, certain embodiments of this invention include combining two polypeptides out of the list of polypeptides that includes for example CRP, TRAIL, PCT, IL-6, IP-10, MX1, for distinguishing between bacterial and viral patients.
In one embodiment, the separation is based on applying dual cutoffs (one for each biomarker) and generating a quadrary separation pattern.
In another embodiment, the separation is based on applying dual cutoffs for one biomarker and a single cutoff for the second biomarker and generating a six unit separation pattern.
In another embodiment, the separation is based on the ratio between the two biomarkers using a defined cutoff.
In yet another embodiment, the combination of the two biomarkers is performed in a cutoff independent manner using statistical classification algorithms.
Some determinants may exhibit trends that depends on the patient age (e.g. the population baseline may rise or fall as a function of age). One can use an ‘Age dependent normalization or stratification’ scheme to adjust for age related differences. Performing age dependent normalization, stratification or distinct mathematical formulas can be used to improve the accuracy of determinants for differentiating between different types of infections. For example, one skilled in the art can generate a function that fits the population mean levels of each determinant as function of age and use it to normalize the determinant of individual subjects levels across different ages. Another example is to stratify subjects according to their age and determine age specific thresholds or index values for each age group independently.
In the context of the present invention the following statistical terms may be used:
“TP” is true positive, means positive test result that accurately reflects the tested-for activity. For example in the context of the present invention a TP, is for example but not limited to, truly classifying a bacterial infection as such.
“TN” is true negative, means negative test result that accurately reflects the tested-for activity. For example in the context of the present invention a TN, is for example but not limited to, truly classifying a viral infection as such.
“FN” is false negative, means a result that appears negative but fails to reveal a situation. For example in the context of the present invention a FN, is for example but not limited to, falsely classifying a bacterial infection as a viral infection.
“FP” is false positive, means test result that is erroneously classified in a positive category. For example in the context of the present invention a FP, is for example but not limited to, falsely classifying a viral infection as a bacterial infection.
“Sensitivity” is calculated by TP/(TP+FN) or the true positive fraction of disease subjects.
“Specificity” is calculated by TN/(TN+FP) or the true negative fraction of non-disease or normal subjects.
“Total accuracy” is calculated by (TN+TP)/(TN+FP+TP+FN).
“Positive predictive value” or “PPV” is calculated by TP/(TP+FP) or the true positive fraction of all positive test results. It is inherently impacted by the prevalence of the disease and pre-test probability of the population intended to be tested.
“Negative predictive value” or “NPV” is calculated by TN/(TN+FN) or the true negative fraction of all negative test results. It also is inherently impacted by the prevalence of the disease and pre-test probability of the population intended to be tested. See, e.g., O'Marcaigh A S, Jacobson R M, “Estimating The Predictive Value Of A Diagnostic Test, How To Prevent Misleading Or Confusing Results,” Clin. Ped. 1993, 32(8): 485-491, which discusses specificity, sensitivity, and positive and negative predictive values of a test, e.g., a clinical diagnostic test.
“MCC” (Matthews Correlation coefficient) is calculated as follows: MCC=(TP*TN−FP*FN)/{(TP+FN)*(TP+FP)*(TN+FP)*(TN+FN)}{circumflex over ( )}0.5 where TP, FP, TN, FN are true-positives, false-positives, true-negatives, and false-negatives, respectively. Note that MCC values range between −1 to +1, indicating completely wrong and perfect classification, respectively. An MCC of 0 indicates random classification. MCC has been shown to be a useful for combining sensitivity and specificity into a single metric (Baldi, Brunak et al. 2000). It is also useful for measuring and optimizing classification accuracy in cases of unbalanced class sizes (Baldi, Brunak et al. 2000).
Often, for binary disease state classification approaches using a continuous diagnostic test measurement, the sensitivity and specificity is summarized by a Receiver Operating Characteristics (ROC) curve according to Pepe et al., “Limitations of the Odds Ratio in Gauging the Performance of a Diagnostic, Prognostic, or Screening Marker,” Am. J. Epidemiol 2004, 159 (9): 882-890, and summarized by the Area Under the Curve (AUC) or c-statistic, an indicator that allows representation of the sensitivity and specificity of a test, assay, or method over the entire range of test (or assay) cut points with just a single value. See also, e.g., Shultz, “Clinical Interpretation Of Laboratory Procedures,” chapter 14 in Teitz, Fundamentals of Clinical Chemistry, Burtis and Ashwood (eds.), 4th edition 1996, W.B. Saunders Company, pages 192-199; and Zweig et al., “ROC Curve Analysis: An Example Showing The Relationships Among Serum Lipid And Apolipoprotein Concentrations In Identifying Subjects With Coronory Artery Disease,” Clin. Chem., 1992, 38(8): 1425-1428. An alternative approach using likelihood functions, odds ratios, information theory, predictive values, calibration (including goodness-of-fit), and reclassification measurements is summarized according to Cook, “Use and Misuse of the Receiver Operating Characteristic Curve in Risk Prediction,” Circulation 2007, 115: 928-935.
“Accuracy” refers to the degree of conformity of a measured or calculated quantity (a test reported value) to its actual (or true) value. Clinical accuracy relates to the proportion of true outcomes (true positives (TP) or true negatives (TN) versus misclassified outcomes (false positives (FP) or false negatives (FN)), and may be stated as a sensitivity, specificity, positive predictive values (PPV) or negative predictive values (NPV), Matthews correlation coefficient (MCC), or as a likelihood, odds ratio, Receiver Operating Characteristic (ROC) curve, Area Under the Curve (AUC) among other measures.
A “formula,” “algorithm,” or “model” is any mathematical equation, algorithmic, analytical or programmed process, or statistical technique that takes one or more continuous or categorical inputs (herein called “parameters”) and calculates an output value, sometimes referred to as an “index” or “index value”. Non-limiting examples of “formulas” include sums, ratios, and regression operators, such as coefficients or exponents, biomarker value transformations and normalizations (including, without limitation, those normalization schemes based on clinical-determinants, such as gender, age, or ethnicity), rules and guidelines, statistical classification models, and neural networks trained on historical populations. Of particular use in combining determinants are linear and non-linear equations and statistical classification analyses to determine the relationship between levels of determinants detected in a subject sample and the subject's probability of having an infection or a certain type of infection.
In panel and combination construction, of particular interest are structural and syntactic statistical classification algorithms, and methods of index construction, utilizing pattern recognition features, including established techniques such as cross-correlation, Principal Components Analysis (PCA), factor rotation, Logistic Regression (LogReg), Linear Discriminant Analysis (LDA), Eigengene Linear Discriminant Analysis (ELDA), Support Vector Machines (SVM), Random Forest (RF), Recursive Partitioning Tree (RPART), as well as other related decision tree classification techniques, Shrunken Centroids (SC), StepAIC, Kth-Nearest Neighbor, Boosting, Decision Trees, Neural Networks, Bayesian Networks, and Hidden Markov Models, among others. Other techniques may be used in survival and time to event hazard analysis, including Cox, Weibull, Kaplan-Meier and Greenwood models well known to those of skill in the art. Many of these techniques are useful either combined with a determinant selection technique, such as forward selection, backwards selection, or stepwise selection, complete enumeration of all potential panels of a given size, genetic algorithms, or they may themselves include biomarker selection methodologies in their own technique. These may be coupled with information criteria, such as Akaike's Information Criterion (AIC) or Bayes Information Criterion (BIC), in order to quantify the tradeoff between additional biomarkers and model improvement, and to aid in minimizing overfit. The resulting predictive models may be validated in other studies, or cross-validated in the study they were originally trained in, using such techniques as Bootstrap, Leave-One-Out (LOO) and 10-Fold cross-validation (10-Fold CV). At various steps, false discovery rates may be estimated by value permutation according to techniques known in the art. A “health economic utility function” is a formula that is derived from a combination of the expected probability of a range of clinical outcomes in an idealized applicable patient population, both before and after the introduction of a diagnostic or therapeutic intervention into the standard of care. It encompasses estimates of the accuracy, effectiveness and performance characteristics of such intervention, and a cost and/or value measurement (a utility) associated with each outcome, which may be derived from actual health system costs of care (services, supplies, devices and drugs, etc.) and/or as an estimated acceptable value per quality adjusted life year (QALY) resulting in each outcome.
The sum, across all predicted outcomes, of the product of the predicted population size for an outcome multiplied by the respective outcome's expected utility is the total health economic utility of a given standard of care. The difference between (i) the total health economic utility calculated for the standard of care with the intervention versus (ii) the total health economic utility for the standard of care without the intervention results in an overall measure of the health economic cost or value of the intervention. This may itself be divided amongst the entire patient group being analyzed (or solely amongst the intervention group) to arrive at a cost per unit intervention, and to guide such decisions as market positioning, pricing, and assumptions of health system acceptance. Such health economic utility functions are commonly used to compare the cost-effectiveness of the intervention, but may also be transformed to estimate the acceptable value per QALY the health care system is willing to pay, or the acceptable cost-effective clinical performance characteristics required of a new intervention.
For diagnostic (or prognostic) interventions of the invention, as each outcome (which in a disease classifying diagnostic test may be a TP, FP, TN, or FN) bears a different cost, a health economic utility function may preferentially favor sensitivity over specificity, or PPV over NPV based on the clinical situation and individual outcome costs and value, and thus provides another measure of health economic performance and value which may be different from more direct clinical or analytical performance measures. These different measurements and relative trade-offs generally will converge only in the case of a perfect test, with zero error rate (a.k.a., zero predicted subject outcome misclassifications or FP and FN), which all performance measures will favor over imperfection, but to differing degrees.
“Analytical accuracy” refers to the reproducibility and predictability of the measurement process itself, and may be summarized in such measurements as coefficients of variation (CV), Pearson correlation, and tests of concordance and calibration of the same samples or controls with different times, users, equipment and/or reagents. These and other considerations in evaluating new biomarkers are also summarized in Vasan, 2006.
“Performance” is a term that relates to the overall usefulness and quality of a diagnostic or prognostic test, including, among others, clinical and analytical accuracy, other analytical and process characteristics, such as use characteristics (e.g., stability, ease of use), health economic value, and relative costs of components of the test. Any of these factors may be the source of superior performance and thus usefulness of the test, and may be measured by appropriate “performance metrics,” such as AUC and MCC, time to result, shelf life, etc. as relevant.
By “statistically significant”, it is meant that the alteration is greater than what might be expected to happen by chance alone (which could be a “false positive”). Statistical significance can be determined by any method known in the art. Commonly used measures of significance include the p-value, which presents the probability of obtaining a result at least as extreme as a given data point, assuming the data point was the result of chance alone. A result is often considered highly significant at a p-value of 0.05 or less.
In the context of the present invention the following abbreviations may be used: Antibiotics (Abx), Adverse Event (AE), Arbitrary Units (A.U.), Complete Blood Count (CBC), Case Report Form (CRF), Chest X-Ray (CXR), Electronic Case Report Form (eCRF), Food and Drug Administration (FDA), Good Clinical Practice (GCP), Gastrointestinal (GI), Gastroenteritis (GE), International Conference on Harmonization (ICH), Infectious Disease (ID), In vitro diagnostics (IVD), Lower Respiratory Tract Infection (LRTI), Myocardial infarction (MI), Polymerase chain reaction (PCR), Per-oss (P.O), Per-rectum (P.R), Standard of Care (SoC), Standard Operating Procedure (SOP), Urinary Tract Infection (UTI), Upper Respiratory Tract Infection (URTI).
As used herein the term “about” refers to ±10%.
The terms “comprises”, “comprising”, “includes”, “including”, “having” and their conjugates mean “including but not limited to”.
The term “consisting of” means “including and limited to”.
The term “consisting essentially of” means that the composition, method or structure may include additional ingredients, steps and/or parts, but only if the additional ingredients, steps and/or parts do not materially alter the basic and novel characteristics of the claimed composition, method or structure.
As used herein, the singular form “a”, “an” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a compound” or “at least one compound” may include a plurality of compounds, including mixtures thereof.
Throughout this application, various embodiments of this invention may be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 3, 4, 5, and 6. This applies regardless of the breadth of the range.
Whenever a numerical range is indicated herein, it is meant to include any cited numeral (fractional or integral) within the indicated range. The phrases “ranging/ranges between” a first indicate number and a second indicate number and “ranging/ranges from” a first indicate number “to” a second indicate number are used herein interchangeably and are meant to include the first and second indicated numbers and all the fractional and integral numerals therebetween.
As used herein the term “method” refers to manners, means, techniques and procedures for accomplishing a given task including, but not limited to, those manners, means, techniques and procedures either known to, or readily developed from known manners, means, techniques and procedures by practitioners of the chemical, pharmacological, biological, biochemical and medical arts.
As used herein, the term “treating” includes abrogating, substantially inhibiting, slowing or reversing the progression of a condition, substantially ameliorating clinical or aesthetical symptoms of a condition or substantially preventing the appearance of clinical or aesthetical symptoms of a condition.
It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable subcombination or as suitable in any other described embodiment of the invention. Certain features described in the context of various embodiments are not to be considered essential features of those embodiments, unless the embodiment is inoperative without those elements.
Although the invention has been described in conjunction with specific embodiments thereof, it is evident that many alternatives, modifications and variations will be apparent to those skilled in the art. Accordingly, it is intended to embrace all such alternatives, modifications and variations that fall within the spirit and broad scope of the appended claims.
All publications, patents and patent applications mentioned in this specification are herein incorporated in their entirety by reference into the specification, to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated herein by reference. In addition, citation or identification of any reference in this application shall not be construed as an admission that such reference is available as prior art to the present invention. To the extent that section headings are used, they should not be construed as necessarily limiting.
Various embodiments and aspects of the present invention as delineated hereinabove and as claimed in the claims section below find experimental support in the following examples.
Reference is now made to the following examples, which together with the above descriptions illustrate some embodiments of the invention in a non limiting fashion.
Generally, the nomenclature used herein and the laboratory procedures utilized in the present invention include molecular, biochemical, microbiological and recombinant DNA techniques. Such techniques are thoroughly explained in the literature. See, for example, “Molecular Cloning: A laboratory Manual” Sambrook et al., (1989); “Current Protocols in Molecular Biology” Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al., “Current Protocols in Molecular Biology”, John Wiley and Sons, Baltimore, Md. (1989); Perbal, “A Practical Guide to Molecular Cloning”, John Wiley & Sons, New York (1988); Watson et al., “Recombinant DNA”, Scientific American Books, New York; Birren et al. (eds) “Genome Analysis: A Laboratory Manual Series”, Vols. 1-4, Cold Spring Harbor Laboratory Press, New York (1998); methodologies as set forth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and 5,272,057; “Cell Biology: A Laboratory Handbook”, Volumes I-III Cellis, J. E., ed. (1994); “Culture of Animal Cells—A Manual of Basic Technique” by Freshney, Wiley-Liss, N. Y. (1994), Third Edition; “Current Protocols in Immunology” Volumes I-III Coligan J. E., ed. (1994); Stites et al. (eds), “Basic and Clinical Immunology” (8th Edition), Appleton & Lange, Norwalk, Conn. (1994); Mishell and Shiigi (eds), “Selected Methods in Cellular Immunology”, W. H. Freeman and Co., New York (1980); available immunoassays are extensively described in the patent and scientific literature, see, for example, U.S. Pat. Nos. 3,791,932; 3,839,153; 3,850,752; 3,850,578; 3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281,521; “Oligonucleotide Synthesis” Gait, M. J., ed. (1984); “Nucleic Acid Hybridization” Hames, B. D., and Higgins S. J., eds. (1985); “Transcription and Translation” Hames, B. D., and Higgins S. J., eds. (1984); “Animal Cell Culture” Freshney, R. I., ed. (1986); “Immobilized Cells and Enzymes” IRL Press, (1986); “A Practical Guide to Molecular Cloning” Perbal, B., (1984) and “Methods in Enzymology” Vol. 1-317, Academic Press; “PCR Protocols: A Guide To Methods And Applications”, Academic Press, San Diego, Calif. (1990); Marshak et al., “Strategies for Protein Purification and Characterization—A Laboratory Course Manual” CSHL Press (1996); all of which are incorporated by reference as if fully set forth herein. Other general references are provided throughout this document. The procedures therein are believed to be well known in the art and are provided for the convenience of the reader. All the information contained therein is incorporated herein by reference.
Methods
Patient recruitment: A total of 1057 patients were recruited to the study of whom 948 had a suspected infectious disease and 109 had a non-infectious disease (control group). Informed consent was obtained from each participant or legal guardian, as applicable. Inclusion criteria for the infectious disease cohort included: clinical suspicion of an acute infectious disease, peak fever >37.5° C. since symptoms onset, and duration of symptoms ≤12 days. Inclusion criteria for the control group included: clinical impression of a non-infectious disease (e.g., trauma, stroke and myocardial infarction), or healthy subjects. Exclusion criteria included: evidence of any episode of acute infectious disease in the two weeks preceding enrollment; diagnosed congenital immune deficiency; current treatment with immunosuppressive or immunomodulatory therapy; active malignancy, proven or suspected human immunodeficiency virus (HIV)-1, hepatitis B virus (HBV), or hepatitis C virus (HCV) infection. Importantly, in order to enable broad generalization, antibiotic treatment at enrollment did not cause exclusion from the study. An overview of study workflow is depicted in
Enrollment process and data collection: For each patient, the following baseline variables were recorded: demographics, physical examination, medical history (e.g. main complaints, underlying diseases, chronically-administered medications, comorbidities, time of symptom onset, and peak temperature), complete blood count (CBC) obtained at enrollment, and chemistry panel (e.g. creatinine, urea, electrolytes, and liver enzymes). A nasal swab was obtained from each patient for further microbiological investigation, and a blood sample was obtained for protein screening and validation. Additional samples were obtained as deemed appropriate by the physician (e.g. urine and stool samples in cases of suspected urinary tract infection [UTI], and gastroenteritis [GI] respectively). Radiological tests were obtained at the discretion of the physician (e.g. chest X-ray for suspected lower respiratory tract infection [LRTI]). All information was recorded in a custom electronic case report form (eCRF).
Establishing the reference standard: Currently, no single reference standard exists for determining bacterial and viral infections in a wide range of clinical syndromes. Therefore, a rigorous reference standard was created following recommendations of the Standards for Reporting of Diagnostic Accuracy (STARD) [21]. First, a thorough clinical and microbiological investigation was performed for each patient as described above. Then, all the data collected throughout the disease course was reviewed by a panel of up to three physicians that assigned one of the following diagnostic labels to each patient: (i) bacterial; (ii) viral; (iii) no apparent infectious disease or healthy (controls); and (iv) indeterminate. Importantly, the panel members were blinded to the labeling of their peers to prevent group pressure or influential personality bias as recommended by NHS-HTA [22], and to the results of the host-proteins measurements.
Samples, procedures and sample processing: Venous blood samples were stored at 4° C. for up to 5 hours, subsequently fractionated into plasma, serum and total leukocytes, and stored at −80° C. Nasal swabs and stool samples were stored at 4° C. for up to 72 hours and subsequently transported to a certified service laboratory for multiplex PCRs. C-reactive protein (CRP) was measured from serum using either Cobas-6000, Cobas-Integra-400/800, or Modular-Analytics-P800 (Roche). Procalcitonin (PCT) was measured using either Elecsys BRAHMS PCT Kit or LIAISON BRAHMS PCT Kit. Other host-determinants were measured using enzyme-linked immunosorbent-assay (ELISA).
Statistical analysis Primary analysis was based on area under the receiver operating curve (AUC), Matthews correlation coefficient (MCC), sensitivity, specificity, total accuracy. positive predictive value (PPV), and negative predictive value (NPV). These measures are defined as follows:
P, N, TP, FP, TN, FN are positives, negatives, true-positives, false-positives, true-negatives, and false-negatives, respectively. Unless mentioned otherwise, positives and negatives refer to patients with bacterial and viral infections, respectively.
Results
Patients characteristics: The studied group of acute infection patients included 47% females and 53% males aged 1 month to 88 years. The patients presented with a variety of clinical syndromes affecting different physiological systems (e.g., respiratory, urinal, central nervous system, systemic). Detailed characterization of studied patients is depicted in
Importantly, as improved identification of bacterial patients was the primary end goal of the inventors, the evaluated cohort was deliberately enriched with hard to diagnose patients, previously classified by individual proteins or the TCP signature as false negative or false positives. Therefore the performance measures of the TCP in the following sections are significantly lower than what would be expected in the general population.
Generating New Host-Protein Signatures with Improved Ability to Identify Bacterial Infected Patients and Distinguish them from Viral Patients:
The TCP signature predictive score is calculated using a non-linear Multinomial Logistic Regression model (MLR; Table 3). The model provides a viral or other (including non-infectious) labels when the predictive score is between 0-35; a bacterial label when the predictive score is between 65-100; and an equivocal result when the predictive score is between 35-65. Its measures of accuracy on the studied cohort are summarized in Table 4.
In trying to improve the sensitivity of the TCP signature we evaluated different ways to combine it with additional proteins such as IL-6 and PCT. We initially evaluated the performance of PCT and IL-6 as individual classifiers in cutoff independent (using logistic regression models; Table 5), and dependent manner (Table 6). The logistic regression model used for calculating IL-6 or PCT measures of accuracy in a cutoff independent manner is:
Statistical Classification Algorithms
Both PCT and IL-6 were poor-medium classifiers in the studied cohort with a maximal sensitivity of 0.68 (IL-6) and 0.47 (PCT). To test whether they are able to improve the sensitivity of the TCP signature requires: i) to mathematically combine them with the TCP model; and ii) to test the new combination on hundreds of real world clinical samples. To combine the TCP signature with IL-6 and PCT, several statistical approaches were applied in order to generate different unique separation hyperplanes that distinguish between bacterial and viral patients with higher levels of accuracy. The inventors first examined multiple statistical classification algorithms and computational models including Artificial Neural Networks (ANN), Support Vector Machines (SVM), Bayesian Networks (BN), K-Nearest Neighbor (KNN) and Logistic Regression. Results using Logistic Regression are provided herein below. The performance (accuracy levels) of the developed models using real world infectious disease clinical samples described above was evaluated (Tables 7-9). A set of quantitative parameters (model coefficients) that specifically define the hyperplane separating between two patient groups are provided in Tables 7-9. As clinically demonstrated, both IL-6 and PCT (and IL-6+PCT) were able to improve the sensitivity of the TCP signature and comprising proteins (Tables 7-9).
Using Fuzzy OR Model to Generate Improved Signatures for Distinguishing Between Bacterial and Viral Patients
The inventors developed the models which incorporates the measurements of PCT and or IL-6 with the results of the TCP model in a manner that allows a significant improvement in model specificity. These models are referred to as “Fuzzy Or models.”
The rationale behind the construction of the Fuzzy or Model is as follows: in the data the inventors found that both IL-6 and PCT have relatively very low sensitivity but reasonable specificity, for distinguishing between bacterial and viral etiologies. This is particularly true for relatively high cutoffs (e.g., IL-6 cutoff of 100 pg/mi gives sensitivity of 31% and specificity of 95%; PCT cutoff of 2 μg/L gives sensitivity of 22%, specificity of 98%; Tables 10-12). Accordingly, the inventors devised a novel model that incorporates the TCP signature with levels of IL-6, PCT or both. In particular the new Fuzzy OR model gives low weight to low or medium levels of IL-6 and PCT, because the inventors found that such low levels add limited information beyond the TCP signature. Accordingly, the Fuzzy OR model was devised such that the signature is by and large dominated by the likelihood of the TCP signature (
However, as IL-6 and PCT levels become higher (for example without limitation 100, 200, 240, 250, 280, 320, and 350 pg/ml for IL-6 and 1, 1.5, 2, 2.5, 5, and 7.5 μg/L for PCT), they start to increase the likelihood of bacterial infection. The hill coefficient, is applied to control over the slope of the transition between TCP signature prediction to IL-6 or PCT. The result of the combined model is a single likelihood score for prediction of bacterial infections that has improved sensitivity compared to the TCP model (
Examples of such models are described in Fuzzy OR formulas #1-6, below:
Fuzzy OR Formula #1
were
TCPprob=TCP signature score/100 (scale of 0-1)
hPCT=PCT model hill coefficient
cPCT=PCT model cutoff
Fuzzy OR Formula #2
TCPprob=TCP signature score/100 (scale of 0-1)
HIL6=IL-6 model hill coefficient
CIL6=IL-6 model cutoff
Fuzzy OR Formula #3
Fuzzy OR Formula #4
In one preferred embodiment a very small constant (ε) is added to the protein concentrations to prevent numeric instability:
TCPprob=TCP signature score/100 (scale of 0-1)
hPCT=PCT model hill coefficient
cPCT=PCT model cutoff
Fuzzy OR Formula #5
TCPprob=TCP signature score/100 (scale of 0-1)
HIL6=IL-6 model hill coefficient
CIL6=IL-6 model cutoff
The inventors further evaluated the performance (accuracy levels) of the developed model in distinguishing between bacterial and viral patients (Tables 10-12), and between bacterial and non-bacterial (viral plus non-infectious) patients (Tables 13-15). The Fuzzy OR models significantly improved the TCP signature sensitivity. For example, combining IL-6 and the TCP signature resulted in sensitivity levels of 0.834-0.888 depending on the cutoff applied (Table 10). Combining PCT and the TCP signature resulted in sensitivity levels of 0.82-0.99 depending on the cutoff applied (Table 11). Combining both PCT and IL-6 with the TCP signature resulted in sensitivity levels of 0.855-0.995 depending on the cutoffs applied (Table 12). Similar improvements were observed for distinguishing between bacterial and non-bacterial (viral plus non-infectious) patients (Tables 13-15). The optimal cutoff of either IL-6, PCT or both depends on the balance between optimal sensitivity and specificity and may vary according to the desired use and/or clinical setting.
Combining TCP Signature with IL-6 and PCT Improves the Ability to Diagnose Early Infections
Interestingly, we find that one class of examples in which the contribution of IL-6 or PCT to the TCP signature, is particularly pronounced, is during early bacterial infections. Indeed, the rise in IL-6 levels in response to bacterial infections can be detected as early as the first day of symptoms onset and precedes the rise in other bacterially induced proteins (
Sub-Group Analysis
The present inventors further evaluated the ability of IL-6 and PCT to improve the sensitivity and accuracy levels of the TCP signature in various patient sub-groups using the Fuzzy OR model. Patients were stratified according to several categories (i.e., clinical syndrome; specific pathogen; and age), and measures of accuracy were calculated for different combinations of IL-6, PCT and the TCP signature generated using the Fuzzy OR model (PCT cutoff=2.5 μg/L; IL-6 cutoff=250 pg/ml; Hill coefficient=10; Tables 17-19). Adding PCT and IL-6 was able to improve the TCP signature performance in various patient sub-groups (Tables 17-19). For example, the combined model improved the sensitivity of the TCP signature in identifying patients with serious bacterial infections (SBI), which are at high risk for adverse outcomes (0.92 vs 0.9; Table 19). This combination was also superior in various clinical syndromes, specific pathogens and age groups (Table 19).
Combining Two Biomarkers to Distinguish Between Bacterial and Viral Infections
In certain clinical settings, for example at the point-of-care or in resource limited settings, it might be beneficial to use a smaller set of biomarkers. There are various ways (and formulations) to combine two biomarkers into one predictive score. For example, using dual cutoffs—one for each biomarker (e.g., one for TRAIL and one for PCT), generates a quadrary separation pattern that can separate between bacterial, viral and mixed (bacterial-viral co-infection) patients (
Alternatively, the separation between bacterial and viral patients could be based on the ratio between the two biomarkers. Using a defined cutoff for the ratio between the two biomarkers generates a line that separates between bacterial (below the line) and viral (above the line) zones (
Distinguishing Between Infectious and Non-Infectious Patients
Distinguishing between infectious and non-infectious patients is a crucial step in many clinical scenarios, in order to guide correct patient management and treatment. Notable examples include: (i) distinguishing between SIRS and sepsis (which is SIRS of infective origin), and (ii) distinguishing between a non-infective exacerbation state and an infective exacerbation state in chronic obstructive pulmonary disease (COPD). In these two examples classifying the patient as infectious will require more aggressive management including antibiotic treatment, follow-up microbiological diagnostics, and even ICU admission.
Therefore, the inventors developed logistic regression models and evaluated the accuracy levels of single biomarker noted above (CRP, IL-6, IP-10, PCT, TRAIL), and their combinations, in distinguishing between infectious (including bacterial, viral and mixed bacterial-viral co infection patients, n=948) and non-infectious patients (n=109).
Some embodiments of the present invention analyze the biological data by calculating a value of a likelihood function using the expression levels. When the value of a likelihood function, as calculated using the expression levels obtained from the subject, is between a lower bound SLB and an upper bound SUB, wherein each of the lower and upper bounds is calculated using a combination δ (e.g., a linear combination) of the expression levels, the value of the likelihood function can be used to provide information pertaining an infection the subject is suffering from.
The lower bound SLB and upper bound SUB can be viewed geometrically as two curved objects, and the combination δ of the expression levels, can be can be viewed geometrically as a non-curved object, as illustrated schematically in
Generally, each of the curved objects S, SLB and SUB is a manifold in n dimensions, where n is a positive integer, and the non-curved object π is a hyperplane in an n+1 dimensional space.
The concept of n-dimensional manifolds and hyperplanes in n+1 dimensions are well known to those skilled in the art of geometry. For example, when n=1 the first curved object is a curved line, and the non-curved object π is a hyperplane in 2 dimensions, namely a straight line defining an axis. When n=2, the first curved object is a curved surface, and the non-curved object π is a hyperplane in 3 dimensions, namely a flat plane, referred to below as “a plane”.
In the simplest case each of S, SLB and SUB is a curved line and π is a straight axis defined by a direction.
Thus, the present embodiments provide information pertaining to the infection by calculating distances between curved and non-curved geometrical objects.
The method begins at 10 and optionally and preferably continuous to 11 at which biological data containing, e.g., expression values of two or more determinants in the blood of a subject are obtained.
The method optionally and preferably continues to 12 at which background and/or clinical data that relate to the subject are obtained. In some embodiments of the present invention the background data includes the age of the subject, in some embodiments of the present invention the background data includes the ethnicity of the subject, in some embodiments of the present invention the background data includes the gender of the subject, in some embodiments of the present invention the clinical data includes a syndrome that the subject is experiencing, in some embodiments of the present invention the clinical data includes a pathogen suspected as being present in the subject.
The method proceeds to 13 at which the distance d between a segment of the curved object S (e.g., a curved line) and a non-curved object 7t (e.g., an axis defined by a direction) is calculated. The distance d is calculated at a point P(δ) over the curved line S defined by a coordinate δ along the direction. The direction is denoted herein using the same Greek letters as the coordinate, except that the direction is denoted by underlined Greek letters to indicate that these are vectors. Thus, when the coordinate is denoted δ, the direction is denoted δ.
The distance d is measured from S to the point P, perpendicularly to π. The segment SROI of S is above a region-of-interest πROI defined in the non-curved object π. For example, when π is an axis, πROI is a linear segment along the axis. Thus, πROI is the projection of SROI on π. For n=1, SROI is preferably a curved segment of (the curve) S.
The coordinate δ is optionally and preferably defined by a combination of expression values of the determinants. For example, δ can be a combination of the determinants, according to the following equation:
δ=a0+a1D1+a2D2+ . . . +ϕ
where a0, a1, . . . are constant and predetermined coefficients, where each of the variables D1, D2, . . . is an expression levels of one of the determinants or some score pertaining to one or more of the determinants, and where ϕ is a function that is nonlinear with respect to at least one of the expression levels.
The function ϕ is optional and may, independently, be set to zero (or, equivalently, not included in the calculation of the respective coordinate). When ϕ=0 the coordinate δ is a linear combination of the determinants.
The nonlinear function ϕ can optionally and preferably be expressed as a sum of powers of expression levels, for example, according to the following equations:
ϕ=ΣiqiXiγi
where i is a summation index, qi and ri are sets of coefficients, Xi∈{D1, D2, . . . }, and γi is a numerical exponent. Note that the number of terms in the nonlinear function π does not necessarily equals the number of the determinants, and that two or more terms in the sum may correspond to the same determinant, albeit with a different numerical exponent.
One or more of the predetermined coefficients (ai, qi, ri) typically depends on the respective type of the determinant, but can also depend on the background and/or clinical data obtained at 12. Thus, the calculation of the distance d can optionally and preferably be based on the background and/or clinical data, because the location of the coordinate δ on π can depend on such data. For example, the coefficient ai for a particular determinant Di can be different when the subject has a particular syndrome or pathogen, than when the subject does not have this particular syndrome or pathogen. In this case, the location of the point P(δ) on π is different for subjects with the particular syndrome or pathogen, than for subjects without the particular syndrome or pathogen. Since the location is different, the distance d can also be different. Similarly, the coefficient ai (hence also the location of the point P(δ) on π) for a particular determinant Di can be different when the subject is of a particular age, gender and/or ethnicity, than when the subject is of a different age, gender and/or ethnicity.
The patient background and/or clinical data can be used for determining the coefficients, in more than one way. In some embodiments of the present invention, a lookup table is used. Such a lookup table can include a plurality of entries wherein each entry includes a determinant, information pertaining to the background and/or clinical data, and a coefficient that is specific to the determinant and the background and/or clinical data of the respective entry. Relevant clinical data includes but is not limited to absolute neutrophil count (abbreviated ANC), absolute lymphocyte count (abbreviated ALC), white blood count (abbreviated WBC), neutrophil % (defined as the fraction of white blood cells that are neutrophils and abbreviated Neu (%)), lymphocyte % (defined as the fraction of white blood cells that are lymphocytes and abbreviated Lym (%)), monocyte % (defined as the fraction of white blood cells that are monocytes and abbreviated Mon (%)), Sodium (abbreviated Na), Potassium (abbreviated K), Bilirubin (abbreviated Bili). Other clinical parameters are described herein below.
As used herein the term “patient background” refers to the history of diseases or conditions of the patient, or which the patient is prone to. For example, the patient medical background may include conditions such as chronic lung diseases and diabetes that affect its immune response to infection (see Example 1, herein below).
In some embodiments of the present invention, the coefficients are initially selected based on the particular determinants, (without taking into account the background and/or clinical data), and thereafter corrected, e.g., by normalization, based on the background and/or clinical data. For example, the coefficients can be normalized according to the age of the subject. In these embodiments, the subject is optionally and preferably stratified according to the subject's age, and the coefficient for the particular determinant is normalized by an age-dependent normalization procedure. In some embodiments, there are different coefficients, normalizations or stratification when the subject is an adult (e.g., older than 18, 21, or 22 years), than when the subject is a child (e.g., younger than 18, 21 or 22 years). In some embodiments, there are different coefficients, normalizations or stratifications when the subject is an adult (e.g., older than 18, 21, or 22 years), an adolescent (e.g., between 12 and 21 years), a child (e.g., between 2 and 12 years), an infant (e.g., 29 days to less than 2 years of age), and a neonates (e.g., birth through the first 28 days of life). In some embodiments, there are different coefficients, normalizations or stratification when the subject is older than 70, 65, 60, 55, 50, 40, 30, 22, 21, 18, 12, 2, 1 years than when the subject is older than 3, 2 and/or 1 month. In some embodiments, there are different coefficients, normalizations or stratification when the subject is younger than 70, 65, 60, 55, 50, 40, 30, 22, 21, 18, 12, 2, 1 year, than when the subject is older than 3, 2 and/or 1 month.
The boundaries of πROI are denoted herein δMIN and δMAX. These boundaries preferably correspond to the physiologically possible ranges of the expression values of the determinants. The range of the expression values can be set by the protocol used for obtaining the respective determinants. Alternatively, the expression values of one or more of the determinants that are used in the calculation of δ can be score values, for example, z-scored values, relative to a group of subjects previously diagnosed with a bacterial infection. These embodiments are particularly useful when the distance d is used for distinguishing between bacterial and viral infections. Still alternatively, the expression values of one or more of the determinants that are used in the calculation of δ can be score values, for example, z-scored values, relative to a group of subjects previously diagnosed with an infection. These embodiments are particularly useful when the distance d is used for distinguishing between infectious and non-infectious subjects. Still alternatively, the expression values of one or more of the determinants that are used in the calculation of δ can be score values, for example, z-scored values, relative to a group of subjects previously diagnosed with a mixed infection. These embodiments are particularly useful when the distance d is used for distinguishing between mixed infection and viral infection.
At least a major part of the segment SROI of curved object S is between two curved objects referred to below as a lower bound curved object SLB and an upper bound curved object SUB.
As used herein “major part of the segment SROI” refers to a part of a smoothed version SROI whose length (when n=1), surface area (when n=2) or volume (when n≥3) is 60% or 70% or 80% or 90% or 95% or 99% of a smoothed version of the length, surface area or volume of SROI, respectively.
As used herein, “a smooth version of the segment SROI” refers to the segment SROI, excluding regions of SROI at the vicinity of points at which the Gaussian curvature is above a curvature threshold, which is X times the median curvature of SROI, where X is 1.5 or 2 or 4 or 8.
The following procedure can be employed for the purpose of determining whether the major part of the segment SROI is between SLB and SUB. Firstly, a smoothed version of the segment SROI is obtained. Secondly, the length (when n=1), surface area (when n=2) or volume (when n≥3) A1 of the smoothed version of the segment SROI is calculated. Thirdly, the length (when n=1) surface area (when n=2) or volume (when n≥3) A2 of the part of the smoothed version of the segment SROI that is between SLB and SUB is calculated. Fourthly, the percentage of A2 relative to A1 is calculated.
For clarity of presentation, SROI is illustrated as a one dimensional segment, but the skilled person would understand that SROI is generally an n-dimensional mathematical object. The Gaussian curvature is calculated for a sufficient number of sampled points on SROI. For example, when the manifold is represented as point cloud, the Gaussian curvature can be calculated for the points in the point cloud. The median of the Gaussian curvature is then obtained, and the curvature threshold is calculated by multiplying the obtained median by the factor X.
When n=1 (namely when S is a curved line), SLB is a lower bound curved line, and SUB an upper bound curved line. In these embodiments, SLB and SUB can be written in the form:
S
LB
=f(δ)−ε0,
S
UB
=f(δ)+ε1
where f(δ) is a probabilistic classification function of the coordinate δ (along the direction δ) which represents the likelihood that the test subject has an infection of a predetermined type (e.g., a bacterial infection, or a viral infection or a mixed infection). Also contemplated, are embodiments in which f(δ) is a probabilistic classification function which represents the likelihood that the test subject has an infection. In some embodiments of the invention f(δ)=1/(1+exp(−δ)). In some embodiments of the invention both SLB and SUB are positive for any value of δ within πROI.
In any of the above embodiments each of the parameters ε0 and ε1 is less than 0.5 or less than 0.4 or less than 0.3 or less than 0.2 or less than 0.1 or less than 0.05.
The method preferably proceeds to 14 at which the calculated distance d is correlated to the presence of, absence of, or likelihood that the subject has, a disease or condition corresponding to the type of the probabilistic function f. For example, when the probabilistic function f represents the likelihood that the test subject has a bacterial infection, the calculated distance d is correlated to the presence of, absence of, or likelihood that the subject has, a bacterial infection, when the probabilistic function f represents the likelihood that the test subject has a viral infection, the calculated distance d is correlated to the presence of, absence of, or likelihood that the subject has, a viral infection, and when the probabilistic function f represents the likelihood that the test subject has a mixed infection, the calculated distance d is correlated to the presence of, absence of, or likelihood that the subject has, a mixed infection.
In various exemplary embodiments of the invention the correlation includes determining that the distance d is the likelihood that the subject has the respective infection (bacterial, viral, mixed). The likelihood is optionally and preferably compared to a predetermined threshold ωB, wherein the method can determine that it is likely that the subject has a bacterial infection when the likelihood is above ωB, and that it is unlikely that the subject has a bacterial infection otherwise. Typical values for ωB include, without limitation, about 0.2, about 0.3, about 0.4, about 0.5, about 0.6 and about 0.7. Other likelihood thresholds are also contemplated.
In some embodiments of the present invention the method proceeds to 15 at which the likelihood is corrected based on the background and/or clinical data. Such a correction can be executed in more than one way. For example, the method can employ different predetermined thresholds ωB for different ages, ethnicities, genders, syndromes, and/or suspected pathogens. The method can alternatively or additionally employ different values for one or both the parameters ε0 and ε1 for different ages, ethnicities, genders, syndromes, and/or suspected pathogens. The method can alternatively or additionally normalize the value of the probabilistic classification function 6, based on the age, ethnicity, gender, syndrome, and/or suspected pathogen.
The method optionally and preferably continues to 16 at which an output of the likelihood(s) is generated. The output can be presented as text, and/or graphically and/or using a color index. The output can optionally include the results of the comparison to the threshold WB. From 16 the method can optionally and preferably loops back to 13 for repeating the analysis using a different set of coefficients for the calculation of the coordinate δ and/or a different probabilistic classification function f. For example, the analysis can be initially executed using a set of coefficients and probabilistic classification function f that are selected for determining the presence of, absence of, or likelihood that the subject has, a bacterial infection or a mixed infection, and then, in a subsequent execution, the analysis can use a set of coefficients and probabilistic classification function f that are selected for determining the presence of, absence of, or likelihood that the subject has, a viral infection.
In some embodiments of the present invention, when the method determines that it is likely that the subject has a bacterial infection, the subject is treated (17) for the bacterial infection, as further detailed herein. In some embodiments of the present invention, when the method determines that it is likely that the subject has a viral infection, the subject is treated (17) for the viral infection, as further detailed herein.
The method ends at 18.
Following are representative examples of coefficients that can be used for defining the coordinate δ according to some embodiments of the present invention.
In some embodiments of the present invention the coordinate δ is calculated as a0+a1X+a2Y, wherein X is a value of the score of the TCP signature as further detailed hereinabove, and Y is a value of the expression level of IL-6 in pg/ml, wherein a0 is from about 2.75 to about 3.40, a1 is from about 4.5 to about 5.5, and a2 is from about 0.0044 to about 0.0055. In these embodiments the probabilistic classification function f represents the likelihood the subject has a bacterial infection. More preferred values for the parameters a0, a1 and a2 in these embodiments are provided in Table 7.
In some embodiments of the present invention the coordinate Bis calculated as a0+a1X+a2Y, wherein X is a value of the calculated score of the TCP signature as further detailed hereinabove, and the Y is a value of the expression level of PCT in μg/L, wherein a0 is from about 2.70 to about 3.30, a1 is from about 4.55 to about 5.60, and a2 is from about 0.176 to about 0.215. In these embodiments the probabilistic classification function f represents the likelihood the subject has a bacterial infection. More preferred values for the parameters a0, a1 and a2 in these embodiments are provided in Table 7.
In some embodiments of the present invention the coordinate δ is calculated as a0+a1X+a2Y+a3Z, wherein X is a value of the expression level of CRP in μg/ml, Y is a value of the expression level of IL-6 in pg/ml and Z is a value of the expression level of TRAIL in pg/ml, wherein a0 is from about −1.05 to about −0.85, a1 is from about 0.025 to about 0.032, a2 is from about 0.004 to about 0.006, and a3 is from about −0.022 to about −0.017. In these embodiments the probabilistic classification function f represents the likelihood the subject has a bacterial infection. More preferred values for the parameters a0, a1, a2 and a3 in these embodiments are provided in Table 8.
In some embodiments of the present invention the coordinate δ is calculated as a0+a1X+a2Y+a3Z, wherein X is a value of the expression level of CRP in μg/ml, Y is a value of the expression level of PCT in μg/L and Z is a value of the expression level of TRAIL in pg/ml, wherein a0 is from about −0.60 to about −0.48, a1 is from about 0.024 to about 0.31, a2 is from about 0.13 to about 0.16, and a3 is from about −0.025 to about −0.019. In these embodiments the probabilistic classification function f represents the likelihood the subject has a bacterial infection. More preferred values for the parameters a0, a1, a2 and a3 in these embodiments are provided in Table 8.
In some embodiments of the present invention the coordinate δ is calculated as a0+a1X+a2Y+a3Z, wherein X is a value of the expression level of IP-10 in μg/ml, Y is a value of the expression level of PCT in μg/L and Z is a value of the expression level of TRAIL in pg/ml, wherein a0 is from about 1.42 to about 1.75, a1 is from about 0.00024 to about 0.00031, a2 is from about 0.23 to about 0.29, and a3 is from about −0.038 to about −0.030. In these embodiments the probabilistic classification function f represents the likelihood the subject has a bacterial infection. More preferred values for the parameters a0, a1, a2 and a3 in these embodiments are provided in Table 8.
In some embodiments of the present invention the coordinate δ is calculated as a0+a1X+a2Y+a3Z, wherein X is a value of the calculated score of the TCP signature as further detailed hereinabove, Y is a value of the expression level of IL-6 in pg/L and the Z is a value of the expression level of PCT in μg/ml, wherein a0 is from about −3.48 to about −2.84, a1 is from about 4.40 to about 5.39, a2 is from about 0.0041 to about 0.0051, and a3 is from about 0.14 to about 0.18. In these embodiments the probabilistic classification function f represents the likelihood the subject has a bacterial infection. More preferred values for the parameters a0, a1, a2 and a3 in these embodiments are provided in Table 8.
In some embodiments of the present invention the coordinate δ is calculated as a0+a1X+a2Y+a3Z+a4T, wherein X is a value of the expression level of CRP in μg/ml, Y is a value of the expression level of IL-6 in pg/ml, Z is a value of the expression level of PCT in μg/L and T is a value of the expression level of TRAIL in pg/ml, wherein a0 is from about −1.13 to about −0.92, a1 is from about 0.025 to about 0.031, a2 is from about 0.0045 to about 0.0055, a3 is from about 0.098 to about 0.13 and a4 is from about −0.021 to about −0.016. In these embodiments the probabilistic classification function f represents the likelihood the subject has a bacterial infection. More preferred values for the parameters a0, a1, a2, a3 and a4 in these embodiments are provided in Table 9.
In some embodiments of the present invention the coordinate δ is calculated as a0+a1X+a2Y+a3Z+a4T, wherein X is a value of the expression level of IL-6 in pg/ml, Y is a value of the expression level of IP-10 in pg/ml, Z is a value of the expression level of PCT in μg/L and T is a value of the expression level of TRAIL in pg/ml, wherein a0 is from about 1.029 to about 1.258, a1 is from about 0.0049 to about 0.0060, a2 is from about 0.00013 to about 0.00017, a3 is from about 0.19 to about 0.24 and a4 is from about −0.033 to about −0.027. In these embodiments the probabilistic classification function f represents the likelihood the subject has a bacterial infection. More preferred values for the parameters a0, a1, a2, a3 and a4 in these embodiments are provided in Table 9.
In some embodiments of the present invention the coordinate δ is calculated as a0+a1X+a2Y+a3Z+a4T+a5W, wherein X is a value of the expression level of CRP in μg/ml, wherein Y is a value of the expression level of IL-6 in pg/ml, Z is a value of the expression level of IP-10 in pg/ml, T is a value of the expression level of PCT in μg/L and the W is a value of the expression level of TRAIL in pg/ml, wherein a0 is from about −3.08 to about −2.52, a1 is from about 0.10 to about 0.13, a2 is from about 0.038 to about 0.047, a3 is from about 0.008 to about 0.010, a4 is from about −0.17 to about −0.13 and as is from about 0.0044 to about 0.0054. In these embodiments the probabilistic classification function f represents the likelihood the subject has an infection. More preferred values for the parameters a0, a1, a2, a3, a4 and as in these embodiments are provided in Table 24.
In some embodiments, the method can be carried out using a system 330, which optionally and preferably, but not necessarily, comprises a hand-held device. The system can comprise two or more compartments, wherein the levels of determinants in the blood is measured in one of the compartments (e.g. using an immunohistochemical method), and wherein an analysis of the obtained levels is executed in the other compartment to provide an output relating to the diagnosis.
A block diagram of representative example of system 330 in embodiments in which system 330 comprises a hand-held device 331 is illustrated in
In some embodiments of the present invention system 330 communicates with a communication network, as schematically illustrated in the block diagram of
In some embodiments of the present invention system 330 communicates with a user, as schematically illustrated in the block diagram of
Measuring the determinant levels is typically affected at the protein level as further described herein below.
Methods of Detecting Expression and/or Activity of Proteins
Expression and/or activity level of proteins expressed in the cells of the cultures of some embodiments of the invention can be determined using methods known in the arts and typically involve the use of antibodies. Such methods may be referred to an immunoassays. Immunoassays may be run in multiple steps with reagents being added and washed away or separated at different points in the assay. Multi-step assays are often called separation immunoassays or heterogeneous immunoassays. Some immunoassays can be carried out simply by mixing the reagents and sample and making a physical measurement. Such assays are called homogenous immunoassays or less frequently non-separation immunoassays. The use of a calibrator is often employed in immunoassays. Calibrators are solutions that are known to contain the analyte in question, and the concentration of that analyte is generally known. Comparison of an assay's response to a real sample against the assay's response produced by the calibrators makes it possible to interpret the signal strength in terms of the presence or concentration of analyte in the sample.
The antibody may be monoclonal, polyclonal, chimeric, or a fragment of the foregoing, and the step of detecting the reaction product may be carried out with any suitable immunoassay.
Suitable sources for antibodies for the detection of the polypeptides include commercially available sources such as, for example, Abazyme, Abnova, AssayPro, Affinity Biologicals, AntibodyShop, Aviva bioscience, Biogenesis, Biosense Laboratories, Calbiochem, Cell Sciences, Chemicon International, Chemokine, Clontech, Cytolab, DAKO, Diagnostic BioSystems, eBioscience, Endocrine Technologies, Enzo Biochem, Eurogentec, Fusion Antibodies, Genesis Biotech, GloboZymes, Haematologic Technologies, Immunodetect, Immunodiagnostik, Immunometrics, Immunostar, Immunovision, Biogenex, Invitrogen, Jackson ImmunoResearch Laboratory, KMI Diagnostics, Koma Biotech, LabFrontier Life Science Institute, Lee Laboratories, Lifescreen, Maine Biotechnology Services, Mediclone, MicroPharm Ltd., ModiQuest, Molecular Innovations, Molecular Probes, Neoclone, Neuromics, New England Biolabs, Novocastra, Novus Biologicals, Oncogene Research Products, Orbigen, Oxford Biotechnology, Panvera, PerkinElmer Life Sciences, Pharmingen, Phoenix Pharmaceuticals, Pierce Chemical Company, Polymun Scientific, Polysiences, Inc., Promega Corporation, Proteogenix, Protos Immunoresearch, QED Biosciences, Inc., R&D Systems, Repligen, Research Diagnostics, Robo screen, Santa Cruz Biotechnology, Seikagaku America, Serological Corporation, Serotec, SigmaAldrich, StemCell Technologies, Synaptic Systems GmbH, Technopharm, Terra Nova Biotechnology, TiterMax, Trillium Diagnostics, Upstate Biotechnology, US Biological, Vector Laboratories, Wako Pure Chemical Industries, and Zeptometrix. However, the skilled artisan can routinely make antibodies, against any of the polypeptides described herein.
Polyclonal antibodies for measuring polypeptides include without limitation antibodies that were produced from sera by active immunization of one or more of the following: Rabbit, Goat, Sheep, Chicken, Duck, Guinea Pig, Mouse, Donkey, Camel, Rat and Horse.
Examples of additional detection agents, include without limitation: scFv, dsFv, Fab, sVH, F(ab′)2, Cyclic peptides, Haptamers, A single-domain antibody, Fab fragments, Single-chain variable fragments, Affibody molecules, Affilins, Nanofitins, Anticalins, Avimers, DARPins, Kunitz domains, Fynomers and Monobody.
The detection agents may be labeled with a label and detected by inspection, or a detector which monitors a particular probe or probe combination is used to detect the detection reagent label. Typical detectors include spectrophotometers, phototubes and photodiodes, microscopes, scintillation counters, cameras, film and the like, as well as combinations thereof. Those skilled in the art will be familiar with numerous suitable detectors that widely available from a variety of commercial sources and may be useful for carrying out the method disclosed herein. Commonly, an optical image of a substrate comprising bound labeling moieties is digitized for subsequent computer analysis. See generally The Immunoassay Handbook (Wild 2005).
Enzyme linked immunosorbent assay (ELISA): Performing an ELISA involves at least one antibody with specificity for a particular antigen. The sample with an unknown amount of antigen is immobilized on a solid support (usually a polystyrene microtiter plate) either non-specifically (via adsorption to the surface) or specifically (via capture by another antibody specific to the same antigen, in a “sandwich” ELISA). After the antigen is immobilized, the detection antibody is added, forming a complex with the antigen. The detection antibody can be covalently linked to an enzyme, or can itself be detected by a secondary antibody that is linked to an enzyme through bioconjugation. Between each step, the plate is typically washed with a mild detergent solution to remove any proteins or antibodies that are a specifically bound. After the final wash step, the plate is developed by adding an enzymatic substrate to produce a visible signal, which indicates the quantity of antigen in the sample.
Enzymes commonly employed in this method include horseradish peroxidase and alkaline phosphatase. If well calibrated and within the linear range of response, the amount of substrate present in the sample is proportional to the amount of color produced. A substrate standard is generally employed to improve quantitative accuracy.
Western blot: This method involves separation of a substrate from other protein by means of an acrylamide gel followed by transfer of the substrate to a membrane (e.g., nylon or PVDF). Presence of the substrate is then detected by antibodies specific to the substrate, which are in turn detected by antibody binding reagents. Antibody binding reagents may be, for example, protein A, or other antibodies. Antibody binding reagents may be radiolabeled or enzyme linked as described hereinabove. Detection may be by autoradiography, colorimetric reaction or chemiluminescence. This method allows both quantitation of an amount of substrate and determination of its identity by a relative position on the membrane which is indicative of a migration distance in the acrylamide gel during electrophoresis.
Fluorescence activated cell sorting (FACS): This method involves detection of a substrate in situ in cells by substrate specific antibodies. The substrate specific antibodies are linked to fluorophores. Detection is by means of a cell sorting machine which reads the wavelength of light emitted from each cell as it passes through a light beam. This method may employ two or more antibodies simultaneously.
Automated Immunoassay: An automated analyzer applied to an immunoassay (often called “Automated Immunoassay”) is a medical laboratory instrument designed to measure different chemicals and other characteristics in a number of biological samples quickly, with minimal human assistance. These measured properties of blood and other fluids may be useful in the diagnosis of disease. Many methods of introducing samples into the analyzer have been invented. This can involve placing test tubes of sample into racks, which can be moved along a track, or inserting tubes into circular carousels that rotate to make the sample available. Some analyzers require samples to be transferred to sample cups. However, the effort to protect the health and safety of laboratory staff has prompted many manufacturers to develop analyzers that feature closed tube sampling, preventing workers from direct exposure to samples. Samples can be processed singly, in batches, or continuously. Examples of automated immunoassay machines include, without limitation, ARCHITECT ci4100, ci8200 (2003), ci16200 (2007), ARCHITECT i1000SR, ARCHITECT i2000, i2000SR, i4000SR, AxSYM/AxSYM Plus, 1994 U.S.,
DS2, AIMS, AtheNA, DSX, ChemWell, UniCel Dxl 860i Synchron Access Clinical System, UniCel DxC 680i Synchron Access Clinical System, Access/Access 2 Immunoassay System, UniCel Dxl 600 Access Immunoassay System, UniCel DxC 600i Synchron Access Clinical System, UniCel Dxl 800 Access Immunoassay System, UniCel DxC 880i Synchron Access Clinical System, UniCel Dxl 660i Synchron Access Clinical System, SPA PLUS (Specialist Protein Analyzer), VIDAS Immunoassay Analyzer, BioPlex 2200, PhD System EVOLIS PR 3100TSC Photometer, MAGO 4S/2011 Mago Plus Automated EIA Processor, LIAISON XL/2010 LIAISON, ETI-MAX 3000 Agility, Triturus, HYTEC 288 PLUSDSX, VITROS ECi Immunodiagnostic System, VITROS 3600 Immunodiagnostic System, Phadia Laboratory System 100E, Phadia Laboratory System 250, Phadia Laboratory System 1000, Phadia Laboratory System 2500, Phadia Laboratory System 5000, cobas e 602/2010, cobas e411, cobas e601, MODULAR ANALYTICS E170, Elecsys 2010, Dimension EXL 200/2011, Dimension Xpand Plus Integrated Chemistry System, Dimension RxL Max/Max Suite Integrated Chemistry System; Dimension RxL Integrated Chemistry System, Dimension EXL with LM Integrated Chemistry System, Stratus CS Acute Care Diagnostic System, IMMULITE 2000 XPi Immunoassay System, ADVIA Centaur CP Immunoassay System, IMMULITE 2000, IMMULITE 1000, Dimension Vista 500 Intelligent Lab System, Dimension Vista 1500 Intelligent Lab System, ADVIA Centaur XP, AIA-900, AIA-360, AIA-2000, AIA-600 II, AIA-1800. Measurements of CRP, IP-10 and TRAIL can also be performed on a Luminex machine.
Lateral Flow Immunoassays (LFIA): This is a technology which allows rapid measurement of analytes at the point of care (POC) and its underlying principles are described below. According to one embodiment, LFIA is used in the context of a hand-held device.
The technology is based on a series of capillary beds, such as pieces of porous paper or sintered polymer. Each of these elements has the capacity to transport fluid (e.g., urine) spontaneously. The first element (the sample pad) acts as a sponge and holds an excess of sample fluid. Once soaked, the fluid migrates to the second element (conjugate pad) in which the manufacturer has stored the so-called conjugate, a dried format of bio-active particles (see below) in a salt-sugar matrix that contains everything to guarantee an optimized chemical reaction between the target molecule (e.g., an antigen) and its chemical partner (e.g., antibody) that has been immobilized on the particle's surface. While the sample fluid dissolves the salt-sugar matrix, it also dissolves the particles and in one combined transport action the sample and conjugate mix while flowing through the porous structure. In this way, the analyte binds to the particles while migrating further through the third capillary bed. This material has one or more areas (often called stripes) where a third molecule has been immobilized by the manufacturer. By the time the sample-conjugate mix reaches these strips, analyte has been bound on the particle and the third ‘capture’ molecule binds the complex.
After a while, when more and more fluid has passed the stripes, particles accumulate and the stripe-area changes color. Typically there are at least two stripes: one (the control) that captures any particle and thereby shows that reaction conditions and technology worked fine, the second contains a specific capture molecule and only captures those particles onto which an analyte molecule has been immobilized. After passing these reaction zones the fluid enters the final porous material, the wick, that simply acts as a waste container. Lateral Flow Tests can operate as either competitive or sandwich assays.
Different formats may be adopted in LFIA. Strips used for LFIA contain four main components. A brief description of each is given before describing format types.
Sample application pad: It is made of cellulose and/or glass fiber and sample is applied on this pad to start assay. Its function is to transport the sample to other components of lateral flow test strip (LFTS). Sample pad should be capable of transportation of the sample in a smooth, continuous and homogenous manner. Sample application pads are sometimes designed to pretreat the sample before its transportation. This pretreatment may include separation of sample components, removal of interferences, adjustment of pH, etc.
Conjugate pad: It is the place where labeled biorecognition molecules are dispensed. Material of conjugate pad should immediately release labeled conjugate upon contact with moving liquid sample. Labeled conjugate should stay stable over entire life span of lateral flow strip. Any variations in dispensing, drying or release of conjugate can change results of assay significantly. Poor preparation of labeled conjugate can adversely affect sensitivity of assay. Glass fiber, cellulose, polyesters and some other materials are used to make conjugate pad for LFIA. Nature of conjugate pad material has an effect on release of labeled conjugate and sensitivity of assay.
Nitrocellulose membrane: It is highly critical in determining sensitivity of LFIA. Nitrocellulose membranes are available in different grades. Test and control lines are drawn over this piece of membrane. So an ideal membrane should provide support and good binding to capture probes (antibodies, aptamers etc.). Nonspecific adsorption over test and control lines may affect results of assay significantly, thus a good membrane will be characterized by lesser non-specific adsorption in the regions of test and control lines. Wicking rate of nitrocellulose membrane can influence assay sensitivity. These membranes are easy to use, inexpensive, and offer high affinity for proteins and other biomolecules. Proper dispensing of bioreagents, drying and blocking play a role in improving sensitivity of assay.
Adsorbent pad: It works as sink at the end of the strip. It also helps in maintaining flow rate of the liquid over the membrane and stops back flow of the sample. Adsorbent capacity to hold liquid can play an important role in results of assay.
All these components are fixed or mounted over a backing card. Materials for backing card are highly flexible because they have nothing to do with LFIA except providing a platform for proper assembling of all the components. Thus backing card serves as a support and it makes easy to handle the strip.
Major steps in LFIA are (i) preparation of antibody against target analyte (ii) preparation of label (iii) labeling of biorecognition molecules (iv) assembling of all components onto a backing card after dispensing of reagents at their proper pads (v) application of sample and obtaining results.
Sandwich format: In a typical format, label (Enzymes or nanoparticles or fluorescence dyes) coated antibody or aptamer is immobilized at conjugate pad. This is a temporary adsorption which can be flushed away by flow of any buffer solution. A primary antibody or aptamer against target analyte is immobilized over test line. A secondary antibody or probe against labeled conjugate antibody/aptamer is immobilized at control zone.
Sample containing the analyte is applied to the sample application pad and it subsequently migrates to the other parts of strip. At conjugate pad, target analyte is captured by the immobilized labeled antibody or aptamer conjugate and results in the formation of labeled antibody conjugate/analyte complex. This complex now reaches at nitrocellulose membrane and moves under capillary action. At test line, label antibody conjugate/analyte complex is captured by another antibody which is primary to the analyte. Analyte becomes sandwiched between labeled and primary antibodies forming labeled antibody conjugate/analyte/primary antibody complex. Excess labeled antibody conjugate will be captured at control zone by secondary antibody. Buffer or excess solution goes to absorption pad. Intensity of color at test line corresponds to the amount of target analyte and is measured with an optical strip reader or visually inspected. Appearance of color at control line ensures that a strip is functioning properly.
Competitive format: Such a format suits best for low molecular weight compounds which cannot bind two antibodies simultaneously. Absence of color at test line is an indication for the presence of analyte while appearance of color both at test and control lines indicates a negative result. Competitive format has two layouts. In the first layout, solution containing target analyte is applied onto the sample application pad and prefixed labeled biomolecule (antibody/aptamer) conjugate gets hydrated and starts flowing with moving liquid. Test line contains pre-immobilized antigen (same analyte to be detected) which binds specifically to label conjugate. Control line contains pre-immobilized secondary antibody which has the ability to bind with labeled antibody conjugate. When liquid sample reaches at the test line, pre-immobilized antigen will bind to the labeled conjugate in case target analyte in sample solution is absent or present in such a low quantity that some sites of labeled antibody conjugate were vacant. Antigen in the sample solution and the one which is immobilized at test line of strip compete to bind with labeled conjugate. In another layout, labeled analyte conjugate is dispensed at conjugate pad while a primary antibody to analyte is dispensed at test line. After application of analyte solution a competition takes place between analyte and labeled analyte to bind with primary antibody at test line.
Multiplex detection format: Multiplex detection format is used for detection of more than one target species and assay is performed over the strip containing test lines equal to number of target species to be analyzed. It is highly desirable to analyze multiple analytes simultaneously under same set of conditions. Multiplex detection format is very useful in clinical diagnosis where multiple analytes which are inter-dependent in deciding about the stage of a disease are to be detected. Lateral flow strips for this purpose can be built in various ways i.e. by increasing length and test lines on conventional strip, making other structures like stars or T-shapes. Shape of strip for LFIA will be dictated by number of target analytes. Miniaturized versions of LFIA based on microarrays for multiplex detection of DNA sequences have been reported to have several advantages such as less consumption of test reagents, requirement of lesser sample volume and better sensitivity.
Labels: Any material that is used as a label should be detectable at very low concentrations and it should retain its properties upon conjugation with biorecognition molecules. This conjugation is also expected not to change features of biorecognition probes. Ease in conjugation with biomolecules and stability over longer period of time are desirable features for a good label. Concentrations of labels down to 10−9 M are optically detectable. After the completion of assay, some labels generate direct signal (as color from gold colloidal) while others require additional steps to produce analytical signal (as enzymes produce detectable product upon reaction with suitable substrate). Hence the labels which give direct signal are preferable in LFA because of less time consumption and reduced procedure.
Gold nanoparticles: Colloidal gold nanoparticles are the most commonly used labels in LFA. Colloidal gold is inert and gives very perfect spherical particles. These particles have very high affinity toward biomolecules and can be easily functionalized. Optical properties of gold nanoparticles are dependent on size and shape. Size of particles can be tuned by use of suitable chemical additives. Their unique features include environment friendly preparation, high affinity toward proteins and biomolecules, enhanced stability, exceptionally higher values for charge transfer and good optical signaling. Optical signal of gold nanoparticles in colorimetric LFA can be amplified by deposition of silver, gold nanoparticles and enzymes.
Magnetic particles and aggregates: Colored magnetic particles produce color at the test line which is measured by an optical strip reader but magnetic signals coming from magnetic particles can also be used as detection signals and recorded by a magnetic assay reader. Magnetic signals are stable for longer time compared to optical signals and they enhance sensitivity of LFA by 10 to 1000 folds.
Fluorescent and luminescent materials: Fluorescent molecules are widely used in LFA as labels and the amount of fluorescence is used to quantitate the concentration of analyte in the sample. Detection of proteins is accomplished by using organic fluorophores such as rhodamine as labels in LFA.
Current developments in nanomaterial have headed to manufacture of quantum dots which display very unique electrical and optical properties. These semiconducting particles are not only water soluble but can also be easily combined with biomolecules because of closeness in dimensions. Owing to their unique optical properties, quantum dots have come up as a substitute to organic fluorescent dyes. Like gold nanoparticles QDs show size dependent optical properties and a broad spectrum of wavelengths can be monitored. Single light source is sufficient to excite quantum dots of all different sizes. QDs have high photo stability and absorption coefficients.
Upconverting phosphors (UCP) are characterized by their excitation in infra-red region and emission in high energy visible region. Compared to other fluorescent materials, they have a unique advantage of not showing any auto fluorescence. Because of their excitation in IR regions, they do not photo degrade biomolecules. A major advantage lies in their production from easily available bulk materials. Although difference in batch to batch preparation of UCP reporters can affect sensitivity of analysis in LFA, it was observed that they can enhance sensitivity of analytical signal by 10 to 100 folds compared to gold nanoparticles or colored latex beads, when analysis is carried out under same set of biological conditions.
Enzymes: Enzymes are also employed as labels in LFA. But they increase one step in LFA which is application of suitable substrate after complete assay. This substrate will produce color at test and control lines as a result of enzymatic reaction. In case of enzymes, selection of suitable enzyme substrate combination is one necessary requirement in order to get a colored product for strip reader or electroactive product for electrochemical detection. In other words, sensitivity of detection is dependent on enzyme substrate combination.
Colloidal carbon: Colloidal carbon is comparatively inexpensive label and its production can be easily scaled up. Because of their black color, carbon NPs can be easily detected with high sensitivity. Colloidal carbon can be functionalized with a large variety of biomolecules for detection of low and high molecular weight analytes.
Detection systems: In case of gold nanoparticles or other color producing labels, qualitative or semi-quantitative analysis can be done by visual inspection of colors at test and control lines. The major advantage of visual inspection is rapid qualitative answer in “Yes” or “NO”. Such quick replies about presence of an analyte in clinical analysis have very high importance. Such tests help doctors to make an immediate decision near the patients in hospitals in situations where test results from central labs cannot be waited for because of huge time consumption. But for quantification, optical strip readers are employed for measurement of the intensity of colors produced at test and control lines of strip. This is achieved by inserting the strips into a strip reader and intensities are recorded simultaneously by imaging softwares. Optical images of the strips can also be recorded with a camera and then processed by using a suitable software. Procedure includes proper placement of strip under the camera and a controlled amount of light is thrown on the areas to be observed. Such systems use monochromatic light and wavelength of light can be adjusted to get a good contrast among test and control lines and background. In order to provide good quantitative and reproducible results, detection system should be sensitive to different intensities of colors. Optical standards can be used to calibrate an optical reader device. Automated systems have advantages over manual imaging and processing in terms of time consumption, interpretation of results and adjustment of variables.
In case of fluorescent labels, a fluorescence strip reader is used to record fluorescence intensity of test and control lines. Fluorescence brightness of test line increased with an increase in nitrated seruloplasmin concentration in human serum when it was detected with a fluorescence strip reader. A photoelectric sensor was also used for detection in LFIA where colloidal gold is exposed to light emitting diode and resulting photoelectrons are recorded. Chemiluminescence which results from reaction of enzyme and substrate is measured as a response to amount of target analyte. Magnetic strip readers and electrochemical detectors are also reported as detection systems in LFTS but they are not very common. Selection of detector is mainly determined by the label employed in analysis.
Immunohistochemical analysis: Immunoassays carried out in accordance with some embodiments of the present invention may be homogeneous assays or heterogeneous assays. In a homogeneous assay the immunological reaction usually involves the specific antibody (e.g., anti-MX1 and CRP antibody), a labeled analyte, and the sample of interest. The signal arising from the label is modified, directly or indirectly, upon the binding of the antibody to the labeled analyte. Both the immunological reaction and detection of the extent thereof can be carried out in a homogeneous solution. Immunochemical labels, which may be employed, include free radicals, radioisotopes, fluorescent dyes, enzymes, bacteriophages, or coenzymes.
In a heterogeneous assay approach, the reagents are usually the sample, the antibody, and means for producing a detectable signal. Samples as described above may be used. The antibody can be immobilized on a support, such as a bead (such as protein A and protein G agarose beads), plate or slide, and contacted with the specimen suspected of containing the antigen in a liquid phase.
According to a particular embodiment, the antibody is immobilized to a porous strip to form a detection site. The measurement or detection region of the porous strip may include a plurality of sites, one for MX1 and one for CRP. A test strip may also contain sites for negative and/or positive controls.
Alternatively, control sites can be located on a separate strip from the test strip. Optionally, the different detection sites may contain different amounts of antibodies, e.g., a higher amount in the first detection site and lesser amounts in subsequent sites.
Upon the addition of test sample, the number of sites displaying a detectable signal provides a quantitative indication of the amount of polypeptides present in the sample. The detection sites may be configured in any suitably detectable shape and are typically in the shape of a bar or dot spanning the width of a test strip.
The support is then separated from the liquid phase and either the support phase or the liquid phase is examined for a detectable signal employing means for producing such signal. The signal is related to the presence of the analyte in the sample. Means for producing a detectable signal include the use of radioactive labels, fluorescent labels, or enzyme labels. For example, if the antigen to be detected contains a second binding site, an antibody which binds to that site can be conjugated to a detectable group and added to the liquid phase reaction solution before the separation step. The presence of the detectable group on the solid support indicates the presence of the antigen in the test sample. Examples of suitable immunoassays are oligonucleotides, immunoblotting, immunofluorescence methods, immunoprecipitation, chemiluminescence methods, electrochemiluminescence (ECL) or enzyme-linked immunoassays.
Those skilled in the art will be familiar with numerous specific immunoassay formats and variations thereof which may be useful for carrying out the method disclosed herein. See generally E. Maggio, Enzyme-Immunoassay, (1980) (CRC Press, Inc., Boca Raton, Fla.); see also U.S. Pat. No. 4,727,022 to Skold et al. titled “Methods for Modulating Ligand-Receptor Interactions and their Application,” U.S. Pat. No. 4,659,678 to Forrest et al. titled “Immunoassay of Antigens,” U.S. Pat. No. 4,376,110 to David et al., titled “Immunometric Assays Using Monoclonal Antibodies,” U.S. Pat. No. 4,275,149 to Litman et al., titled “Macromolecular Environment Control in Specific Receptor Assays,” U.S. Pat. No. 4,233,402 to Maggio et al., titled “Reagents and Method Employing Channeling,” and U.S. Pat. No. 4,230,767 to Boguslaski et al., titled “Heterogenous Specific Binding Assay Employing a Coenzyme as Label.”
Antibodies can be conjugated to a solid support suitable for a diagnostic assay (e.g., beads such as protein A or protein G agarose, microspheres, plates, slides or wells formed from materials such as latex or polystyrene) in accordance with known techniques, such as passive binding. Antibodies as described herein may likewise be, conjugated to detectable labels or groups such as radiolabels (e.g., 35S, 125I, 131I), enzyme labels (e.g., horseradish peroxidase, alkaline phosphatase), and fluorescent labels (e.g., fluorescein, Alexa, green fluorescent protein, rhodamine) in accordance with known techniques.
Examples of monoclonal antibodies for measuring CRP include without limitation: Mouse, Monoclonal (108-2A2); Mouse, Monoclonal (108-7G41D2); Mouse, Monoclonal (12D-2C-36), IgG1; Mouse, Monoclonal (1G1), IgG1; Mouse, Monoclonal (5A9), IgG2a kappa; Mouse, Monoclonal (63F4), IgG1; Mouse, Monoclonal (67A1), IgG1; Mouse, Monoclonal (8B-5E), IgG1; Mouse, Monoclonal (B893M), IgG2b, lambda; Mouse, Monoclonal (C1), IgG2b; Mouse, Monoclonal (C11F2), IgG; Mouse, Monoclonal (C2), IgG1; Mouse, Monoclonal (C3), IgG1; Mouse, Monoclonal (C4), IgG1; Mouse, Monoclonal (C5), IgG2a; Mouse, Monoclonal (C6), IgG2a; Mouse, Monoclonal (C7), IgG1; Mouse, Monoclonal (CRP103), IgG2b; Mouse, Monoclonal (CRP11), IgG1; Mouse, Monoclonal (CRP135), IgG1; Mouse, Monoclonal (CRP169), IgG2a; Mouse, Monoclonal (CRP30), IgG1; Mouse, Monoclonal (CRP36), IgG2a; Rabbit, Monoclonal (EPR283Y), IgG; Mouse, Monoclonal (KT39), IgG2b; Mouse, Monoclonal (N-a), IgG1; Mouse, Monoclonal (N1G1), IgG1; Monoclonal (P5A9AT); Mouse, Monoclonal (S5G1), IgG1; Mouse, Monoclonal (SB78c), IgG1; Mouse, Monoclonal (SB78d), IgG1 and Rabbit, Monoclonal (Y284), IgG, Human C-Reactive Protein/CRP Biot MAb (Cl 232024), Mouse IgG2B, Human C-Reactive Protein/CRP MAb (Clone 232007), Mouse IgG2B, Human/Mouse/Porcine C-Reactive Protein/CRP MAb (Cl 232026), Mouse IgG2A.
Antibodies for measuring CRP include monoclonal antibodies for measuring CRP and polyclonal antibodies for measuring CRP.
Antibodies for measuring CRP also include antibodies that were developed to target epitopes from the list comprising of: Human plasma derived CRP, Human serum derived CRP, Mouse myeloma cell line NSO-derived recombinant human C-Reactive Protein/CRP (Phe17-Pro224 Accession #P02741).
As mentioned, the present invention also contemplates measuring determinants at the RNA level.
Methods of analyzing the amount of RNA are known in the art and are summarized infra:
Northern Blot analysis: This method involves the detection of a particular RNA in a mixture of RNAs. An RNA sample is denatured by treatment with an agent (e.g., formaldehyde) that prevents hydrogen bonding between base pairs, ensuring that all the RNA molecules have an unfolded, linear conformation. The individual RNA molecules are then separated according to size by gel electrophoresis and transferred to a nitrocellulose or a nylon-based membrane to which the denatured RNAs adhere. The membrane is then exposed to labeled DNA probes. Probes may be labeled using radio-isotopes or enzyme linked nucleotides. Detection may be using autoradiography, colorimetric reaction or chemiluminescence. This method allows both quantitation of an amount of particular RNA molecules and determination of its identity by a relative position on the membrane which is indicative of a migration distance in the gel during electrophoresis.
RT-PCR analysis: This method uses PCR amplification of relatively rare RNAs molecules. First, RNA molecules are purified from the cells and converted into complementary DNA (cDNA) using a reverse transcriptase enzyme (such as an MMLV-RT) and primers such as, oligo dT, random hexamers or gene specific primers. Then by applying gene specific primers and Taq DNA polymerase, a PCR amplification reaction is carried out in a PCR machine. Those of skills in the art are capable of selecting the length and sequence of the gene specific primers and the PCR conditions (i.e., annealing temperatures, number of cycles and the like) which are suitable for detecting specific RNA molecules. It will be appreciated that a semi-quantitative RT-PCR reaction can be employed by adjusting the number of PCR cycles and comparing the amplification product to known controls.
RNA in situ hybridization stain: In this method DNA or RNA probes are attached to the RNA molecules present in the cells. Generally, the cells are first fixed to microscopic slides to preserve the cellular structure and to prevent the RNA molecules from being degraded and then are subjected to hybridization buffer containing the labeled probe. The hybridization buffer includes reagents such as formamide and salts (e.g., sodium chloride and sodium citrate) which enable specific hybridization of the DNA or RNA probes with their target mRNA molecules in situ while avoiding non-specific binding of probe. Those of skills in the art are capable of adjusting the hybridization conditions (i.e., temperature, concentration of salts and formamide and the like) to specific probes and types of cells. Following hybridization, any unbound probe is washed off and the bound probe is detected using known methods. For example, if a radio-labeled probe is used, then the slide is subjected to a photographic emulsion which reveals signals generated using radio-labeled probes; if the probe was labeled with an enzyme then the enzyme-specific substrate is added for the formation of a colorimetric reaction; if the probe is labeled using a fluorescent label, then the bound probe is revealed using a fluorescent microscope; if the probe is labeled using a tag (e.g., digoxigenin, biotin, and the like) then the bound probe can be detected following interaction with a tag-specific antibody which can be detected using known methods.
In situ RT-PCR stain: This method is described in Nuovo G J, et al. [Intracellular localization of polymerase chain reaction (PCR)-amplified hepatitis C cDNA. Am J Surg Pathol. 1993, 17: 683-90] and Komminoth P, et al. [Evaluation of methods for hepatitis C virus detection in archival liver biopsies. Comparison of histology, immunohistochemistry, in situ hybridization, reverse transcriptase polymerase chain reaction (RT-PCR) and in situ RT-PCR. Pathol Res Pract. 1994, 190: 1017-25]. Briefly, the RT-PCR reaction is performed on fixed cells by incorporating labeled nucleotides to the PCR reaction. The reaction is carried on using a specific in situ RT-PCR apparatus such as the laser-capture microdissection PixCell I LCM system available from Arcturus Engineering (Mountainview, Calif.).
DNA Microarrays/DNA Chips:
The expression of thousands of genes may be analyzed simultaneously using DNA microarrays, allowing analysis of the complete transcriptional program of an organism during specific developmental processes or physiological responses. DNA microarrays consist of thousands of individual gene sequences attached to closely packed areas on the surface of a support such as a glass microscope slide. Various methods have been developed for preparing DNA microarrays. In one method, an approximately 1 kilobase segment of the coding region of each gene for analysis is individually PCR amplified. A robotic apparatus is employed to apply each amplified DNA sample to closely spaced zones on the surface of a glass microscope slide, which is subsequently processed by thermal and chemical treatment to bind the DNA sequences to the surface of the support and denature them. Typically, such arrays are about 2×2 cm and contain about individual nucleic acids 6000 spots. In a variant of the technique, multiple DNA oligonucleotides, usually 20 nucleotides in length, are synthesized from an initial nucleotide that is covalently bound to the surface of a support, such that tens of thousands of identical oligonucleotides are synthesized in a small square zone on the surface of the support. Multiple oligonucleotide sequences from a single gene are synthesized in neighboring regions of the slide for analysis of expression of that gene. Hence, thousands of genes can be represented on one glass slide. Such arrays of synthetic oligonucleotides may be referred to in the art as “DNA chips”, as opposed to “DNA microarrays”, as described above [Lodish et al. (eds.). Chapter 7.8: DNA Microarrays: Analyzing Genome-Wide Expression. In: Molecular Cell Biology, 4th ed., W. H. Freeman, New York. (2000)].
Oligonucleotide microarray—In this method oligonucleotide probes capable of specifically hybridizing with the polynucleotides of some embodiments of the invention are attached to a solid surface (e.g., a glass wafer). Each oligonucleotide probe is of approximately 20-25 nucleic acids in length. To detect the expression pattern of the polynucleotides of some embodiments of the invention in a specific cell sample (e.g., blood cells), RNA is extracted from the cell sample using methods known in the art (using e.g., a TRIZOL solution, Gibco BRL, USA). Hybridization can take place using either labeled oligonucleotide probes (e.g., 5′-biotinylated probes) or labeled fragments of complementary DNA (cDNA) or RNA (cRNA). Briefly, double stranded cDNA is prepared from the RNA using reverse transcriptase (RT) (e.g., Superscript II RT), DNA ligase and DNA polymerase I, all according to manufacturer's instructions (Invitrogen Life Technologies, Frederick, Md., USA). To prepare labeled cRNA, the double stranded cDNA is subjected to an in vitro transcription reaction in the presence of biotinylated nucleotides using e.g., the BioArray High Yield RNA Transcript Labeling Kit (Enzo, Diagnostics, Affymetix Santa Clara Calif.). For efficient hybridization the labeled cRNA can be fragmented by incubating the RNA in 40 mM Tris Acetate (pH 8.1), 100 mM potassium acetate and 30 mM magnesium acetate for 35 minutes at 94° C. Following hybridization, the microarray is washed and the hybridization signal is scanned using a confocal laser fluorescence scanner which measures fluorescence intensity emitted by the labeled cRNA bound to the probe arrays.
For example, in the Affymetrix microarray (Affymetrix®, Santa Clara, Calif.) each gene on the array is represented by a series of different oligonucleotide probes, of which, each probe pair consists of a perfect match oligonucleotide and a mismatch oligonucleotide. While the perfect match probe has a sequence exactly complimentary to the particular gene, thus enabling the measurement of the level of expression of the particular gene, the mismatch probe differs from the perfect match probe by a single base substitution at the center base position. The hybridization signal is scanned using the Agilent scanner, and the Microarray Suite software subtracts the non-specific signal resulting from the mismatch probe from the signal resulting from the perfect match probe.
RNA sequencing: Methods for RNA sequence determination are generally known to the person skilled in the art. Preferred sequencing methods are next generation sequencing methods or parallel high throughput sequencing methods. An example of an envisaged sequence method is pyrosequencing, in particular 454 pyrosequencing, e.g. based on the Roche 454 Genome Sequencer. This method amplifies DNA inside water droplets in an oil solution with each droplet containing a single DNA template attached to a single primer-coated bead that then forms a clonal colony. Pyrosequencing uses luciferase to generate light for detection of the individual nucleotides added to the nascent DNA, and the combined data are used to generate sequence read-outs. Yet another envisaged example is Illumina or Solexa sequencing, e.g. by using the Illumina Genome Analyzer technology, which is based on reversible dye-terminators. DNA molecules are typically attached to primers on a slide and amplified so that local clonal colonies are formed. Subsequently one type of nucleotide at a time may be added, and non-incorporated nucleotides are washed away. Subsequently, images of the fluorescently labeled nucleotides may be taken and the dye is chemically removed from the DNA, allowing a next cycle. Yet another example is the use of Applied Biosystems' SOLiD technology, which employs sequencing by ligation. This method is based on the use of a pool of all possible oligonucleotides of a fixed length, which are labeled according to the sequenced position. Such oligonucleotides are annealed and ligated. Subsequently, the preferential ligation by DNA ligase for matching sequences typically results in a signal informative of the nucleotide at that position. Since the DNA is typically amplified by emulsion PCR, the resulting bead, each containing only copies of the same DNA molecule, can be deposited on a glass slide resulting in sequences of quantities and lengths comparable to Illumina sequencing. A further method is based on Helicos' Heliscope technology, wherein fragments are captured by polyT oligomers tethered to an array. At each sequencing cycle, polymerase and single fluorescently labeled nucleotides are added and the array is imaged. The fluorescent tag is subsequently removed and the cycle is repeated. Further examples of sequencing techniques encompassed within the methods of the present invention are sequencing by hybridization, sequencing by use of nanopores, microscopy-based sequencing techniques, microfluidic Sanger sequencing, or microchip-based sequencing methods. The present invention also envisages further developments of these techniques, e.g. further improvements of the accuracy of the sequence determination, or the time needed for the determination of the genomic sequence of an organism etc.
According to one embodiment, the sequencing method comprises deep sequencing.
As used herein, the term “deep sequencing” refers to a sequencing method wherein the target sequence is read multiple times in the single test. A single deep sequencing run is composed of a multitude of sequencing reactions run on the same target sequence and each, generating independent sequence readout.
It will be appreciated that the expression level of the determinants described herein can be an absolute expression level, a normalized expression and/or a relative expression level.
In general scientific context, normalization is a process by which a measurement raw data is converted into data that may be directly compared with other so normalized data. In the context of the present invention, measurements of expression levels are prone to errors caused by, for example, unequal degradation of measured samples, different loaded quantities per assay, and other various errors. More specifically, any assayed sample may contain more or less biological material than is intended, due to human error and equipment failures. Thus, the same error or deviation applies to both the polypeptide of the invention and to the control reference, whose expression is essentially constant. Thus, division of MX1 or CRP raw expression value by the control reference raw expression value yields a quotient which is essentially free from any technical failures or inaccuracies (except for major errors which destroy the sample for testing purposes) and constitutes a normalized expression value of the polypeptide. Since control reference expression values are equal in different samples, they constitute a common reference point that is valid for such normalization.
According to a particular embodiment, each of the polypeptide expression values are normalized using the same control reference.
Once the tests are carried out to determine the level of the determinants, a subject specific dataset is optionally generated which contains the results of the measurements.
The subject-specific dataset may be stored in a computer readable format on a non-volatile computer readable medium, and is optionally and preferably accessed by a hardware processor, such as a general purpose computer or dedicated circuitry.
As mentioned, the levels of the determinants (e.g. polypeptides) in the test subjects blood are compared to the levels of the identical polypeptides in a plurality of subjects' blood, when the subjects have already been verified as having a bacterial infection, viral infection or non-bacterial/non-viral disease on the basis of parameters other than the blood level of the polypeptides. The levels of the polypeptides of the plurality of subjects together with their verified diagnosis can be stored in a second dataset, also referred to herein as the “group dataset” or “prediagnosed dataset”, as further described herein below.
The phrase “non-bacterial/non-viral disease” refers to disease that is not caused by a bacteria or virus. This includes diseases such as acute myocardial infarction, physical injury, epileptic attack, inflammatory disorders etc, fungal diseases, parasitic diseases etc.
The phrase “viral infection” as used herein refers to a disease that is caused by a virus and does not comprise a bacterial component.
Methods of analyzing a dataset, for example, for the purpose of calculating one or more probabilistic classification function representing the likelihood that a particular subject has a bacterial infection, or the likelihood that a particular subject has a viral infection or the likelihood that a particular subject has a non-bacterial non-viral disease, may be performed as described in the Examples section below.
For example, diagnosis may be supported using PCR diagnostic assays such as (i) Seeplex® RV15 for detection of parainfluenza virus 1, 2, 3, and 4, coronavirus 229E/NL63, adenovirus A/B/C/D/E, bocavirus 1/2/3/4, influenza virus A and B, metapneumovirus, coronavirus 0C43, rhinovirus A/B/C, respiratory syncytial virus A and B, and Enterovirus, or (ii) Seeplex® PB6 for detection of Streptococcus pneumoniae, Haemophilus influenzae, Chlamydophila pneumoniae, Legionella pneumophila, Bordetella pertussis, and Mycoplasma pneumoniae.
Blood cultures, urine cultures and stool cultures may be analyzed for Shigella spp., Campylobacter spp. and Salmonella spp.; serological testing (IgM and/or IgG) for cytomegalovirus (CMV), Epstein-Barr virus (EBV), Mycoplasma Pneumonia, and Coxiella burnetii (Q-Fever).
Radiological tests (e.g. chest X-ray for suspected lower respiratory tract infection [LRTI]) may be used to confirm chest infections.
Alternatively, or additionally at least one trained physician may be used to establish the diagnosis.
Methods of determining the expression level of the polypeptides in the pre-diagnosed subjects have been described herein above.
Preferably, the same method which is used for determining the expression level of the polypeptides in the pre-diagnosed subjects is used for determining the level of the polypeptides in the test subject. Thus, for example if an immunoassay type method is used for determining the expression level of the polypeptides in the pre-diagnosed subjects, then an immunoassay type method should be used for determining the level of the polypeptides in the test subject.
It will be appreciated that, the type of blood sample need not be identical in the test subject and the pre-diagnosed subjects. Thus, for example, if a serum sample is used for determining the expression level of the polypeptides in the pre-diagnosed subjects, then a plasma sample may be used for determining the level of the polypeptides in the test subject.
The additional dimensions of the datasets provides additional information pertaining to the subject under analysis, to the other subjects and/or to levels of polypeptides other than CRP and MX1.
“Traditional laboratory risk factors” also referred to as “clinical data” encompass biomarkers isolated or derived from subject samples and which are currently evaluated in the clinical laboratory and used in traditional global risk assessment algorithms. Examples of same are provided herein above.
Preferably, at least one of the traditional laboratory risk factors of the subject under analysis is included in the subject specific dataset, and at least one of the traditional laboratory risk factors of one or more (more preferably all) of the other subjects is included in the group dataset. When the subject specific dataset includes at least one of the traditional laboratory risk factors, the risk factors can be included as a separate entry. When the group dataset includes the risk factors, the risk factors is optionally and preferably included per subject. Thus, for example, a group dataset entry can be described by the tuple (S, G, D, L {R}), where S, G, D and L have been introduced before and {R} is the at least one risk factor of subject S.
“Clinical parameters” encompass all non-sample or non-analyte biomarkers of subject health status or other characteristics, such as, without limitation, age (Age), ethnicity (RACE), gender (Sex), core body temperature (abbreviated “temperature”), maximal core body temperature since initial appearance of symptoms (abbreviated “maximal temperature”), time from initial appearance of symptoms (abbreviated “time from symptoms”), pregnancy, or family history (abbreviated FamHX).
Preferably, at least one of the clinical parameters of the subject under analysis is included in the subject specific dataset, and at least one of the clinical parameters of one or more (more preferably all) of the other subjects is included in the group dataset. When the subject specific dataset includes at least one of the clinical parameters, the clinical parameters can be included as a separate entry. When the group dataset includes the clinical parameters, the clinical parameters is optionally and preferably included per subject. Thus, for example, a group dataset entry can be described by the tuple (S, G, D, L {C}), where S, G, D and L have been introduced before and {C} is the clinical parameter of subject S.
As used herein “blood chemistry” refers to the concentration, or concentrations, of any and all substances dissolved in, or comprising, the blood. Representative examples of such substances, include, without limitation, albumin, amylase, alkaline phosphatase, bicarbonate, total bilirubin, BUN, C-reactive protein, calcium, chloride, LDL, HDL, total cholesterol, creatinine, CPK, γ-GT, glucose, LDH, inorganic phosphorus, lipase, potassium, total protein, AST, ALT, sodium, triglycerides, uric acid and VLDL.
Once the diagnosis has been made, it will be appreciated that a number of actions may be taken.
Thus, for example, if a bacterial infection is ruled in, then the subject may be treated with an antibiotic agent.
Examples of antibiotic agents include, but are not limited to Daptomycin; Gemifloxacin; Telavancin; Ceftaroline; Fidaxomicin; Amoxicillin; Ampicillin; Bacampicillin; Carbenicillin; Cloxacillin; Dicloxacillin; Flucloxacillin; Mezlocillin; Nafcillin; Oxacillin; Penicillin G; Penicillin V; Piperacillin; Pivampicillin; Pivmecillinam; Ticarcillin; Aztreonam; Imipenem; Doripenem; Meropenem; Ertapenem; Clindamycin; Lincomycin; Pristinamycin; Quinupristin; Cefacetrile (cephacetrile); Cefadroxil (cefadroxyl); Cefalexin (cephalexin); Cefaloglycin (cephaloglycin); Cefalonium (cephalonium); Cefaloridine (cephaloridine); Cefalotin (cephalothin); Cefapirin (cephapirin); Cefatrizine; Cefazaflur; Cefazedone; Cefazolin (cephazolin); Cefradine (cephradine); Cefroxadine; Ceftezole; Cefaclor; Cefamandole; Cefmetazole; Cefonicid; Cefotetan; Cefoxitin; Cefprozil (cefproxil); Cefuroxime; Cefuzonam; Cefcapene; Cefdaloxime; Cefdinir; Cefditoren; Cefetamet; Cefixime; Cefmenoxime; Cefodizime; Cefotaxime; Cefpimizole; Cefpodoxime; Cefteram; Ceftibuten; Ceftiofur; Ceftiolene; Ceftizoxime; Ceftriaxone; Cefoperazone; Ceftazidime; Cefclidine; Cefepime; Cefluprenam; Cefoselis; Cefozopran; Cefpirome; Cefquinome; Fifth Generation; Ceftobiprole; Ceftaroline; Not Classified; Cefaclomezine; Cefaloram; Cefaparole; Cefcanel; Cefedrolor; Cefempidone; Cefetrizole; Cefivitril; Cefmatilen; Cefmepidium; Cefovecin; Cefoxazole; Cefrotil; Cefsumide; Cefuracetime; Ceftioxide; Azithromycin; Erythromycin; Clarithromycin; Dirithromycin; Roxithromycin; Telithromycin; Amikacin; Gentamicin; Kanamycin; Neomycin; Netilmicin; Paromomycin; Streptomycin; Tobramycin; Flumequine; Nalidixic acid; Oxolinic acid; Piromidic acid; Pipemidic acid; Rosoxacin; Ciprofloxacin; Enoxacin; Lomefloxacin; Nadifloxacin; Norfloxacin; Ofloxacin; Pefloxacin; Rufloxacin; Balofloxacin; Gatifloxacin; Grepafloxacin; Levofloxacin; Moxifloxacin; Pazufloxacin; Sparfloxacin; Temafloxacin; Tosufloxacin; Besifloxacin; Clinafloxacin; Gemifloxacin; Sitafloxacin; Trovafloxacin; Prulifloxacin; Sulfamethizole; Sulfamethoxazole; Sulfisoxazole; Trimethoprim-Sulfamethoxazole; Demeclocycline; Doxycycline; Minocycline; Oxytetracycline; Tetracycline; Tigecycline; Chloramphenicol; Metronidazole; Tinidazole; Nitrofurantoin; Vancomycin; Teicoplanin; Telavancin; Linezolid; Cycloserine 2; Rifampin; Rifabutin; Rifapentine; Bacitracin; Polymyxin B; Viomycin; Capreomycin.
If a viral infection is ruled in, the subject may be treated with an antiviral agent. Examples of antiviral agents include, but are not limited to Abacavir; Aciclovir; Acyclovir; Adefovir; Amantadine; Amprenavir; Ampligen; Arbidol; Atazanavir; Atripla; Balavir; Boceprevirertet; Cidofovir; Combivir; Dolutegravir; Darunavir; Delavirdine; Didanosine; Docosanol; Edoxudine; Efavirenz; Emtricitabine; Enfuvirtide; Entecavir; Ecoliever; Famciclovir; Fomivirsen; Fosamprenavir; Foscarnet; Fosfonet; Fusion inhibitor; Ganciclovir; Ibacitabine; Imunovir; Idoxuridine; Imiquimod; Indinavir; Inosine; Integrase inhibitor; Interferon type III; Interferon type II; Interferon type I; Interferon; Lamivudine; Lopinavir; Loviride; Maraviroc; Moroxydine; Methisazone; Nelfinavir; Nevirapine; Nexavir; Oseltamivir; Peginterferon alfa-2a; Penciclovir; Peramivir; Pleconaril; Podophyllotoxin; Raltegravir; Reverse transcriptase inhibitor; Ribavirin; Rimantadine; Ritonavir; Pyramidine; Saquinavir; Sofosbuvir; StavudineTelaprevir; Tenofovir; Tenofovir disoproxil; Tipranavir; Trifluridine; Trizivir; Tromantadine; Truvada; traporved; Valaciclovir; Valganciclovir; Vicriviroc; Vidarabine; Viramidine; Zalcitabine; Zanamivir; Zidovudine; RNAi antivirals; inhaled rhibovirons; monoclonal antibody respigams; neuriminidase blocking agents.
The information gleaned using the methods described herein may aid in additional patient management options. For example, the information may be used for determining whether a patient should or should not be admitted to hospital. It may also affect whether or not to prolong hospitalization duration. It may also affect the decision whether additional tests need to be performed or may save performing unnecessary tests such as CT and/or X-rays and/or MRI and/or culture and/or serology and/or PCR assay for specific bacteria and/or PCR assays for viruses and/or perform procedures such as lumbar puncture.
Although the invention has been described in conjunction with specific embodiments thereof, it is evident that many alternatives, modifications and variations will be apparent to those skilled in the art. Accordingly, it is intended to embrace all such alternatives, modifications and variations that fall within the spirit and broad scope of the appended claims.
It is the intent of the Applicant(s) that all publications, patents and patent applications referred to in this specification are to be incorporated in their entirety by reference into the specification, as if each individual publication, patent or patent application was specifically and individually noted when referenced that it is to be incorporated herein by reference. In addition, citation or identification of any reference in this application shall not be construed as an admission that such reference is available as prior art to the present invention. To the extent that section headings are used, they should not be construed as necessarily limiting. In addition, any priority document(s) of this application is/are hereby incorporated herein by reference in its/their entirety.
This application is a continuation U.S. patent application Ser. No. 16/238,582 filed on Jan. 3, 2019, which is a continuation of PCT Patent Application No. PCT/IL2017/050780 having International Filing Date of Jul. 10, 2017, which claims the benefit of priority under 35 USC § 119(e) of U.S. Provisional Patent Application No. 62/360,418 filed on Jul. 10, 2016. The contents of the above applications are all incorporated by reference as if fully set forth herein in their entirety.
| Number | Date | Country | |
|---|---|---|---|
| 62360418 | Jul 2016 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 16238582 | Jan 2019 | US |
| Child | 17372575 | US | |
| Parent | PCT/IL2017/050780 | Jul 2017 | US |
| Child | 16238582 | US |
