Patent Application
20140092933
1. Field of the Invention
The present invention relates to systems and methods for calibrating thermal sensors. More particularly, aspects of the present invention relate to systems and methods for using a single slug comprising one or more calibrators or multiple slugs comprising one or more calibrators to calculate a relationship between temperature and an electrical characteristic of the thermal sensor for use in connection with calibrating thermal sensors.
2. Description of the Background
Devices for performing chemical, biological, or other reactions (e.g., a microfluidic device for performing polymerase chain reaction (PCR) amplification of DNA molecules, or a microfluidic molecular diagnostic platform that performs PCR on a patient sample and then uses the PCR product for genotyping by performing a high resolution melt analysis) often feature one or more thermal control elements that are used to subject reactants to a desired thermal profile. A description of PCR amplification, and an example of one possible microfluidic device including thermal control elements for PCR amplification and thermal melt analysis, are provided in U.S. patent application Ser. No. 12/165,043, which is hereby incorporated herein by reference. A description of the field trial unit (FTU) referred to in the present application can be found in U.S. patent application Ser. No. 13/223,290, which is hereby incorporated herein by reference.
In many applications of such microfluidic devices (e.g., PCR and/or thermal melt analysis), the thermal control elements of those devices must be precisely calibrated. That is, the correspondence between the temperature of the thermal control element and an electrical characteristic of the thermal control element must be precisely determined. For example, in the case of a resistance temperature detector, the correspondence between temperature and resistance must be precisely determined. Additional types of thermal control elements can include platinum resistive heaters, thermistors, diode temperature sensors, thermocouples, or any other suitable temperature measuring devices. Additional electrical characteristics of thermal control elements that correspond to temperature can include capacitance or inductance of an element, frequency, pulse width, or amplitude of a signal, or other sensor characteristics known in the art. Methods of calibrating thermal control elements often include generating a lookup table or a series of coefficients that define a calibration equation, i.e., a lookup table or an equation relating the temperature of the thermal control element with the electrical characteristic.
Calibration can be performed by sending the device to a third party laboratory for taking accurate measurements and generating the lookup table or series of coefficients; however, this procedure is generally expensive and time consuming. Furthermore, for many devices (e.g., many common microfluidic devices) there may be many thermal control elements (e.g. dozens or even hundreds of heaters and sensors), each of which requires its own precise calibration, making third-party calibration impractical.
The present microfluidic system utilizes a microfluidic chip referred to herein as a U chip, which is contained with a cartridge. Throughout the present invention, U chip and microfluidic chip will be used interchangeably. Several variables can cause fluid temperature variance within U chip microfluidic channels. Heater calibration is utilized to correct for these combination of factors to provide a more accurate result with functional testing by melting amplicon, measuring the melting temperature (Tm), and then adjusting software settings for how power is delivered to the heaters. The heater calibration process itself introduces some error into temperature correction due to calibrator formulation variation and melting curve smoothing/calculations to match the reference melting curve for heater parameter adjustment.
Accordingly, what is desired is robust calibration of thermal sensors that can be accurate, reduce downtime and maintain high throughput.
The present invention relates to systems and methods for calibrating a thermal control element. More particularly, the present invention relates to systems and methods of calibrating thermal control elements in connection with a microfluidic chip.
Thus, in one aspect, the present invention relates to a method and system for calibrating thermal control elements comprising introducing a single slug of fluid into a microfluidic chip. The method may comprise the steps of (a) providing a calibrator in thermal contact with the thermal control element, (b) utilizing the thermal control element to perform a thermal variation to generate a thermal response profile for the compound calibrator, (c) identifying at least one feature of the thermal response profile and generating at least one relation between a known temperature of the at least one feature and at least one measurement value of the thermal control element, and (e) calculating one or more calibration coefficients for the thermal control element based on the at least one relation.
In further embodiments, the thermal response profile may be a thermal melt curve. In a yet further embodiment, the at least one feature may correspond to a melting temperature of the calibrator, and an optional second feature may correspond to a second melting temperature of the calibrator. In other embodiments, the measurement value may be the resistance of the thermal control element.
In other embodiments, the calibrator may be an amplicon of a nucleic acid, and the compound calibrator may be a mixture of at least one amplicon(s) of a nucleic acid. The amplicons may be Ultra-Conserved Elements of the human genome, for example. In another embodiment, the calibrant may comprise at least one amplicon derived from synthetic sequences, such as that which is described herein as RFCal.
Another embodiment of the invention includes a method for calibrating one or more thermal control elements in a thermal device having more than one thermal zone. This method may include the steps of (a) providing a calibrator in a first thermal zone, wherein the first thermal zone is in thermal contact with a first of said plurality of thermal control elements, (b) utilizing the first thermal control element to perform a thermal variation, generating a first thermal response profile for the calibrator, (c) identifying at least one feature of the first thermal response profile and generating a first relation between a known temperature of the first feature and a first measurement value of the first thermal control element, (d) identifying a second feature of the first thermal response profile and generating a second relation between a known temperature of the second feature and a second measurement value of the first thermal control element, and (e) calculating one or more calibration coefficients for the first thermal control element based on at least the first and second relations.
In a further embodiment, the first thermal zone may be thermally isolated from the second thermal zone. The first thermal zone and the second thermal zone may be calibrated in parallel, or in serial, or only one thermal zone may be calibrated.
In yet a further embodiment, the calibrator may be introduced into the thermal zone or placed in thermal contact with the thermal control element by being introduced into a microfluidic chip as a component in a fluid slug. In one embodiment, the microfluidic chip may contain at least one microfluidic channel. In another embodiment, the at least one microfluidic channel may be thermal contact with at least one thermal zone. In some embodiments, the microfluidic channel may be in thermal contact with at least two thermal zones.
In another embodiment, the calibrator may be introduced into the microfluidic channel such that the calibrator fills the entire portion of the microfluidic channel that is in thermal contact with the first thermal zone, and such that the calibrator fills less than the entire portion of the microfluidic channel that is in thermal contact with the second thermal zone. In a further embodiment, the calibrator filling less than the entire portion of the microfluidic channel that is in thermal contact with the second thermal zone provides a leading “edge” to the fluid slug containing the calibrator that allows the system to control the movement of the slug within the microfluidic channel.
In one embodiment, the method of calibrating one or more thermal control elements as previously described herein occurs while a fluid slug containing the calibrator fills the entire portion of the microfluidic channel that is in thermal contact with the first thermal zone, and while said calibrator fills less than the entire portion of the microfluidic channel that is in thermal contact with the second thermal zone.
In a further embodiment, the fluid slug that fills the entire portion of the microfluidic channel that is in thermal contact with the first thermal zone and fills less than the entire portion of the microfluidic channel that is in thermal contact with the second thermal zone is moved through the channel, such that the fluid slug then fills the entire portion of the microfluidic channel that is in thermal contact with the second thermal zone and fills less than the entire portion of the microfluidic channel that is in thermal contact with the first thermal zone. In this embodiment, the fluid slug filling only a portion of the microfluidic channel that is in thermal contact with the first thermal zone would provide a rear “edge” to the fluid slug containing the calibrator that allows the system to control the movement of the slug within the microfluidic channel.
In one embodiment of the invention, the method of calibrating one or more thermal control elements as previously described herein may then be repeated in order to calibrate the thermal control elements associated with the second thermal zone. In additional embodiments, this process of moving the fluid slug and calibrating the thermal control elements may be repeated for any number of thermal zones.
In a further embodiment, any of the methods for calibrating a thermal control element provided herein may more particularly include the steps of (a) providing a calibrator in thermal contact with the thermal control element, (b) utilizing the thermal control element to perform a thermal ramp, (c) generating a melt curve for the calibrator, (d) identifying a first feature of the melt curve and generating a first relation between a known temperature of the first feature and a first measurement value of the thermal control element, (e) optionally identifying a second feature of the melt curve and generating a second relation between a known temperature of the second feature and a second measurement value of the thermal control element, and (f) calculating one or more calibration coefficients for the thermal control element based on at least the first and/or optional second relations.
In yet another embodiment, the present invention provides a method of calibrating at least one of a plurality of thermal control elements in a thermal device, wherein the thermal device comprises a microfluidic chip having more than one thermal zones, each thermal zone being in thermal contact with at least one of said plurality of thermal control elements, wherein the microfluidic chip comprises at least one microfluidic channel that is in thermal contact with each of the more than one thermal zones, the method comprising: a) introducing a fluid slug comprising a calibrator into the microfluidic channel such that the fluid slug fills the entire portion of the microfluidic channel that is in thermal contact with a first thermal zone and fills less than the entire portion of the microfluidic channel that is in thermal contact with a second thermal zone; b) utilizing at least one thermal control element to perform a thermal variation within the first thermal zone, generating a first thermal response profile for said calibrator; c) identifying a first feature of said first thermal response profile and generating a first relation between a known temperature of said first feature and a first measurement value of said first thermal control element; and d) calculating one or more calibration coefficients for said at least one thermal control element based on at least said first relation.
In another embodiment, there is provided a method calibrating at least one of a plurality of thermal control elements in a thermal device, wherein the thermal device comprises a microfluidic chip having more than one thermal zones, each thermal zone being in thermal contact with at least one of said plurality of thermal control elements, wherein the microfluidic chip comprises at least one microfluidic channel that is in thermal contact with each of the more than one thermal zones, the method comprising: a) introducing a fluid slug comprising a calibrator into the microfluidic channel such that the fluid slug fills the entire portion of the microfluidic channel that is in thermal contact with a first thermal zone and fills less than the entire portion of the microfluidic channel that is in thermal contact with a second thermal zone; b) utilizing at least one thermal control element to perform a thermal variation within the first thermal zone, generating a first thermal response profile for said calibrator; c) identifying a first feature of said first thermal response profile and generating a first relation between a known temperature of said first feature and a first measurement value of said first thermal control element; and d) calculating one or more calibration coefficients for said at least one thermal control element based on at least said first relation, wherein the method further comprises: moving the fluid slug such that the fluid slug fills the entire portion of the microfluidic channel that is in thermal contact with a second thermal zone and fills less than the entire portion of the microfluidic channel that is in thermal contact with said first thermal zone; repeating steps a)-d) using the calibrator in said second thermal zone, wherein the second thermal zone is in thermal contact with at least one thermal control element.
In a further embodiment, these steps may be repeated for each additional thermal zone in addition to a first and second thermal zone.
In one embodiment, the systems and methods provided herein can be utilized with any desired calibrator, including individual and/or compound calibrators.
In one aspect, the present invention includes an additional method for calibrating a thermal control element. The method may comprise the steps of (a) providing a compound calibrator in thermal contact with the thermal control element, (b) utilizing the thermal control element to perform a thermal variation to generate a thermal response profile for the compound calibrator, (c) identifying a first feature of the thermal response profile and generating a first relation between a known temperature of the first feature and a first measurement value of the thermal control element, (d) identifying a second feature of the thermal response profile and generating a second relation between a known temperature of the second feature and a second measurement value of the thermal control element, and (e) calculating one or more calibration coefficients for the thermal control element based on the first and second relations.
In further embodiments, the thermal response profile may be a thermal melt curve. In a yet further embodiment, the first feature may correspond to a first melting temperature of the compound calibrator, and the second feature may correspond to a second melting temperature of the compound calibrator. In other embodiments, the measurement value may be the resistance of the thermal control element.
In other embodiments, the compound calibrator may be a mixture of two or more amplicons of a nucleic acid. The amplicons may be Ultra-Conserved Elements of the human genome, for example. In a further embodiment, the amplicons may be synthetically generated. In still another embodiment, the calibration coefficients may be the coefficients of a linear calibration equation. In still another embodiment, the first feature may be at a melting temperature of a first of the two or more amplicons in the compound calibrator, and the second feature may be at a melting temperature of a second of the two or more amplicons in the compound calibrator.
In a further embodiment, the method further comprises the steps of identifying a third feature of the thermal response profile, as well as generating a third relation between a known temperature of the third feature and a third measurement value of the thermal control element. In this embodiment, the step of calculating one or more calibration coefficients includes calculating one or more calibration coefficients for said thermal control element based on said first, second, and third relations. In an embodiment of this method, the calibration coefficients may be the coefficients of a quadratic calibration equation. In another embodiment of this method, the first feature is at a melting temperature of a first of three or more amplicons in the compound calibrator, the second feature is at a melting temperature of a second of the three or more amplicons in the compound calibrator, and the third feature is at a melting temperature of a third of the three or more amplicons in the compound calibrator. In another embodiment, one of the first, second, and third features may be at a melting temperature of a first amplicon in the compound calibrator, and the other two of the first, second, and third features are at melting temperatures of a second amplicon in the compound calibrator.
In another embodiment, the method may further include the additional steps of identifying a third relation between a known ambient temperature and a measurement value of the thermal control element. In this embodiment, the step of calculating one or more calibration coefficients may further be based on at least the first, second, and third relations.
Another embodiment of the invention includes a method for calibrating a plurality of thermal control elements in a thermal device. This method may include the steps of (a) providing a compound calibrator in a first thermal zone, wherein the first thermal zone is in thermal contact with a first of said plurality of thermal control elements, (b) utilizing the first thermal control element to perform a thermal variation, generating a first thermal response profile for the compound calibrator, (c) identifying a first feature of the first thermal response profile and generating a first relation between a known temperature of the first feature and a first measurement value of the first thermal control element, (d) identifying a second feature of the first thermal response profile and generating a second relation between a known temperature of the second feature and a second measurement value of the first thermal control element, (e) calculating one or more calibration coefficients for the first thermal control element based on at least the first and second relations; and f) repeating steps a-e using the compound calibrator in a second thermal zone, wherein the second thermal zone is in thermal contact with a second thermal control element.
In a further embodiment, the method may include repeating steps a-e for each additional thermal element in the thermal device. In a further aspect, the thermal device may be a microfluidic channel in thermal communication with a plurality of thermal control elements.
In a further embodiment, the first thermal zone may be thermally isolated from the second thermal zone. The first thermal zone and the second thermal zone may be calibrated in parallel. In another embodiment, the first thermal zone and the second thermal zone may be calibrated in series. In still another embodiment, the compound calibrator may be a mixture of two or more amplicons of a nucleic acid.
Another aspect of the present invention is a method for calibrating a plurality of thermal control elements in a thermal device. In this aspect, the method may include the steps of (a) providing a compound calibrator in a first thermal zone, wherein the first thermal zone is in thermal contact with a first of the plurality of thermal control elements, (b) utilizing the first thermal control element to perform a thermal variation, generating a first thermal response profile for the compound calibrator, (c) identifying a first feature of the first thermal response profile and generating a first relation between a known temperature of said first feature and a first measurement value of the first thermal control element, (d) identifying a second feature of the first thermal response profile and generating a second relation between a known temperature of the second feature and a second measurement value of the first thermal control element, (e) identifying a third relation between a known ambient temperature and measurement value of the first thermal control element, (f) calculating one or more calibration coefficients for the first thermal control element based on at least the first, second, and third relations, and (g) repeating steps a-f using the compound calibrator in a second thermal zone, wherein the second thermal zone is in thermal contact with a second thermal control element.
In another embodiment, a method for calibrating a thermal control element is provided which may include the steps of (a) providing a compound calibrator in thermal contact with the thermal control element, (b) utilizing the thermal control element to perform a thermal ramp, (c) generating a melt curve for the compound calibrator, (d) identifying a first feature of the melt curve and generating a first relation between a known temperature of the first feature and a first measurement value of the thermal control element, (e) identifying a second feature of the melt curve and generating a second relation between a known temperature of the second feature and a second measurement value of the thermal control element, and (f) calculating one or more calibration coefficients for the thermal control element based on at least the first and second relations.
In this embodiment, the method may further comprise identifying a third relation between a known ambient temperature and a third measurement value of the thermal control element, wherein the step of calculating one or more calibration coefficients is further based at least on the third relation.
In a further embodiment, a method for serially calibrating a plurality of thermal control elements in a microfluidic channel which may include the steps of (a) providing a compound calibrator in thermal contact with a first of the plurality of thermal control elements, (b) utilizing the first thermal control element to perform a thermal ramp, generating a first melt curve for the compound calibrator, (c) identifying a first feature of the first melt curve and generating a first relation between a known temperature of the first feature and a first measurement value of the first thermal control element, (d) identifying a second feature of the first melt curve and generating a second relation between a known temperature of the second feature and a second measurement value of the first thermal control element, (e) calculating one or more calibration coefficients for the first thermal control element based on at least the first and second relations, (f) providing the compound calibrator in thermal contact with a second of said plurality of thermal control elements, (f) utilizing the second thermal control element to perform a thermal ramp, generating a second melt curve for the compound calibrator, (g) identifying a third feature of the second melt curve and generating a third relation between a known temperature of the third feature and a third measurement value of the second thermal control element, (h) identifying a fourth feature of the second melt curve and generating a fourth relation between a known temperature of the second feature and a fourth measurement value of the second thermal control element, and (i) calculating one or more calibration coefficients for the second thermal control element based on at least the third and fourth relations.
The above and other embodiments of the present invention are described below with reference to the accompanying drawings.
The accompanying drawings, which are incorporated herein and form part of the specification, illustrate various embodiments of the present invention. In the drawings, like reference numbers indicate identical or functionally similar elements. Additionally, the left-most digit(s) of the reference number identifies the drawing in which the reference number first appears.
In one aspect, the present invention provides a method for calibrating thermal control elements in situ using a single compound calibrator. In some embodiments, the present invention uses a compound calibrator to calibrate thermal control elements on a microfluidic device. In a non-limiting embodiment, the compound calibrator can be a droplet, plug, slug, segment or continuous flow of any appropriate solution that, when heated, yields a thermal response profile with a plurality of features (e.g., maxima, minima, inflection points, linear regions, etc.).
The above and other aspects and features of the present invention, as well as the structure and application of various embodiments of the present invention, are described below with reference to the accompanying drawings.
The present invention has several embodiments and relies on patents, patent applications and other references for details known to those of the art. Therefore, when a patent, patent application, or other reference is cited or repeated herein, it should be understood that it is incorporated by reference in its entirety for all purposes as well as for the proposition that is recited.
The practice of the present invention may employ, unless otherwise indicated, conventional techniques and descriptions of organic chemistry, polymer technology, molecular biology (including recombinant techniques), cell biology, biochemistry, and immunology, which are within the skill of the art. Such conventional techniques include amplification techniques such as the polymerase chain reaction and other techniques such as high-resolution thermal melting.
As used herein, “thermal control element” includes those elements known in the art, including but not limited to “thermal sensors”. Where used herein, “thermal sensor” is to be read as an example of a thermal control element, and any statement relating to a “thermal sensor” should be broadly interpreted as also pertaining the larger class of “thermal control elements.”
As used herein, “genetic material” means any nucleic acid, including DNA and RNA. Thus, genetic material may include a gene, a part of a gene, a group of genes, a fragment of many genes, a molecule of DNA or RNA, molecules of DNA or RNA, a fragment of a DNA or RNA molecule, or fragments of many DNA or RNA molecules. Genetic material can refer to anything from a small fragment of DNA or RNA to the entire genome of an organism.
The use of the terms “a” and “an” and “the” and similar referents in the context of describing the invention (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. The terms “comprising,” “having,” “including,” and “containing” are to be construed as open-ended terms (i.e., meaning “including, but not limited to,”) unless otherwise noted. Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. For example, if the range 10-15 is disclosed, then 11, 12, 13, and 14 are also disclosed. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., “such as”) provided herein, is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention unless otherwise claimed. No language in the specification should be construed as indicating any non-claimed element as essential to the practice of the invention.
In an embodiment, the microfluidic device 100 further includes thermal control elements in the form of thin film resistive heaters 112 associated with the microfluidic channels 102. In one non-limiting embodiment, the thin film resistive heaters 112 may be platinum resistive heaters whose resistances are measured in order to control their respective temperatures. In the embodiment illustrated in
The microfluidic device 100 may include a plurality of heater electrodes 110 connected to the various thin-film heaters 112a and 112b. In non-limiting embodiments, heater electrodes 110 may include PCR section leads 118, one or more PCR section common lead 116a, thermal melt section leads 120, and one or more thermal melt section common lead 116b. According to one embodiment of the present invention, a separate PCR section lead 118 is connected to each of the thin-film PCR heaters 112a, and a separate thermal melt section lead 120 is connected to each of the thin-film thermal melt heaters 112b.
The temperature in the PCR zone 104 can be controlled by the PCR zone temperature controller 210. The PCR zone temperature controller 210, which may be a programmed computer or other microprocessor, sends signals to the heater device 212 (e.g., a PCR heater 112a) based on the temperature determined by a temperature sensor 214 (such as, for example, an RTD or thin-film thermistor, or a thin-film thermocouple thermometer). In this way, the temperature of the PCR zone 104 can be maintained at the desired level. According to some embodiments of the present invention, the PCR zone 104 may also be cooled by a cooling device 216 (for example, to quickly bring the channel temperature from 92° C. down to 55° C.), which may also be controlled by the PCR zone temperature controller 210. In exemplary embodiments, the cooling device 216 could be a peltier device, heat sink or forced convection air cooled device, for example.
The flow of sample through the microfluidic channels 102 can be measured by a PCR zone flow monitoring system 218. In one embodiment, the flow monitoring system can be a fluorescent dye diffusion imaging and tracking system illustrated in U.S. patent application Ser. No. 11/505,358, incorporated herein by reference. According to one embodiment of the present invention, the channels in the PCR zone can be excited by an excitation device 220 and light fluoresced from the sample can be detected by a detection device 222. An example of one possible excitation device and detection device forming part of an imaging system is illustrated in U.S. patent application Ser. Nos. 11/606,006 and 11/505,358, incorporated herein by reference in their entireties.
The thermal melt zone temperature controller 224, e.g. a programmed computer or other microprocessor, can be used to control the temperature of the thermal melt zone 106. As with the PCR zone temperature controller 210, the thermal melt zone temperature controller 224 sends signals to the heating component 226 (e.g., a thermal melt heater 112b) based on the temperature measured by a temperature sensor 228 which can be, for example, an RTD or thin-film thermocouple. Additionally, the thermal melt zone 106 may be independently cooled by cooling device 230. In exemplary embodiments, the cooling device 230 could be a peltier device, heat sink or forced convection air cooled device, for example. The fluorescent signature of the sample can be measured by the thermal melt zone fluorescence measurement system 232. The fluorescence measurement system 232 excites the sample with an excitation device 234, and the fluorescence of the sample can be detected by a detection device 236. An example of one possible fluorescence measurement system is illustrated in U.S. patent application Ser. Nos. 11/606,006 and 11/505,358, incorporated herein by reference in their entireties.
In accordance with aspects of the present invention, the thin film heaters 112 may function as both heaters and temperature detectors. Thus, in one embodiment of the present invention, the functionality of heating element 212 and 226 and temperature sensors 214 and 228 can be accomplished by the thin film heaters 112.
In one embodiment, the system 200 sends power to the thin-film heaters 112a and/or 112b, thereby causing them to heat up, based on a control signal sent by the PCR zone temperature controller 210 or the thermal melt zone temperature controller 224. The control signal can be, for example, a pulse width modulation (PWM) control signal. An advantage of using a PWM signal to control the heaters 212 is that with a PWM control signal, the same voltage potential across the heaters may be used for all of the various temperatures required. In another embodiment, the control signal could utilize amplitude modulation or alternating current. In some embodiments, it may be advantageous to use a control signal that is amplitude modulated to control the heaters 212 because a continuous modest change in voltage, rather than large voltage steps, may avoid slew rate limits and improve settling time. Further discussion of amplitude modulation can be found in U.S. patent application Ser. No. 12/825,476, filed Jun. 29, 2010, which is incorporated herein by reference. In some embodiments, the desired temperature for the heaters is reached by changing the duty cycle of the control signal. For example, the duty cycle of the control signal for achieving 95° C. in a PCR heater might be about 50%, the duty cycle of the control signal for achieving 72° C. in a PCR heater might be about 25%, and the duty cycle of the control signal for achieving 55° C. in a PCR heater might be about 10%.
The microfluidic device 100 and the system 200 can be used in conjunction with aspects of the present invention. For example, one can use the microfluidic device 100 in connection with the system 200 described above to calibrate the heaters 112 on the microfluidic device 100 using a droplet, plug, slug, segment, or continuous flow of a compound calibrator, in accordance with aspects of the invention.
In some embodiments, calibration of a thermal control element can include determining the coefficients of a calibration equation, i.e., an equation that models the relationship between the temperature of the thermal control element and a measurement value. In an embodiment, that measurement value may be an electrical characteristic of the thermal control element. For example, a calibration equation for a resistive heater 112 may model the relationship between the temperature of the heater 112 and the resistance of the heater 112. In this embodiment, the calibration equation may model a linear relationship as shown in Equation 1:
T=k
0
+k
1
R Equation 1
In this case, T is temperature of the thermal control element, R is the resistance of the thermal control element, and k0 and k1 are constants (i.e., the coefficients) to be determined by calibration. Two calibration coefficients can be determined by, for example, measuring the resistance R at two known temperatures (T1 and T2). In some aspects of the present invention, these measurements can be obtained by heating the thermal control element (e.g., a heater 112) in thermal contact with a droplet, plug, slug, segment or continuous flow of a compound calibrator (e.g., while a compound calibrator is in a microfluidic channel 102 corresponding with the heater 112) and measuring the resistance of the thermal control element (e.g., measuring the resistance of the heater 112) at temperatures that coincide with two or more features of the thermal response profile of the compound calibrator.
In other embodiments, the calibration equation may model the relation between other electrical factors, such as the current, electric potential, applied power, resistivity, conductivity, or other related quantities. In some aspects, the measurement value may be an independently controlled aspect of the thermal control element that is related to the temperature of the thermal control element. In other aspects, the measurement value could be any factor related to the temperature of the thermal control element.
In some embodiments, the calibration equation may contain more coefficients to be determined. For example, in the case where the measurement value is resistance, some calibration equations can model a quadratic relationship as shown in Equation 2:
T=k
0
+k
1
R+k
2
R
2 Equation 2
In this case, a compound calibrator having three or more features in its thermal response profile is preferable to more accurately determine all of the coefficients. Further, one of ordinary skill will comprehend that this approach may be expanded for a compound calibrator having n or more features, using Equation 3:
T=k
0
+k
1
R+k
2
R
2
+ . . . k
n-1
R
n-1 Equation 3
Furthermore, in some embodiments, more accurate values for the coefficients may be obtained by utilizing a compound calibrator having more features than there are coefficients to be determined (i.e., determine more correspondences between temperature and resistance of the thermal control element than there are coefficients). The resulting over-determined system can be solved, for example, using the least squares method.
The process 300 can begin at step 302 at which an in situ thermal response profile is obtained for the compound calibrator. As used herein, a “thermal response profile” refers to the analysis of a dependent variable related to a solution that is subject to a thermal variation, i.e., the relationship between a solution's temperature and the dependent variable. In some embodiments, the thermal response profile may be a “melt curve,” i.e. the fluorescent melt analysis of a solution to determine the relationship between the amount of fluorescence and the solution's temperature. Other possible thermal response profiles may be based on the absorbance, transmittance, reflectance, or emissivity of the compound calibrator. In some embodiments, generating such a thermal response profile can include loading a microfluidic chip (e.g., the microfluidic chip 100) into a system for controlling reactions in the microfluidic chip (e.g., system 200), loading a droplet, plug, slug, segment, or continuous flow of the compound calibrator into the chip (e.g., into a microfluidic channel 102), and controlling a thermal control element that is in thermal communication with the compound calibrator (e.g., heater 112) to heat the compound calibrator while monitoring the temperature of the thermal control element and while monitoring the dependent variable (e.g., fluorescence in the case in which a melt curve is obtained) of the compound calibrator.
In accordance with one embodiment, an initial estimate of the calibration coefficients (e.g., k0′ and k1′, which are respectively estimates of k0 and k1 of Equation 1) can be used to control the thermal control element for an initial thermal variation. The thermal variation may be any variation of the temperature of the thermal control element over a period of time. One example of such a thermal variation is a thermal ramp (e.g., heating the thermal control element at, for example, 0.5 degrees Celsius per second over a range of temperatures that includes temperatures corresponding to the features of the compound calibrator thermal response profile). During the thermal ramp, the dependent variable (e.g., fluorescence intensity) of the calibration plug (for example) and the measurement value of the thermal control element is monitored to generate a thermal response profile.
vs. T). In some embodiments, the derivative plot can be generated using a Savitsky-Golay filter. The melt curves illustrated in
Referring back to process 300, at step 304, the apparent temperatures of each feature (e.g., the apparent melt temperatures Tm1′ and Tm2′ respectively corresponding to each amplicon) are identified from the in situ thermal response profile generated in step 302. In some embodiments, the apparent temperatures can be determined from the derivative plot using peak-picking. In other embodiments, the apparent temperatures can be determined by cross-correlating the derivative plot with a known template (i.e., an expected thermal response profile) for each feature, or shifting and stretching the thermal response profile to match a predefined template.
At step 306, the initial calibration coefficients k0′ and k1′ are used to convert the apparent temperatures of each feature (e.g., the apparent melt temperatures Tm1′ and Tm2′) into measurement values corresponding to each feature Mm1 and Mm2 (e.g., when the measured value is resistance, the measured values Mm1 and Mm2 may be resistances Rm1 and Rm2 of the thermal control element respectively at the melt transitions of the compound calibrator).
At step 308, the measurement values corresponding to each feature are matched, respectively, with the known true temperatures of each feature (e.g., the true melt temperatures Tm1 and Tm2 respectively corresponding to the known melt transitions in the compound calibrator) to determine the calibration coefficients (e.g., k0 and k1 of Equation 1). As long as the number of features in the thermal response profile is greater than or equal to the number of calibration coefficients, the relations between measured values and known true temperatures (e.g., (Mm1,Tm1) and (Mm2,Tm2)) can be used to solve a system of equations to determine the calibration coefficients.
The calibrant described herein and referred to as RFCal comprises at least one amplicon derived from synthetic sequences. FRCal was previously described in U.S. patent application Ser. No. 13/223,258 filed Aug. 31, 2011, which is incorporated herein by reference.
In a preferred embodiment, the at least one amplicon(s) are designed from synthetic sequences so that they may be readily produced. In some embodiments, the sequences are chosen such that they are not present in human genomic DNA. In other embodiments, the sequences are chosen such that they are not present in mammalian genomic DNA. In additional embodiments, such sequences are chosen such that they are not present in vertebrate DNA. In some embodiments, for instance where more than one amplicon is being used (i.e., a compound calibrator), the sequences are chosen to produce amplicons with a Tm span greater than 5 degrees Celsius, preferably greater than 10 degrees Celsius, and more preferably greater than 20 degrees Celsius. In one embodiment, an amplicon is named RFCal-100. In another embodiment, an amplicon is named RFCal-200. RFCAL-100 has a melt temperature TM around 70° C., and RFCAL-200 has a melt temperature TM around 90° C. In certain embodiments, the at least one amplicon is cloned in a vector. Any suitable vector well known to the skilled artisan may be used, such as a virus, and the like.
The present invention provides an improvement over current cartridge heater calibration methods used within a microfluidic platform which consists of filling the entire U chip with RFCal, as seen in
Thus, one embodiment of the present invention provides a solution to mitigate this potential cause for calibration inaccuracy by performing the calibration while in slug configuration, as seen in
In U.S. patent application Ser. No. 13/223,270, incorporated herein by reference, the invention of performing calibration within multiple slugs was described. In the present invention, a revised slug configuration has been developed which also uses calibration in slugs. This improved method consists of a single slug that fills the entire Zone 1 and a portion of Zone 2 of the microfluidic chip, with edge detection taking place in Zone 2, as seen in
An additional concern with the microfluidic systems can be the long start-up/set-up time to receiving the first result. The time required to calibrate the heaters can be 45 min and which is followed by the slug training process which is an additional 30 min.
The present invention of calibration in slugs combines heater calibration with slug training (during which a series of slugs are introduced into the microfluidic chip prior to addition of a slug containing a DNA sample (‘sample slug’) so that the sample slug can undergo edge detection with the associated tracking and movement control from its initial entry onto the chip) to decrease the total start-up time. The single slug method allows calibration to finish in less than 10 min and no slug training is required. Instead, following calibration, the first test slug is pulled in to the microfluidic chip for PCR and then DNA melting directly following the calibration slug. This is possible because the single slug method places a single slug throughout the entire zone 1 and part of zone 2. The tracking and management of multiple slugs throughout Zone 1 and Zone 2 are unnecessary when using the single slug method. However, the time between results for the single slug configuration is increased due to only one slug being thermocycled at a time as opposed to the multi-slug configuration where multiple sample slugs (separated by spacer slugs) are present in the chip and undergo thermocycling simultaneously.
That is, it is an aspect of the present invention that calibration occurs as described herein, wherein a slug containing one or more calibrants flows within a channel 102 through the PCR zone 104, and partially into the thermal melt zone 106, where edge detection in the thermal melt zone 106 will hold the slug in place within the PCR zone 104 while calibration is being performed. Alternatively, calibration occurs as described herein, wherein a slug containing one or more calibrants flows within a channel 102 through the PCR zone 104, and fully into the thermal melt zone 106 (while a portion of the calibrant remains in the PCR zone 104), where edge detection in the PCR zone 104 will hold the slug in place within the thermal melt zone 106 while calibration is being performed. Alternatively, it is a further aspect of the present invention that the calibrant may fill both the PCR zone 104 and the thermal melt zone 106 while calibration is performed in either the PCR zone 104 and/or the thermal melt zone 106.
As described above, flow of the one or more calibrants into the microfluidic chip 100 can be controlled by a flow controller 208. In one embodiment, the flow controller may comprise one or more pressure monitoring devices (e.g., MEMS pressure sensors) and one or more pumping elements (e.g., peristaltic pumps). A control system 250 may comprise, for example, a flow controller 208, a PCR zone temperature controller 210, a PCR flow monitor 218, a thermal melt zone temperature controller 224, and a zone fluorescence measurement system 232.
The compound calibrators useful in the present invention may be any compound or mixture of compounds that undergo a physical change when subject to a change in temperature. In one embodiment, the compound calibrator may be a nucleic acid that undergoes denaturation (i.e., a “melt”), when subject to a thermal variation. The compound calibrator may be a single nucleic acid having two melting features (e.g., a nucleic acid containing the MTHFR 667 gene, as shown in FIGS. 19-22 of U.S. patent application Ser. No. 12/759,415, which is herein incorporated by reference in its entirety.) Other compounds, such as proteins, protein complexes, or other compounds and complexes that undergo a thermal transition when heated may also be used as compound calibrators. As described above, in some embodiments, the compound calibrator may contain a mixture of two or more amplicons of a nucleic acid. The amplicons in this embodiment may be from any organism's genome including the human genome. In a further embodiment, the amplicons in the compound calibrator could also be from so called “Ultra Conserved” regions of the human genome (so called Ultra Conserved Elements, see, e.g., U.S. patent application Ser. No. 13/223,258 filed Aug. 31, 2011, which is incorporated herein in its entirety).
Further, in another embodiment, one or more amplicons may be entirely synthetic and not found in any organism's genome. In some embodiments, synthetic amplicons may be preferable because the melt characteristics can be finely engineered by varying the number of GC and AT bonds in the amplicon (or amplicons) to alter the melt temperature thereof. Further, the number of base pairs can be designed to alter melt temperature and melt characteristics. Further deletions and other alterations can be used to alter the melt characteristics.
In some embodiments, the compound calibrator may be based on a snap-back or other assay with a probe region separate from the amplicon region. An exemplary embodiment of such compound calibrators is illustrated in
In certain embodiments, the compound calibrator will result in a thermal response profile with many easily distinguishable features. Furthermore, the thermal response profile of the compound calibrator will preferably be very repeatable. The compound calibrator preferably exhibits a strong feature signal in comparison to the background and noise level inherent in the measuring instrument. In the instance where thermal melt data is used for the thermal response profile, for example, the melt transition of individual components is preferably much larger than the decay in fluorescence due to temperature in the absence of melting, which allows software to detect the melt transition from the background noise. Also, the melt transition of individual components is preferably large compared to the random variation in fluorescence due to detector limits, which allows software to distinguish a true feature from noise.
The relative relationship between adjacent features can also impact the accuracy of calibration. In some embodiments, if one feature is too small, it may be difficult to distinguish next to the larger feature. Specifically, the smaller feature will appear like it is part of the background. In certain embodiments, the concentrations of the constituents in a compound calibrator containing a mixture of compounds may be adjusted to make the features easier to distinguish. For example, the concentrations of two amplicons may be adjusted to make feature sizes similar. In some embodiments, the molarities of the constituents may be a fixed ratio. In other embodiments, the molarities may be equal, for example, between the first and second compounds in the compound calibrator.
As described above, in some embodiments, the compound calibrator can yield a thermal response profile with three or four or more features. With three features, a quadratic relationship (three calibration coefficients) can be readily determined. With four features, a cubic relationship (four calibration coefficients) can be readily determined. This same concept could be extended to higher orders as well. Further, in some embodiments, the calibration equations need not be polynomial, but could instead follow a number of different mathematical relationships, such as, for example, power law, exponential, logarithmic, and trigonometric relationships. Also as discussed above, with three or four or more features, the additional features could be used to improve the quality of the calibration without using more calibration coefficients (i.e., the system could be over-determined). For example, with 3 features yielding 3 known points, a linear calibration (2 coefficients) can be determined using a least squares fit. Other data fitting techniques could also be used as will be apparent to one skilled in the art, including, for example, both ordinary and total least squares fitting methods. Other examples include those methods that minimize the absolute maximum difference or minimize the sum of absolute differences (e.g., least absolute deviation method) or other robust regression techniques.
In some embodiments, the thermal control element can be calibrated using an ambient temperature (i.e., room temperature) in addition to one or more temperatures determined based on features of thermal response profiles.
In an embodiment, unwanted self-heating of the thermal control element may be minimized. In the embodiment where the thermal control element is a resistive heater, and the measurement value is an electrical characteristic such as resistance, current, applied potential, or other such electrical characteristic, the thermal control element is preferably read using the minimum power or current necessary to obtain an accurate reading. Further, in an embodiment, the ambient temperature calibration point may be defined to include a temperature rise due to self-heating properties of the thermal control element (e.g., Tcal=Tamb+ΔTself). In some embodiments, self-heating properties of the thermal control element can be determined analytically, with a model, or experimentally.
The measurement value of the thermal control element at the ambient temperature and the ambient temperature define an additional correspondence that, in some embodiments, can be used as a point to define a full-rank system or could be used in an over-determined system to improve the quality of the calibration. For instance, in the embodiment where the measurement value is resistance of the heating element, the measured resistance at ambient temperature (i.e., Ramb of the heater 112) and the ambient temperature, (i.e., Tamb) may define the additional correspondence (Ramb, Tamb) that can be used along with two other measured correspondences (e.g., (RTm1,Tm1) and (RTm2,Tm2)).
The ambient temperature calibration may be particularly useful in low temperature applications since it may be difficult to create features in a thermal response profile at low temperatures.
Aspects of the present invention can be utilized, for example, in a stopped or continuous flow system or a “stop-and-go” system that alternates between movement and pauses of samples through a microfluidic device.
Aspects of the present invention can be used to calibrate resistive sensors, thermistors, diode temperature sensors, thermocouples, or any other suitable temperature measuring devices. The present invention can further be used to calibrate resistive sensors that are also used for heating such as thin-film platinum elements (or nickel or copper or any other material as would be understood by those skilled in the art).
Embodiments of the present invention can be used in a variety of instruments, but are particularly useful in PCR and thermal melt systems that perform in vitro diagnostics. Embodiments of the present invention can be used to calibrate sensors and heaters that are intended for thermal melt of samples (diagnostics) as well as other heaters and sensors within the instrument that perform entirely different functions (e.g., sample prep or PCR). Other applications are appropriate, such as, for example, machines or systems used for nucleic acid manufacturing or sample preparation, or any application where temperature calibration of a device is desired and/or appropriate.
In one preferred embodiment, the instrument may create sample plugs wherein the plugs contain samples for assays preceded or proceeded by compound calibration plugs. A compound calibration plug may, in one embodiment, be a plug that includes a compound calibrator. The calibration plugs can be loaded and used as needed on whatever frequency the system designers require to maintain the desired accuracy. In another embodiment, the compound calibrator can be introduced to an instrument in a continuous fluid flow prior to the introduction of a sample. In one embodiment, the compound calibrator can be introduced to an instrument and held in place for the duration of the entire calibration.
Before the next step (step 1006), and index variable (i) is set to an initial value. As described below and illustrated in
At step 1006, a droplet, plug, slug, segment, or continuous flow of the compound calibrator (e.g., a mixture of two or more amplicons) may be loaded into a first thermal zone. This first thermal zone may be a first thermal zone of a microfluidic chip (e.g., the system 200 may load the compound calibrator into an inlet port 103 and move the compound calibrator to the PCR zone 104 of the microchannel 102). However, the first thermal zone may also be a thermal zone in other applications, such as, for example, a device for sample preparation, DNA extraction, or to “hot start” a polymerase (e.g., Taq). As illustrated in
At step 1008, a thermal melt analysis is performed to determine the calibration coefficients (e.g., k0 and k1) for the thermal control element associated with the thermal zone (e.g., the heater 112a). In some embodiments, the step 1008 may include one or more of the steps described above with reference to the process 300. As long as the adjacent thermal zones are thermally isolated, an assay sample present in the next adjacent thermal zone may undergo independent processing or analysis in parallel with the calibration of the thermal control element in the first thermal zone.
After step 1008, a determination may be made as to whether there are additional thermal control elements to calibrate by checking the index counter against the known number of thermal control elements N in step 1010. If there are additional elements to calibrate, the index counter may be incremented in step 1012 (e.g., i=i+1) and the process 1000 returns to step 1006. The droplet, plug, slug, segment or continuous flow of the compound calibrator may be moved to a next thermal zone of the device (e.g., the system 200 moves the compound calibrator to the thermal melt zone 106). As illustrated in
The process 1000 then repeats the step 1008 using the thermal control element associated with the second thermal zone (e.g., using heater 112b). In an alternate embodiment, an assay sample in the first thermal zone may undergo independent processing or analysis in parallel with the calibration of the thermal control element in a second thermal zone. In some embodiments, the second thermal zone may be thermally isolated from the first zone.
In some embodiments, the microfluidic chip may have more than two thermal zones. As illustrated in
In some embodiments where the thermal control elements are thermally isolated, the calibration of thermal control elements along a microfluidic channel (e.g., heaters 112a and 112b along a single microfluidic channel 102) can be performed in parallel. In some embodiments, this can include filling the entire channel with the compound calibrator. As illustrated in
This example compared channel to channel temperature accuracy by calculating Tms of check (control) melts during the heater calibration process to determine if temperature accuracy was improved within a slug format, including as to single slugs. The time to first result of the current process was also compared with calibration in slugs methods.
Methods and Results
It was noticed that for the first Zone 1 calibration the blanking solution fluorescence intensity would decrease well below the software threshold of 50 counts and would cause the slugs to move to varying degrees due to the software's inability to track the edge of the blanking solution. This occurred because the initial heater k value estimate often provided temperatures >10° C. hotter than the actual target temperature which caused increased fluorescence decay of the blanking solution dye due to its temperature dependence for intensity. This slug tracking failure caused artifacts in the melting curves, as seen in
A high channel failure rate during calibration was seen for calibration in slugs experiments. Eleven channels failed across six cartridges. It is unknown what caused all channel failures at this time. A subset of these failures was caused by the inability to detect the edge of the blanking solution during first Zone 1 heater calibration while the other failures are probably related to FTU/cartridge variability.
The FTU Software version was changed to evaluate the single slug calibration process. All investigation for this method was performed on the FTU designated Larry. This system had a few advantages over the other calibration in slugs system. One advantage was that fluid filling steps within the cartridge can be redone if something does not fill correctly. This allowed for a much lower channel failure rate for the calibration process. Another advantage was that the edge detection took place in Zone 2 during Zone 1 heater calibration and so losing track of the edge did not occur due to temperature dependent fluorescence decay. Lastly, only Zone 1 heater calibration was required which reduced calibration time.
The Tm standard deviation for the current calibration method where the chip is entirely filled with calibration fluid, calibration in slugs, and single slug calibration were calculated by using the Tm of the check melt for both RF100 and RF200 melting transitions provided in the FTU batch report. The RF100 and RF200 standard deviations were calculated separately and then averaged together for each cartridge for both Zone 1 and Zone 2 (if applicable). The average of Zone 1 and Zone 2 standard deviations were then averaged to provide a Tm standard deviation for each cartridge. The Tm standard deviation presented in Table 1 is the average standard deviation for all cartridges analyzed within each configuration. It was seen that calibration in slugs methods did provide a lower Tm standard deviation from the current calibration process with the small test sample size analyzed.
The time to first result was reported in Table 2 for each heater calibration method. These times reported cartridge tests where no channel failures occurred, which can cause delays in the process. It was also important to note that for the calibration in slugs method heater calibration was performed twice for each heater zone while the other two methods report times when only single heater calibration was performed for each zone. Therefore it was conceivable that calibration in slugs' time could be reduced ˜10 min by performing single calibration for each heater zone. Additionally, the single slug system performed 20 s cycle PCR whereas the other two methods performed 10 s cycle PCR. If 10 s cycle PCR was to be performed then the single slug system time to first result would be approximately 28 min. The time between answers was longer for the single slug system than the other two methods due to the fact that only one test slug was thermocycled at a time.
Therefore, it appeared that the temperature standard deviation across all channel heaters within a cartridge was decreased when calibrating heaters within a slug format. It was presumed that this improved performance was due to the fact that fluid was not able to travel freely, which could cause temperature measurement inaccuracies.
It was seen that time to first result was reduced when using the calibration in slugs format by up to 40 min.
Using a compound calibrator consisting of amplicons from the sickle cell gene and ultra-conserved element 415 on chromosome 17, a set of calibration data was generated in accordance with the above-described systems and processes.
Embodiments of the present invention have been fully described above with reference to the drawing figures. Although the invention has been described based upon these preferred embodiments, it would be apparent to those of skill in the art that certain modifications, variations, and alternative constructions could be made to the described embodiments within the spirit and scope of the invention. The inventors expect skilled artisans to employ such variations as appropriate, and the inventors intend for the invention to be practiced otherwise than as specifically described herein. Accordingly, this invention includes all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the invention unless otherwise indicated herein or otherwise clearly contradicted by context.
The present application claims the benefit of priority to U.S. provisional patent application Ser. No. 61/613,242, filed on Mar. 20, 2012, and to U.S. patent application Ser. No. 13/838,411 filed Mar. 15, 2013, the entire disclosures of which is incorporated herein by reference.
| Number | Date | Country | |
|---|---|---|---|
| 61613242 | Mar 2012 | US |
