Method for Diagnosing Prognosing Inflammatory Bowel Disease and Crohn's Disease

Information

  • Patent Application
  • 20100254971
  • Publication Number
    20100254971
  • Date Filed
    October 26, 2009
    15 years ago
  • Date Published
    October 07, 2010
    14 years ago
Abstract
Disclosed are methods for diagnosing and prognosing Inflammatory Bowel disease or Crohn's disease (CD) by measuring levels of antibodies to glycans in a biological sample.
Description
FIELD OF THE INVENTION

The invention relates generally to a method for diagnosing and/or predicting the prognosis of digestive diseases such as Inflammatory Bowel Disease (IBD), Crohn's disease (CD) and CD subtypes, as well as CD complications by detecting levels of antibodies to glycans in a subject.


BACKGROUND OF THE INVENTION

Inflammatory bowel disease (IBD), which occurs world-wide and afflicts millions of people, is the collective term used to describe several gastrointestinal disorders of unknown etiology: Crohn's disease (CD), ulcerative colitis (UC) and Indeterminate Colitis (IC). IBD, Celiac disease and irritable bowel syndrome (IBS) will affect one-half of all Americans during their lifetimes, at a cost of several billion dollars. A primary determinant of these high medical costs is the difficulty of diagnosing digestive diseases. The cost associated with IBD and IBS is compounded by lost productivity, with persons suffering from these disorders missing an average of at least eight more days of work annually than persons not suffering from these disorders.


Symptoms associated with IBD, CD, UC, IC and IBS include, e.g., abdominal pain, chronic diarrhea, rectal bleeding, weight loss and cramping. These symptoms occur in very similar forms in IBD (i.e., CD or UC or IC), as well as in irritable bowel syndrome or other non-IBD bowel diseases. This makes a definitive diagnosis of IBD, CD or UC extremely difficult. In fact, only about one-tenth of the several million people suspected of suffering from CD are actually diagnosed with the disease.


The difficulty in differentially diagnosing IBD or CD from other digestive diseases like IBS hampers early and effective treatment of these diseases. In addition, Crohn's disease does not have a constant appearance. It varies according to locations, behaviors, severities and activities.


SUMMARY OF THE INVENTION

The invention is based in part on the discovery that patients with Inflammatory Bowel Disease, or Crohn's disease (CD) subtype, have elevated serum levels of certain IgG, IgA, and IgM isotype antibodies specific for certain glycan structures, as compared to the serum levels of these antibodies in healthy individuals, or individuals with IBS other types of gastrointestinal diseases.


Among the advantages of the invention is a highly sensitive and specific serological testing method for definitively distinguishing IBD patients from those with other digestive diseases, distinguishing patients with CD from UC, and for distinguishing CD patients with complicated disease from CD patients with less severe disease. The discrimination offered by the methods of the invention considerably shortens the time for initiating appropriate treatment and reduces significantly the amount of time and number of other procedures a patient must undergo until a diagnosis is made.


A further advantage of the invention is a panel of serological antibodies to certain sugar structures that provide these three different levels of information: first, whether or not a patient has IBD: second, if a patient does not have IBD, whether the patient has Crohn's disease; and third, for a patient that is diagnosed with Crohn's disease the severity and complications of the disease. This information can considerably shorten the period time for initiating appropriate treatment as well as reduce significantly the amount of time and number of procedures a patient will undergo until his diagnosis is accomplished. This facilitates earlier and more appropriate therapeutic intervention and minimizing uncertainty for patients and their families.


In one aspect, the invention provides a method of diagnosing IBD or Crohn's disease or predicting CD complications in a subject by providing a test sample from the subject and detecting in the test sample at least one of the following anti-glycan antibodies: an anti β-Glc antibody, an anti-Glc(β1,4)Glc(β) antibody, an anti-Glc(β1,3)Glc(β) antibody, an anti-Glc(β1,6)Glc(β) antibody, an anti-β-GlcNAc 6-sulfate antibody, an anti-Dextran antibody, an anti-Xylan antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody, an anti-β-Gal 3-sulphate antibody, an anti-GlcNAc(β1,3)GalNAc(β) antibody, an anti-GlcNAc(β1,3)Gal(β1,4)Glc(β) antibody, an anti-α-Gal antibody, an anti-Gal(β) antibody, an anti-GalNAc(α) antibody, an anti-β-GalNAc antibody, an anti-α-Glc antibody, an anti-Gal(β1,6)Gal(β) antibody, an anti-Laminarin antibody, and an anti-GlcNAc(β1,6)GalNAc(α) antibody. The presence of one or more of the antibodies in the test sample indicates the subject has Crohn's disease.


In some embodiments, levels of the anti-glycan antibody or antibodies in the test sample are compared to the levels of anti-glycan antibodies in a control sample. The control sample is chosen from a group that includes one or more individuals known to have or not to have a gastrointestinal disorder, or to have or not to have a gastrointestinal disorder other than Crohn's disease. When the control sample is from an individual or individuals that do not have Crohn's disease, or has a gastrointestinal disease other than Crohn's disease, elevated levels in the test sample relative to the control sample indicates that the subject has Crohn's disease.


In some embodiments, the control sample is from one or more individuals with a gastrointestinal disorder that is irritable bowel syndrome, ulcerative colitis or other digestive diseases. In some embodiments, the control sample is from one or more individuals that do not have a gastrointestinal disorder.


In some embodiments, the control sample is from one or more individuals with a Crohn's disease with inflammation type of disease not suffering from fistulas or structuring disease.


In some embodiments, the control sample is from one or more individuals with a Crohn's disease that not underwent surgery.


In various embodiments, at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or all of these antibodies are detected.


In some embodiments, the method further includes determining whether the test sample has an anti-Mannan antibody, which is also known as an anti-Saccharomyces cerevisiae antibody (ASCA). The presence of the anti-Mannan antibody in the sample indicates the subject has Crohn's Disease.


In some embodiments, the method further includes determining whether the test sample has an anti-neutrophil cytoplasmic antibody (ANCA). The presence of ANCA indicates the subject has IBD, may have Ulcerative Colitis, but probably does not have does not have Crohn's Disease.


The test sample can be, e.g., a biological fluid. Examples of biological fluids include, e.g., whole blood, serum, plasma, spinal cord fluid, urine, or saliva.


In some embodiments, one, two, three, four or all five of an anti-Glc(β1,3)Glc(β) antibody, an anti-Man(α1,3)Man(α) antibody, an anti Man(α1,3)[Man(α1,6)]Man(α) antibodies, anti-α-Man and/or anti-Mannan antibodies are detected.


The method can optionally include determining the isotype of the antibody. For example the method can include determining whether the antibody is an IgM, IgA, or IgG-type antibody. In some embodiments, the method is used to identify and compare one or more of an anti-Glc(β) IgG antibody, an anti-Glc(β1,3)Glc(β) IgG antibody, an anti-Glc(β1,6)Glc(β) IgG antibody, an anti-β-GalNAc antibody, an anti-α-GalNAc antibody, an anti-Glc(β1,4)Glc(β) IgG antibody, an anti-β-GlcNAc 6-sulfate IgG antibody, an anti-α-Man IgG antibody, an anti-Man(α1,3)[Man(α1-6)]Man(β) IgG antibody, an anti-Man(α1,3)Man(α) IgG antibody, an anti-Mannan IgG antibody an anti-Mannan IgA antibody, an anti-Laminarin antibody, an anti-Xylan IgG antibody, or an anti-Man(α1,2)Man(α) IgG antibody.


In some embodiments, a subject is scored as having CD if the test sample has elevated levels of one or more of an IgG anti-Glc(β1,3)Glc(β), IgG anti-Man(α1,3)Man(α), IgG anti Mannan (ASCA) antibodies, or IgA anti Mannan (ASCA) antibodies, but does not have elevated levels of ANCA.


In some embodiments, a subject is scored as having IBD if the test sample has elevated levels of IgG anti-Glc(β1,3)Glc(β), IgG anti anti-Man(α1,3)Man(α), IgG anti Mannan (ASCA) antibodies, IgA anti Mannan (ASCA) antibodies, or ANCA.


In some embodiments, the anti-glycan antibody or antibodies are detected using a fluorescent antibody, or are detected using an enzyme-linked immunoabsorbent assay (ELISA).


The test sample can be, e.g., a biological fluid. Examples of biological fluids include, e.g., whole blood, serum, plasma, spinal cord fluid, urine, or saliva.


The method can optionally include determining the isotype of the antibody. For example the method can include determining whether the antibody is an IgM, IgA, or IgG-type antibody.


In another aspect, the invention provides a method for diagnosing Crohn's disease in a subject. The method includes providing a test sample from a subject and determining whether an anti-glycan antibody is present in the test sample. At least one anti-glycan antibody is an IgG Glc(β1,3)Glc(β) antibody or an IgG anti-Man(α1,3)Man(α) antibody. The presence of at least one antibody in the test sample indicates the subject has Crohn's disease.


In some embodiments, levels of the anti-glycan antibody or antibodies in the test sample are compared to the levels of anti-glycan antibodies in a control sample. The control sample is chosen from a group that includes one or more individuals known to have or not to have a gastrointestinal disorder, or to have or not to have a gastrointestinal disorder other than Crohn's disease. When the control sample is from an individual or individuals that do not have Crohn's disease, or has a gastrointestinal disease other than Crohn's disease, elevated levels in the test sample relative to the control sample indicates that the subject has Crohn's disease.


In some embodiments, the control sample is from one or more individuals with a gastrointestinal disorder that is irritable bowel syndrome or ulcerative colitis or other digestive diseases. In some embodiments, the control sample is from one or more individuals that do not have a gastrointestinal disorder.


In a further aspect, the invention provides a method of differentially diagnosing Crohn's disease or inflammatory bowel disease in a subject. The method includes providing a test sample from a subject and determining whether the sample has an antibody that is an anti-neutrophil cytoplasmic antibody (ANCA), an IgG anti-Glc(β1,3)Glc(β) antibody, an IgG ASCA and/or IgA ASCA. The absence of ANCA and the presence of at least one of the IgG anti-Glc(β1,3)Glc(β) IgG ASCA, and IgA ASCA antibodies in the test sample indicates the subject has Crohn's disease, and the presence of at least one of the antibodies in the test sample indicates the subject has inflammatory bowel disease (IBD).


In some embodiments, the anti-glycan antibody or antibodies are detected using a fluorescent antibody, or are detected using an enzyme-linked immunoabsorbent assay (ELISA).


The test sample can be, e.g., a biological fluid. Examples of biological fluids include, e.g., whole blood, serum, plasma, spinal cord fluid, urine, or saliva.


The invention additionally provides a method of differentially diagnosing Crohn's disease colitis and ulcerative colitis in a subject. The method includes providing a test sample from a subject and determining levels of at least one an anti-glycan antibody in the sample. The anti-glycan antibody can be one or more of an IgG anti-Gal(α1,4)GlcNAc(α) antibody, an IgG anti-Gal(β1,4)GlcNAc(β) antibody, an IgG anti-α-GalNAc antibody, an IgG anti-α-Glc antibody, an IgG anti-β-Glc antibody, an IgG anti-β-GlcNAc(6-Sulphate) antibody, an IgG anti-β-GlcNAc antibody, an IgG anti-GlcNAc(β1,6)GalNAc(α) antibody, an IgA anti-Gal(α1,3)Gal(β1,4)GlcNAc(β1,3)Gal(β1,4)Glc(β) antibody, an IgA anti-Gal(α1,4)Gal(β1,4)Glc(β) antibody, an IgA anti-β-Gal antibody, an IgA anti-Gal(β1,3)[GlcNAc(β1,6)]GalNAc(α) antibody, an IgA anti-Gal(β1,3)GlcNAc(β) antibody, an IgA anti-Gal(β1,6)Gal(β) antibody, an IgA anti-GalNAc(α) antibody, an IgA anti-β-GalNAc antibody, IgA an anti-Glc(β) antibody, an IgA anti-Glc(β1,3)Glc(β) antibody, an IgA anti-β-GlcNAc antibody, an IgA anti-GlcNAc(β1,3)Gal(β1,4)Glc(β) antibody, an IgA anti-GlcNAc(β1,3)GalNAc(α) antibody, an IgA anti-GlcNAc(β1,4)GlcNAc(β) antibody, an IgA anti-GlcNAc(β1,6)GalNAc(α) antibody, and an IgA anti-β-Xyl antibody. The presence of the at least one antibody in the test sample indicates the subject has Crohn's disease colitis.


In some embodiments, the method further includes comparing the levels of the at least one anti-glycan antibody in the test sample to the levels of the at least one anti-glycan antibody in a control sample, wherein the control sample is selected from the group consisting of one or more individuals known to have or not to have Crohn's disease colitis or known to have or not to have ulcerative colitis (UC).


In some embodiments, the method includes determining whether an additional anti-glycan antibody or antibodies are present in the sample. The additional anti-glycan antibody can be one or more of an IgG anti-α-Gal antibody, an IgG anti-α-Man antibody, an IgG anti-Man(α1,3)Man(α1,6)Man(β) antibody, an IgG anti-Man(α1,3)Man(α1,6)Man(β) antibody, an IgG anti-Man(α1,3)Man(α) antibody, an IgA anti-Man(α) antibody, an IgA anti-Man(α1,2)Man(α) antibody, an IgA anti-Man(α1,3)Man(α1,6)Man(β) antibody, an IgA anti-Man(β1,3)Man(α) antibody, an IgA anti-Man(α1,6)Man(α) antibody, an IgA anti-β-Man antibody, and an IgA anti-α-Xyl antibody. The presence of the additional antibody or antibodies in the test sample indicates the subject has Crohn's disease colitis.


In some embodiments, the additional antibody or antibodies is an IgA anti-GlcNAc(β1,4)GlcNAc(β) antibody and/or and an IgG anti-Man(α1,3)Man(α) antibody.


In some embodiments, the method includes detecting at least two, three, four, five, six seven, eight, nine, ten, eleven or twelve of the antibodies.


In some embodiments, the test sample is a biological fluid (e.g., whole blood, serum, plasma, urine, or saliva).


In some embodiments, the anti-glycan antibody or antibodies are detected using a fluorescent antibody, or are detected using an enzyme-linked immunoabsorbent assay (ELISA).


The test sample can be, e.g., a biological fluid. Examples of biological fluids include, e.g., whole blood, serum, plasma, spinal cord fluid, urine, or saliva.


In a further aspect, the invention provides a method for diagnosing severe Crohn's disease in a subject. The invention includes providing a test sample from a subject with symptoms of Crohn's disease and determining whether the sample includes one or more of an anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody. The presence of the antibodies in the test sample indicates the subject has severe Crohn's disease. In various embodiments, 1, 2, 3, 4, 5, 6, or 7 of the antibodies are detected.


In some embodiments, the method further includes determining whether the sample includes one or more of an anti mannan antibody (gASCA), an anti-Man(α1,3)Man(α) antibody (AMCA), an anti-Man(α1,6)Man(α) antibody (AMBA), an anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA). In various embodiments, 1, 2, 3, 4, or 5 of the antibodies are detected.


In some embodiments, the method includes further determining whether the sample includes an anti-neutrophil cytoplasmic antibody (ANCA).


In some embodiments, the method additionally includes determining whether the subject has a CARD15 allele associated with Crohn's disease. In some embodiments, the CARD15 allele is the R702W, G908R, or 1007fs CARD15 allele.


In some embodiments, the method includes further comprising determining whether the subject with severe Crohn's disease has strictures or fistulas.


In some embodiments, the method includes treating the subject with the antibodies for symptoms associated with severe Crohn's disease. In some embodiments, the treatment is surgery.


In some embodiments, one or more of the anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, the anti-α-GalNAc antibody (AGCA), and the anti-laminarin antibody are IgG antibodies and one or both of the anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA) and the anti-β-GalNAc antibody are IgA antibodies.


In some embodiments, one or more of the gASCA) antibody, anti-Man(α1,3)Man(α) antibody (AMCA) antibody, anti-Man(α1,6)Man(α) antibody (AMBA), anti-Man(α1,2)Man(α) antibody (AMNA) and anti-α-Man antibody (AMA) are IgG antibodies.


In some embodiments, the test sample is serum.


In some embodiments, the presence of antibodies in the sample are determined using an enzyme-linked immunosorbent assay (ELISA).


In some embodiments, a subject is determined to have the indicated disease if the level of the measured antibody is above a cut-off value, which can be independently determined for each antibody. The cut-off values can be independently selected to achieve an optimized clinical parameter including, e.g., sensitivity, specificity, negative predictive value, positive predictive value and overall agreement.


Thus, in some embodiments, the subject is determined to have severe Crohn's disease if when the anti-β-GalNAc is above S, the anti-Glc(β1,6)Glc(β) antibody is above T, the ALCA level is above W, the AGCA is above X, the anti-laminarin antibody is above Y, and the ACCA level is above Z, where S, T, W, X, Y, and Z are selected to optimize sensitivity, specificity, negative predictive value, positive predictive value and overall agreement.


Similarly, in other embodiments, the subject is determined to have severe Crohn's disease, if when the gASCA level is above U, and the AMCA is above V, U and V are independently selected to achieve an optimized clinical parameter selected from the group consisting of: sensitivity, specificity, negative predictive value, positive predictive value and overall agreement. Additional variables (denoted by an arbitrary identifier such as a letter) can be assigned for assessing levels of other anti-glycan antibodies in the assays disclosed herein.


In other embodiments, the method comprises determining the aggregate amount of ALCA, anti-Glc(β1,6)Glc(β) antibody, AGCA, anti-β-GalNAc antibodies, anti-laminarin antibodies and ACCA, the subject is determined to have severe Crohn's disease if the aggregate amount of the antibodies is greater than R


In other embodiments, the method includes determining the aggregate amount of ALCA, anti-Glc(β1,6)Glc(β) antibody, AGCA, anti-β-GalNAc anti-laminarin antibodies and ACCA, the subject is determined to have severe Crohn's disease if the aggregate amount of the antibodies is greater than R.


In some embodiments, the method further comprises determining the aggregate amount of gASCA, AMCA, AMBA, AMNA and AMA antibodies, and the subject is determined to have severe Crohn's disease if the aggregate amount of the antibodies is greater than R.


In a still further aspect, the invention provides a method for assessing the prognosis of Crohn's disease complications in a subject by providing a test sample from a subject with symptoms of Crohn's disease, and determining whether the sample includes an anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, an anti-Glc(α1,6)Glc(α) antibody, and/or an anti-laminarin antibody. The presence of the antibodies in the test sample indicates a severe Crohn's disease prognosis for the subject.


In a further aspect, the invention provides a method for assessing the prognosis of Crohn's disease complications in a subject. The method includes providing a test sample from a subject with symptoms of Crohn's disease and determining whether the sample includes one or more of an anti-Glc(β1,3)Glc(β) antibody (ALCA), an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-Man(α1,3)Man(α) antibody (AMBA), and an anti-Mannan antibody. The presence of the antibodies in the test sample indicates a severe Crohn's disease prognosis for the subject.


In a further aspect, the invention features a method for differentiating inflammatory bowel disease (IBD) from a disease other than IBD in subject. The method includes providing a test sample from a subject with symptoms of IBD and determining whether the sample includes determining whether the sample includes one or more of an anti-Glc(β1,3)Glc(β) antibody (ALCA), an anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, an anti-Glc(α1,6)Glc(α) antibody and an anti-Glc(α1,6)Glc(α) antibody, and an anti-laminarin antibody. The presence of the antibodies in the test sample indicates the subject has inflammatory bowel disease.


In some embodiments, the method includes determining whether the sample includes 2, 3, 4, 5, 6, 7, or 8 of an anti-Glc(β1,3)Glc(β) antibody (ALCA), an anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, an anti-Glc(α1,6)Glc(α) antibody, and/or an anti-laminarin antibody.


In some embodiments, the method further includes further comprising determining whether the sample includes one or more of an anti mannan antibody (gASCA), an anti-Man(α1,3)Man(α) antibody (AMCA), an anti-Man(α1,6)Man(α) antibody (AMBA), anti-Man(α1,2)Man(α) antibody (AMNA), and anti-α-Man antibody (AMA). In some embodiments, the method includes detecting 2, 3, 4, or 5 of these antibodies.


In some embodiments, the method further comprises determining whether the sample includes an anti-neutrophil cytoplasmic antibody (ANCA).


In some embodiments, the method includes further comprising determining whether the subject has a CARD15 allele associated with Crohn's disease. The allele can be, e.g., a R702W, G908R, or 1007fs CARD15 allele.


In some embodiments, the method includes further determining whether the subject with inflammatory bowel disease has strictures or fistulas.


In some embodiments, the method includes further treating the subject with the antibodies for symptoms associated with severe Crohn's disease. In some embodiments, the treatment is surgery.


In some embodiments, the anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, the anti-α-GalNAc antibody (AGCA), the anti-β-GalNAc, and/or the anti-laminarin antibody is an IgG antibody, and the anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA) and/or the anti-β-GalNAc antibody is an IgA antibody.


In some embodiments, the gASCA antibody, anti-Man(α1,3)Man(α) antibody (AMCA) antibody, anti-Man(α1,6)Man(α) antibody (AMBA), anti-Man(α1,2)Man(α) antibody (AMNA) and/or or anti-α-Man antibody (AMA) is an IgG antibody.


In some embodiments, the anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, the anti-α-GalNAc antibody (AGCA), the anti-β-GalNAc antibody, and the anti-laminarin antibody are IgG antibodies and the anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA) and the anti-β-GalNAc antibodies are IgA antibodies.


In some embodiments, the test sample is serum.


In some embodiments, the presence of antibodies in the sample are determined using an enzyme-linked immunosorbent assay (ELISA).


In some embodiments, the subject is determined to have severe Crohn's disease if when the ALCA level is above W, the AGCA is above X, the anti-laminarin antibody is above Y, and the ACCA level is above Z, wherein W, X, Y, and Z are independently selected to achieve an optimized clinical parameter selected from the group consisting of: sensitivity, specificity, negative predictive value, positive predictive value and overall agreement.


In some embodiments, the subject is determined to have severe Crohn's disease, if when the gASCA level is above U, and the AMCA is above V, where U and V are independently selected to achieve an optimized clinical parameter selected from the group consisting of: sensitivity, specificity, negative predictive value, positive predictive value and overall agreement.


In some embodiments, the method comprises determining the aggregate amount of ALCA, AGCA, anti-laminarin antibodies and ACCA, the subject is determined to have severe Crohn's disease if the aggregate amount of the antibodies is greater than T.


The invention additionally provides reagents for detecting anti-glycan antibodies that reveal the presence of Crohn's Disease. The reagents include one or more carbohydrates that specifically react with an anti-β-Glc antibody, an anti-Glc(β1,4)Glc(β) antibody, an anti-Glc(β1,3)Glc(β) antibody, an anti-Glc(β1,6)Glc(β) antibody, an anti-β-GalNAc antibody, an anti-α-GalNAc antibody, an anti-GlcNAc(β) 6-sulfate antibody, an anti-Man(α1,2)Man(α) antibody, an anti-Man(α1,3)Man(α) antibody, an anti-Man(α1,6)Man(α) antibody, an anti-Man(α) antibody, an anti-Man(α1,3)[Man(α1,6)]Man(α), an anti-Mannan antibody, an anti-Dextran antibody, an anti-Xylan antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody, an anti-β-Gal 3-sulphate antibody, an anti-aGlcNAc(β1,3)GalNAc(β) antibody, an anti-GlcNAc(β1,3)Gal(β1,4)Glc(β) antibody, and/or an anti-Gal(α1,3)Gal(β1,4)GlcNAc(β) antibody. In some embodiments, the reagents are attached to a solid phase.


Also within the invention are arrays that include reagents (preferably carbohydrate reagents) that specifically detect the disease-detecting antibodies disclosed herein. For example, an array useful for detecting CD can include one or more reagents that detect an anti-β-Glc antibody, an anti-Glc(β1,4)Glc(β) antibody, an anti-Glc(β1,3)Glc(β) antibody, anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β) 6-sulfate antibody, an anti-Man(α1,2)Man(α) antibody, an anti-Man(α1,3)Man(α) antibody, an anti-Man(α1,6)Man(α) antibody, an anti-α-Man antibody, an anti-Man(α1,3)[Man(α1,6)]Man(α), an anti-Mannan antibody, an anti-Dextran antibody, an anti-Xylan antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody, an anti-Gal 3-sulphate(β) antibody, an anti-GlcNAc(β1,3)GalNAc(β) antibody, an anti-GlcNAc(β1,3)Gal(β1-4)Glc(β) antibody, Gal(α1,3)Gal(β1,4)GlcNAc(β) antibody.


In some embodiments, the reagents that are used to specifically bind and detect those anti glycans antibodies are the specific glycan structures. In other embodiments, the reagents are other molecules or macromolecules that include the specific glycan structure. The glycan or sugar structures can be only the a carbohydrate moiety (including monosaccharides an oligosaccharide or a polysaccharide) or displaying on any solid phase or other macromoleculeor any other molecular structure that includes the glycan. The glycan-containing structure can be naturally occurring, e.g., extracted from an organism, or synthetic.


For example, the anti-Glc(β1,3)Glc(β) antibody can be detected using the polysaccharide β-D(1,3) Glucan, a polymer of glucose units connected in a (β1,3) glycosidic bond. Thus, the glycan itself can be used for detecting the corresponding antibody or antibodies, as can any carbohydrate, peptide, protein, or any other molecular structure that includes the glycan.


In some embodiments, the reagents that are used to specifically bind and detect the anti glycans antibodies of the invention are peptides that mimic the carbohydrate antigens of the invention. The peptides can be used to identify specific anti glycan antibodies.


The array may additionally include a reagent or reagent, e.g., a carbohydrate reagent or reagents, that detect an anti-Mannan (ASCA) antibody or a ANCA.


In some embodiments, the glycans are attached to the array via a linker. A suitable linker includes at least one ethylene glycol derivative, at least two cyanuric chloride derivatives and an anilino group.


In some embodiments, at least two of the reagent or reagents are provided at the same location on the addressable array.


In some embodiments, the array includes a reagent, e.g., a glycan reagent that detects an anti-Glc(β1,3)Glc(β) antibody and/or an IgG anti-Man(α1,3)Man(α) antibody.


Other arrays include arrays useful for differentially diagnosing Crohn's disease or inflammatory bowel disease in a subject. The array includes one or more reagents (e.g., glycan or peptide reagents) that detect an anti-neutrophil cytoplasmic antibody (ANCA), an anti-Glc(β1,3)Glc(β) antibody, an ASCA; or an ASCA. In some embodiments, the array includes, one, two, or three of these reagents.


The invention additionally provides an array of reagents (e.g., glycan or peptide reagents) useful for differentially diagnosing Crohn's disease colitis and ulcerative colitis in a subject. The arrays include one or more reagents that detect an anti-Gal(α1,4)GlcNAc(α) antibody, an anti-Gal(β1,4)GlcNAc(β) antibody, an anti-GalNAc(α) antibody, an anti-α-Glc antibody, an anti-β-Glc antibody, an anti-β-GlcNAc(6-Sulphate) antibody, an anti-β-GlcNAc antibody, an anti-GlcNAc(β1,6)GalNAc(α) antibody, an anti-Gal(α1,3)Gal(β1,4)GlcNAc(β1,3)Gal(β1,4)Glc(β) antibody, an anti-Gal(α1,4)Gal(β1,4)Glc(β) antibody, an anti-β-Gal antibody, an anti-Gal(β1,3)[GlcNAc(β1,6)]GalNAc(α) antibody, an anti-Gal(β1,3)GlcNAc(β) antibody, an anti-Gal(β1,6)Gal(β) antibody, an anti-α-GalNAc antibody, an anti-β-GalNAc antibody, an anti-β-Glc antibody, an anti-Glc(β1,3)Glc(β) antibody, an anti-β-GlcNAc antibody, an anti-GlcNAc(β1,3)Gal(β1,4)Glc(β) antibody, an anti-GlcNAc(β1,3)GalNAc(α) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody, an anti-GlcNAc(β1,6)GalNAc(α) antibody, and an anti-Xyl(β) antibody.


In some embodiments, the array includes reagents that bind 2, 3, 4, 6, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 of these antibodies.


The array may additionally include a reagent, e.g, a glycan or peptide reagent, that detects an anti-Gal(α) antibody, an anti-Man(α) antibody, anti-Man(α1,3)Man(α1,6)Man(β) antibody, an anti-Man(α1,3)Man(α1,6)Man(β) antibody, an anti-Man(α1,3)Man(α) antibody, an anti-Man(α) antibody, an anti-Man(α1,2)Man(α) antibody, an anti-Man(α1,3)Man(α1,6)Man(β) antibody, an anti-Man(β1,3)Man(α) antibody, an an anti-Man(α1,6)Man(α) antibody, an anti-β-Man antibody, and/or an anti-α-Xyl antibody.


In some embodiments, the array includes reagents that bind 2, 3, 4, 6, 6, 7, 8, 9, 10, 11, or 12 of these antibodies.


The array may additionally include a reagent (e.g., a glycan or peptide reagent) that detects an anti-GlcNAc(β1,4)GlcNAc(β) antibody and/or an anti-Man(α1,3)Man(α) antibody.


Also provided by the invention is an array useful for differentially diagnosing inflammatory bowel disease (IBD) or non-IBD digestive disease (NIC). The array includes a reagent (e.g., a glycan or peptide reagent) that detects anti chitobioside (GlcNAc(β1,4)GlcNAc(β)) carbohydrate antibodies (ACCA) and/or anti-mannan (ASCA) antibodies. The array may optionally include a reagent that detects anti-laminarobioside (Glc(β1,3)Glc(β)) Carbohydrate Antibodies (ALCA).


The invention additionally provides kits that include reagents for detecting anti-glycan antibodies that reveal the presence of Crohn's Disease. The kits include one or more carbohydrate reagent(s) that specifically reacts with an anti-Glc(β) antibody, an anti-Glc(β1,4)Glc(β) antibody, an anti-Glc(β1,3)Glc(β) antibody, an anti-GlcNAc(β) 6-sulfate antibody, an anti-Man(α1,2)Man(α) antibody, an anti-Man(α1,3)Man(α) antibody, an anti-Man(α1,6)Man(α) antibody, an anti-α-Man antibody, an anti-Man(α1,3)[Man(α1,6)]Man(α), an anti-Mannan antibody, an anti-Dextran antibody, an anti-Xylan antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody, an anti-Gal 3-sulphate(β) antibody, an anti-aGlcNAc(β1,3)GalNAc(β) antibody, an anti-GlcNAc(β1,3)Gal(β1-4)Glc(β) antibody, and/or an anti-Gal(α1,3)Gal(β1,4)GlcNAc(β) antibody. The kits may be provided in one or more containers. In some embodiments, the kits contain directions for using the kits to perform the methods described herein. The kits may optionally include reagents for detecting antibody isotypes (e.g., IgA, IgG, and IgM antibodies).


In some embodiments, the kits include reagents that are used to specifically bind and detect those anti glycans antibodies that are the specific glycan structures. In other embodiments, the reagents in the kits are other molecules or macromolecules that include the specific glycan structure. For example, the anti-Glc(β1,3)Glc(β) antibody can be detected using the polysaccharide β-D(1,3) Glucan, a polymer of glucose units connected in a (β1,3) glycosidic bond. Thus, the glycan itself can be used for detecting the corresponding antibody or antibodies, as can any carbohydrate, peptide, protein, or any other molecular structure that includes the glycan.


In some embodiments, the kits include reagents that are used to specifically bind and detect ASCA and/or ANCA.


Also provided by the invention are kits useful for differentially diagnosing Crohn's disease or inflammatory bowel disease in a subject. The kit includes one or more reagents (e.g., glycan or peptide reagents) that detect an anti-neutrophil cytoplasmic antibody (ANCA), an anti-Glc(β1,3)Glc(β) antibody, an ASCA; or an ASCA. In some embodiments, the kit includes, one, two, or three of these reagents.


The invention additionally provides a kit of reagents (e.g., glycan or peptide reagents) useful for differentially diagnosing Crohn's disease colitis and ulcerative colitis in a subject. The kits include one or more reagents that detect an anti-Gal(α1,4)GlcNAc(α) antibody, an anti-Gal(β1,4)GlcNAc(β) antibody, an anti-α-GalNAc antibody, an anti-α-Glc antibody, an anti-β-Glc, antibody, an anti-β-GlcNAc(6-Sulphate) antibody, an anti-β-GlcNAc antibody, an anti-GlcNAc(β1,6)GalNAc(α) antibody, an anti-Gal(α1,3)Gal(β1,4)GlcNAc(β1,3)Gal(β1,4)Glc(β) antibody, an anti-Gal(α1,4)Gal(β1,4)Glc(β) antibody, an anti-β-Gal antibody, an anti-Gal(β1,3)[GlcNAc(β1,6)]GalNAc(α) antibody, an anti-Gal(β1,3)GlcNAc(β) antibody, an anti-Gal(β1,6)Gal(β) antibody, an anti-α-GalNAc antibody, an anti-β-GalNAc antibody, an anti-Glc(β) antibody, an anti-Glc(β1,3)Glc(β) antibody, an anti-GlcNAc(β) antibody, an anti-GlcNAc(β1,3)Gal(β1,4)Glc(β) antibody, an anti-GlcNAc(β1,3)GalNAc(α) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody, an anti-GlcNAc(β1,6)GalNAc(α) antibody, and an anti-β-Xyl antibody In some embodiments, the kit includes reagents that bind 2, 3, 4, 6, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 of these antibodies.


The kit may additionally include a reagent, e.g, a glycan or peptide reagent, that detects an anti-Gal(α) antibody, an anti-Man(α) antibody, anti-Man(α1,3)Man(α1,6)Man(β) antibody, an anti-Man(α1,3)Man(α1,6)Man(β) antibody, an anti-Man(α1,3)Man(α) antibody, an anti-Man(α) antibody, an anti-Man(α1,2)Man(α) antibody, an anti-Man(α1,3)Man(α1,6)Man(β) antibody, an anti-Man(β1,3)Man(α) antibody, an anti-Man(α1,6)Man(α) antibody, an anti-β-Man antibody, and/or an anti-α-Xyl antibody. In some embodiments, the kit includes reagents that bind 2, 3, 4, 6, 6, 7, 8, 9, 10, 11, or 12 of these antibodies.


The kit may additionally include a reagent (e.g., a glycan or peptide reagent) that detects an anti-GlcNAc(β1,4)GlcNAc(β) antibody and/or an anti-Man(α1,3)Man(α) antibody.


Also provided by the invention is a kit useful for differentially diagnosing inflammatory bowel disease (IBD) or non-IBD digestive disease (NIC). The kit includes a reagent (e.g., a glycan or peptide reagent) that detects anti chitobioside (GlcNAc(β1,4)GlcNAc(β)) carbohydrate antibodies (ACCA) and/or anti-mannan (ASCA) antibodies. The kit may optionally include a reagent that detects anti-laminarobioside (Glc(β1,3)Glc(β)) Carbohydrate Antibodies (ALCA).


Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by a person of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patent, and other references mentioned herein are incorporated by reference in their entirety. In the case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.


Other features and advantages of the invention will be apparent from the following detailed description and claims.





BRIEF DESCRIPTION OF THE DRAWINGS


FIG. 1 is a graph showing a Receiver Operator Characteristic (ROC) curve for differentiation between individuals with CD and individuals with other digestive diseases using IgG anti-Glc(β1,3)Glc(β) (Gb3Gb) and IgG anti-Mannan antibodies



FIG. 2A is a box plot graph of the difference between CD colitis and UC groups for the levels of some antiglycan IgG antibodies.



FIG. 2B is a box plot graph of the difference between CD colitis and UC groups for the levels of some antiglycan IgA antibodies.



FIG. 3 is ROC curves differentiating between CD patients with complicated diseases and CD patients non-complicated disease courses using a combination of gASCA and CARD15 variants, and using a combination of gASCA, ACCA, ALCA and CARD15 variants.



FIG. 4 are ROC curves comparing the prediction performance of the known predictors gASCA and CARD15 to the combination of ALCA, ACCA, gASCA and number of CARD15.



FIG. 5 are ROC curves comparing the diagnosis performance of the known predictors gASCA and CARD15 to the combination of ALCA, ACCA, gASCA and CARD15



FIG. 6 are ROC curves differentiating between CD patients (n=133) and UC (n=75) according to anti-laminarin IgG and ALCA IgG levels.



FIG. 7 shows ALCA IgG and anti-laminarin IgG antibodies in CD patients (n=133) and UC (n=75).





DETAILED DESCRIPTION OF THE INVENTION

The invention provides methods for differentially diagnosing inflammatory Bowel Disease (IBD) patients (including Crohn's disease (CD), ulcerative colitis and indeterminate colitis) and non-IBD patients (including, for example, irritable bowel syndrome (IBS), Celiac disease or any other bowel condition which is not IBD) by examining a test sample from a subject for antibodies to one or more specific glycans. The presence of the antibodies in the test sample indicates the subject has IBD, CD and not disease other than IBD (such as IBS). In some embodiments, elevated levels of glycans in a test sample from the subject as compared to the levels of the glycan or glycans in a reference sample that does not have CD indicates that the subject has CD. The methods can be used distinguish the presence of CD in a subject from other inflammatory bowel diseases (including ulcerative colitis).


Certain antibodies to glycan structures are discussed herein. A translation of LinearCode™ syntax used to describe glycan structure in IUPAC nomenclature can be found in Table 1. The glycans are presented either in the International Union of Pure and Applied Chemistry (IUPAC) condensed form for nomenclature carbohydrate representation or in LINEARCODE® syntax, for linear code syntax principles see (Banin et al., Trends in Glycoscience and Glycotechnology, 14:127-37, 2002). A translation of the LINEARCODE® representation to IUPAC representation is presented in Table 1. All the glycan structures that discussed herein, unless mentioned otherwise, are connected in the indicated anomericity α or β to another molecular structure, linker, or solid phase.


In some embodiments, the reagents that are used to specifically bind and detect those anti glycans antibodies are the specific glycan structures. In other embodiments, the reagents are other molecules or macromolecules that include the specific glycan structure. The glycan or sugar structures can be only the a carbohydrate moiety (including monosaccharides an oligosaccharide or a polysaccharide) or displaying on any solid phase or other macromoleculeor any other molecular structure that includes the glycan. The glycan-containing structure can be naturally occurring, e.g., extracted from an organism, or synthetic.


For example, the anti-Glc(β1,3)Glc(β) antibody can be detected using the polysaccharide β-D(1,3) Glucan, a polymer of glucose units connected in a (β1,3) glycosidic bond. Thus, the glycan itself can be used for detecting the corresponding antibody or antibodies, as can any carbohydrate, peptide, protein, or any other molecular structure that includes the glycan.


In some embodiments, the reagents that are used to specifically bind and detect the anti glycans antibodies of the invention are peptides that mimic the carbohydrate antigens of the invention. The peptides can be used to identify specific anti glycan antibodies.


As used herein, the term “inflammatory bowel disease” is synonymous with “IBD” and is a collective term referring to both Crohn's disease and ulcerative colitis. Thus, an individual having either Crohn's disease or ulcerative colitis is defined herein as having IBD. Conversely, an individual having neither ulcerative colitis nor Crohn's disease does not have IBD as defined herein. The term “inflammatory bowel disease” distinguishes Crohn's disease and ulcerative colitis from all other disorders, syndromes or abnormalities of the gastroenterological tract including irritable bowel syndrome.


As used herein, the term “Non inflammatory bowel disease” is synonymous with “Non-IBD” and is a collective term referring to all other disorders, syndromes or abnormalities of the gastroenterological tract including irritable bowel syndrome (IBS).


The methods for diagnosing IBD may additionally include determining whether a sample is positive for anti-neutrophil cytoplasmic antibodies (ANCA). Anti-neutrophil cytoplasmic antibodies that produce a perinuclear staining pattern (pANCA) are elevated in 60-80% of UC patients and less frequently in CD and other disorders of the colon. Serum titers of ANCA are elevated in UC patients regardless of clinical status and, thus, do not reflect disease activity. High levels of serum ANCA also persist in UC patients five years post-colectomy. Although pANCA is found only very rarely in healthy adults and children, healthy relatives of UC patients have an increased frequency of pANCA, indicating that pANCA may be an immunogenetic susceptibility marker. ANCA reactivity is also present in a small portion of patients with Crohn's disease. The reported prevalence in CD varies, with most studies reporting that 10 to 30% of CD patients express ANCA (Saxon et al., J. Allergy Clin. Immunol. 86:202-210 (1990); Cambridge et al., Gut 33:668-674 (1992); Pool et al., Gut 3446-50 (1993); and Brokroelofs et al., Dig. Dis. Sci. 39:545-549 (1994)).


As used herein, the term “anti-neutrophil cytoplasmic antibody” is synonymous with “ANCA” and means antibodies to cytoplasmic components of a neutrophil. ANCA, such as serum or saliva ANCA, can be detected using an enzyme-linked immunosorbent assay with alcohol-fixed neutrophils. As disclosed herein, ANCA activity is divided into several broad categories: perinuclear to nuclear staining or cytoplasmic staining with perinuclear highlighting (pANCA); cytoplasmic neutrophil staining without perinuclear highlighting (cANCA); and diffuse staining with speckling across the entire neutrophil (SAPPA). The term ANCA, as used herein, encompasses all varieties of anti-neutrophils cytoplasmic reactivity, including pANCA, cANCA and SAPPA. Similarly, the term “ANCA” encompasses all immunoglobulin isotypes including, for example, immunoglobulin A and G.


The determination of whether a sample is positive for ANCA using non-histological means is made using an antigen specific for ANCA using methods described in, e.g., U.S. Pat. No. 6,218,129. Such an antigen specific for ANCA can be, for example, whole fixed neutrophils; an unpurified or partially purified neutrophil extract; a purified UC pANCA antigen such as a purified protein, protein fragment or synthetically produced peptide; an anti-ANCA idiotypic antibody; or the like. Particularly useful antigens specific for ANCA are peptides, which can be chemically synthesized or expressed on the surface of phage. Purified antigens specific for ANCA can be, for example, histone H1, or an ANCA-reactive fragment of histone H1, as described in U.S. Pat. No. 6,074,835; an ulcerative colitis pANCA secretory vesicle antigen or an ANCA-reactive fragment thereof; or a microbial UC pANCA antigen, such as a histone H1-like antigen, porin antigen, Bacteroides antigen, or ANCA-reactive fragment thereof, as described in U.S. Pat. No. 6,033,864. One skilled in the art understands that additional antigens specific for ANCA, including antigenic fragments and ANCA-reactive peptides, can be identified, for example, using a representative UC pANCA monoclonal antibody.


Generating an Anti-Glycan Antibody Profile

An anti-glycan antibody profile is generated using a sample obtained from the subject to be diagnosed. The term “sample,” as used herein, means any biological specimen obtained from an individual that contains antibodies. A sample can be, for example, whole blood, plasma, saliva or other bodily fluid or tissue having antibodies, preferably a serum sample. In some embodiments, the sample is obtained surgically. In other embodiments, the sample is obtained non-surgically.


Samples can be diluted if desired before they are analyzed for anti-glycan antibodies. The subject can be, e.g., a human, a non-human primate (including a chimpanzee, ape, gorilla, old world primate), cow, horse, dog, cat, pig, goat, sheep, rodent (including, e.g., a mouse, rat, or guinea pig) Anti-glycan profiles can be determined by using methods known in the art for identifying antibodies to glycans. The methods include those disclosed in e.g., WO00/49412, or WO02/064556, or Schwarz et al., Glycobiology 13:749-54, 2003.


The methods are typically performed using reagents that specifically bind to the anti-glycan antibodies. The reagents can be, e.g., the specific glycan structures. Alternatively, the reagents can be other molecules or macromolecules that include the specific glycan structure. For example, the anti-Glc(β1,3)Glc(β) antibody can be detected using the polysaccharide β-D(1,3) Glucan, a polymer of glucose units connected in a (β1,3) glycosidic bond. Thus, the glycan itself can be used for detecting the corresponding antibody or antibodies, as can any carbohydrate, peptide, protein, or any other molecular structure that includes the glycan.


If desired, peptides that mimic carbohydrate antigens can be used in the methods and compositions described herein. The peptides can be used to identify specific anti glycan antibodies. Peptides which mimic structures recognized by antiglycan antibodies can be identified using methods known in the art, e.g., by screening a filamentous phage-displayed random peptide library (Zhan et al., Biochem Biophys Res Commun. 308:19-22, 2003; Hou et al., J Immunol. 17:4373-79, 2003).


Glycan antigens used to identify various anti-glycan antibodies can be obtained from a variety of other sources so long as the antigen is capable of binding specifically to the given anti-glycan Binding to anti-glycan antibodies can be performed using variety of other immunoassay formats known in the art, including competitive and non-competitive immunoassay formats can also be used (Self and Cook, Curr. Opin. Biotechnol. 7:60-65 (1996), which is incorporated by reference). Other assays include immunoassays, such as enzyme-linked immunosorbent assays (ELISAs). An enzyme such as horseradish peroxidase (HRP), alkaline phosphatase (AP), β-galactosidase or urease can be linked to a secondary antibody selective for a primary anti-glycan antibody of interest. A horseradish-peroxidase detection system can be used, for example, with the chromogenic substrate tetramethylbenzidine (TMB), which yields a soluble product in the presence of hydrogen peroxide that is detectable at 450 nm. An alkaline phosphatase detection system can be used with the chromogenic substrate p-nitrophenyl phosphate, for example, which yields a soluble product readily detectable at 405 nm. Similarly, a β-galactosidase detection system can be used with the chromogenic substrate o-nitrophenyl-a β-D-galactopyranoside (ONPG), which yields a soluble product detectable at 410 nm, or a urease detection system can be used with a substrate such as urea-bromocresol purple (Sigma Immunochemicals, St. Louis, Mo.). A useful secondary antibody linked to an enzyme can be obtained from a number of commercial sources; goat F(ab′)2 anti-human IgG-alkaline phosphatase, for example, can be purchased from Jackson Immuno-Research (West Grove, Pa.).


Immunoassays encompass capillary electrophoresis based immunoassays (CEIA) and can be automated, if desired. Immunoassays also can be used in conjunction with laser induced fluorescence (see, for example, Schmalzing and Nashabeh, Electrophoresis 18:2184-93 (1997)); Bao, J. Chromatogr. B. Biomed. Sci. 699:463-80 (1997), each of which is incorporated herein by reference). Liposome immunoassays, such as flow-injection liposome immunoassays and liposome immunosensors, also can be used (Rongen et al., J. Immunol. Methods 204:105-133 (1997)).


A radioimmunoassay can also be used for determining whether a sample is positive for a glycan antibody, or for determining the level of anti-glycan antibodies in a sample. A radioimmunoassay using, for example, an 125Iodine-labeled secondary antibody (Harlow and Lane, Antibodies A Laboratory Manual Cold Spring Harbor Laboratory: New York, 1988, which is incorporated herein by reference) is encompassed within the invention.


A secondary antibody may alternatively be labeled with a chemiluminescent marker. Such a chemiluminescent secondary antibody is convenient for sensitive, non-radioactive detection of anti-glycan antibodies and can be obtained commercially from various sources such as Amersham Lifesciences, Inc. (Arlington Heights, Ill.).


A detectable reagent may also be labeled with a fluorochrome. Appropriate fluorochromes include, for example, DAPI, fluorescein, Hoechst. 33258, R-phycocyanin, B-phycoerythrin, R-phycoerythrin, rhodamine, Texas red or lissamine. A particularly useful fluorochrome is fluorescein or rhodamine. Secondary antibodies linked to fluorochromes can be obtained commercially. For example, goat F(ab′)2 anti-human IgG-FITC is available from Tago Immunologicals (Burlingame, Calif.).


A signal from the detectable reagent can be analyzed, for example, using a spectrophotometer to detect color from a chromogenic substrate; a radiation counter to detect radiation, such as a gamma counter for detection of 125Iodine; or a fluorometer to detect fluorescence in the presence of light of a certain wavelength. For detection of enzyme-linked reagents, a quantitative analysis of the amount of anti-glycan antibodies can be made using a spectrophotometer such as an EMAX Microplate Reader (Molecular Devices, Menlo Park, Calif.) in accordance with the manufacturer's instructions. If desired, the assays of the invention can be automated or performed robotically, and the signal from multiple samples can be detected simultaneously.


Other methods include, e.g., flow cytometry (including bead based immunoassays), and phage display technology for expressing a recombinant antigen specific for an anti-glycan antibody. Phage particles expressing the antigen specific for a desired anti-glycan antibody can be anchored, if desired, to a multiwell plate using an antibody such as an anti phage monoclonal antibody (Felici et al., “Phage-Displayed Peptides as Tools for Characterization of Human Sera” in Abelson (Ed.), Methods in Enzymol. 267, San Diego: Academic Press, Inc. (1996), which is incorporated by reference herein).


Anti-glycan antibodies are conveniently detected by simultaneously analyzing multiple sample for the presence of one or more anti-glycan antibodies. For example, the antibodies can be detected using an array of reagents that can bind specifically to the anti glycan antibodies. Preferably, each reagent is provided in a different location with a defined address on the array. By exposing the sample to array all the anti glycan antibodies that bind to the reagent on the array can be detected in one test. Suitable arrays that include reagents (preferably carbohydrate reagents) that specifically detect the CD-detecting antibodies disclosed herein, e.g., an anti-β-Glc( ) antibody, an anti-Glc(β1,4)Glc(β) antibody, an anti-Glc(β1,3)Glc(β) antibody, an anti-GlcNAc(β) 6-sulfate antibody, an anti-Man(α1,2)Man(α) antibody, an anti-Man(α1,3)Man(α) antibody, an anti-Man(α1,6)Man(α) antibody, an anti-Man(α) antibody, an anti-Man(α1,3)[Man(α1,6)]Man(α), an anti-Manna antibody, an anti-Dextran antibody, an anti-Xylan antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody, an anti-Gal 3-sulphate(β) antibody, an anti-aGlcNAc(β1,3)GalNAc(β) antibody, an anti-GlcNAc(β1,3)Gal(β1,4)Glc(β) antibody, an anti-α-Gal antibody, an anti-β-Gal antibody, an anti-α-GalNAc, an anti-α-Glc antibody, an anti-Gal(β1,6)Gal(β) antibody, an anti anti-GlcNAc(β1,6)GalNAc(α) or an anti-Gal(α1,3)Gal(β1,4)GlcNAc(β) antibody for diagnosing CD.


In some embodiments, the reagents that are used to specifically bind and detect those anti glycans antibodies are the specific glycan structures. In other embodiments, the reagents are other molecules or macromolecules that include the specific glycan structure. For example, the anti-Glc(β1,3)Glc(β) antibody can be detected using the polysaccharide β-D(1,3) Glucan, a polymer of glucose units connected in a (β1,3) glycosidic bond. Thus, the glycan itself can be used for detecting the corresponding antibody or antibodies, as can any carbohydrate, peptide, protein, or any other molecular structure that includes the glycan.


The array may additionally include a reagent or reagent, e.g., a carbohydrate reagent or reagents, that detect an anti-Mannan antibodies or a ANCA. In some embodiments, the glycans are attached to the array via a linker. A suitable linker includes at least one ethylene glycol derivative, at least two cyanuric chloride derivatives and an anilino group.


If desired, peptides that mimic carbohydrate antigens can be used in the methods and compositions described herein. The peptides can be used to identify specific anti glycan antibodies. Peptides which mimic structures recognized by antiglycan antibodies can be identified using methods known in the art, e.g., by screening a filamentous phage-displayed random peptide library (Zhan et al., Biochem Biophys Res Commun. 308:19-22, 2003; Hou et al., J Immunol. 17:4373-79, 2003.)


Interpreting Anti-Glycan Antibody Binding Data

Typically, binding of anti-glycan antibodies to glycans in a sample is compared to a reference population, and differences in levels of the anti-glycan antibodies in the two samples are compared. The threshold for determining whether a test sample is scored positive for CD or APS, or Non-IBD based on its ant-glycan antibody profile can be altered depending on the sensitivity or specificity desired. The clinical parameters of sensitivity, specificity, negative predictive value, positive predictive value and overall agreement are calculated using true positives, false positives, false negatives and true negatives. A “true positive” sample is a sample positive for CD according to colonoscopy, radiologic and/or histologic analysis, which is also diagnosed positive according to a method of the invention. A “false positive” sample is a sample negative for CD by colonoscopic, radiologic and/or histologic analysis, which is diagnosed positive according to a method of the invention. Similarly, a “false negative” is a sample positive for CD by colonoscopic, radiologic and/or histologic analysis, which is diagnosed negative according to a method of the invention. A “true negative” is a sample negative for CD by colonoscopic, radiologic and/or histologic analysis, and also negative for CD according to a method of the invention. See, for example, Mousy (Ed.), Intuitive Biostatistics New York: Oxford University Press (1995), which is incorporated herein by reference.


As used herein, the term “sensitivity” means the probability that a laboratory method is positive in the presence of CD. Sensitivity is calculated as the number of true positive results divided by the sum of the true positives and false negatives. Sensitivity essentially is a measure of how well a method correctly identifies those with disease. In a method of the invention, the anti-glycan antibody values can be selected such that the sensitivity of diagnosing an individual is at least about 60%, and can be, for example, at least about 65%, 70%, 75%, 80%, 85%, 90% or 95%.


As used herein, the term “specificity” means the probability that a method is negative in the absence of CD. Specificity is calculated as the number of true negative results divided by the sum of the true negatives and false positives. Specificity essentially is a measure of how well a method excludes those who do not have CD. The anti-glycan cut-off value can be selected such that, when the sensitivity is at least about 70%, the specificity of diagnosing an individual is in the range of 30-60%, for example, 35-60%, 40-60%, 45-60% or 50-60%.


The term “positive predictive value,” as used herein, is synonymous with “PPV” and means the probability that an individual diagnosed as having CD actually has the disease. Positive predictive value can be calculated as the number of true positives divided by the sum of the true positives and false positives. Positive predictive value is determined by the characteristics of the diagnostic method as well as the prevalence of the disease in the population analyzed. In a method of the invention, the anti-glycan antibody cut-off values can be selected such that the positive predictive value of the method in a population having a CD disease prevalence of 15% is at least about 5%, and can be, for example, at least about 8%, 10%, 15%, 20%, 25%, 30% or 40%.


As used herein, the term “overall agreement” means the accuracy with which a method diagnoses a disease state. Overall agreement is calculated as the sum of the true positives and true negatives divided by the total number of sample results and is affected by the prevalence of CD in the population analyzed. The anti-glycan antibody cut-off values can be selected such that the overall agreement of a method of the invention in a patient population having an CD disease prevalence of 15% is at least about 45%, and can be, for example, at least about 50%, 55% or 60%.


The invention will be illustrated in the following non-limiting examples.


Example 1
Comparative Antiglycan Antibody Levels in the Serum of Crohn's Disease Patients and Patients with Other Digestive Diseases

An anti-glycan antibody profile for IgG, IgA and IgM in the serum of the patients was obtained using GlycoChip® arrays (Glycominds, Ltd., Lod, Israel, Cat No. 9100). The arrays were constructed using procedures described in Schwarz et. al. Glycobiology, 13: 749-54, 2003. Anti-glycan antibody profiles of 45 CD patients and 27 patients with other digestive diseases were compared.


All serum samples were tested using GlycoChip® plates (Glycominds Ltd., Lod, Israel, Cat No. 9100), which was an array of mono and oligosaccharides covalently attached to a reduced volume 384-well micro titer plate. The mono and oligosaccharides displayed on the array are listed in Table 1. A translation of the LinearCode™ syntax used to describe glycan structure to IUPAC nomenclature can be found in Table 1.


The sera from patients volunteers who had signed an informed consent form were collected by Dr. Iris Dotan from the Gastroenterology and Liver Disease Institute in the Tel Aviv Sorasky Medical Center, Israel. All patients were diagnosed by Dr. Iris Dotan. The sera were collected in evacuated silicon coated gel containing tubes (Estar Technologies Cat #616603GLV). The sera were separated from the blood cells and kept frozen at −25° C. until use. The volume of all solutions added to the glycan array was 10 μl/well. The sera were diluted (1:20; saturating concentration) in 0.15M Tris-HCl pH 7.2, 0.085M Mg2SO4, 0.05% Tween 20 (TBST) containing 1% BSA (Sigma), dispensed into glycan array plates using a Tecan Genesis Workstation 200 automated handling system, and incubated for 60 min at 37° C. The plates were then washed with 250 μL/well Phosphate buffered Saline with 0.05% Tween 20 (PBST, Sigma) in an automatic plate washer (Tecan, POWERWASHER™). At this point the following reagents, diluted in TBST with 1% BSA, were added using a Multidrop 384 dispenser (Thermo Labsystems) and incubated for 60 min at 37° C.: for IgG, IgA, and IgM determination—the respective sub-class specific biotinylated goat anti-human Ig antibody (Jackson, Pa., USA) at 2.8 μg/ml, 3 μg/ml, and 0.9 μg/ml, respectively. Following washing with PBST, Streptavidin-conjugated europium (0.1 μg/ml) diluted in TBST with 1% BSA was added to each well followed by incubation for 30 min at 37° C. in the dark, and washing with PBST. DELFIA™ enhancement solution was then added to the wells and the plates were incubated for 30 to 45 min in the dark at room temperature. The fluorescence of the wells was read with a Victor 1420 (Wallac, Finland) plate reader using time resolved fluorescence settings of 340/612 nm (Excitation/Emission).


Some patients were tested for the presence of antibodies to perinuclear anti neutrophil cytoplasmic antibodies (pANCA) and anti-Saccharomyces cerevisiae (ASCA) IgG and IgA using a commercial kits made by INOVA, San-Diego, Calif. Cat. No 708290, 708865, 708870 respectively, according to the manufacturer instructions.


Tables 2, 3 and 4 present levels of IgG, IgA and IgM type antiglycan antibodies that were detected at significantly different levels between the CD patient population and the patient population with other digestive diseases. The values presented for IgG and IgA are absolute values. The values presented for IgM are absolute values after reduction of background. The back ground signal was measured as the signal received from wells with covalently bound p-nithrophenol. If the result was negative the signal was scored as zero.


Comparison of the average and median values of anti-carbohydrate antibodies in the CD and other digestive disease populations reveals a significant elevation in most of the anti glycans antibodies in the CD group as compared to the group containing individuals with the other digestive diseases group. None of the CD patients was found to be positive for pANCA antibodies. All the anti glycans levels that are displayed in Tables 2, 3 and 4 show statistically significant (α=0.05; p<0.05) differences between the CD groups and the other digestive disease or normal group. Statistically significant differences between the medians of signals of CD and other digestive disease population and normal population were observed for antibodies bound to the following glycans: β-Glc, Glc(β1,4)Glc(β), Glc(β1,3)Glc(β), β-GlcNAc 6-sulfate, Man(α1,2)Man(α), Man(α1,3)Man(α), Man(α1,6)Man(α), Man(α), Man(α1,3)[Man(α1,6)]Man(α), Mannan, Dextran, Xylan, GlcNAc(β1,4)GlcNAc(β), Gal 3-sulphate(β), GlcNAc(β1,3)GalNAc(β), GlcNAc(β1,3)Gal(β1,4)Glc(β), α-Gal, β-Gal, α-GalNAc, α-Glc, Gal(β1,6)Gal(β), GlcNAc(β1,6)GalNAc(α) and Gal(α1,3)Gal(β1,4)GlcNAc(β).


Table 5 shows the specificity and sensitivity of the different IgG anti glycans for differentiation between CD and other digestive diseases using different cut-off values. The cutoff values for each glycans where set as the 89th percentile of the non CD group.


These results reveal a set of chemically defined glycan antigens that are useful for diagnosing CD. The levels of antibodies to those glycans are higher in the CD population than in the population of normal individuals or individuals with other digestive diseases. The antibodies that showed the greatest differentiation between CD and other digestive diseases in these studies are a set of antibodies to mannose based glycan fragment as well as antibodies to on β-Glc, Glc(β1,4)Glc(β), Glc(β1,3)Glc(β). Antibodies to Glc(β1,3)Glc(β), Man(α1,3)Man(α) and Man(α1,3)[Man(α1,6)]Man(α) were in particular able to differentiate between CD and other digestive disease at 57-62% sensitivity and 89%-93% specificity. The separation of those structures was better that what was achieved with Mannan (ASCA) 47% sensitivity and 89% specificity. Table 6 demonstrates that it is possible to use different cut of levels and to achieve higher sensitivity but lower specificity. Table 6 describe the sensitivity, specificity, True Positives (TP), True Negative (TN), False Positives (FP), and False Negatives (FN) and positive Predictive value (PPV) in different cut-of value for differentiation between CD and other digestive disease according to the level of anti Glc(β1,3)Glc(β), IgG and anti Mannan IgG. FIG. 1 is a Receiver Operator Characteristic (ROC) curve differentiating between individuals with CD and individuals with other digestive diseases according to levels of anti Glc(β1,3)Glc(β), IgG and anti Manna IgG antibodies.


By using combination of two or more glycans it is possible to improve the sensitivity with without reducing the specificity. For example, by setting cut-offs of 2000,000 for anti Glc(β1,3)Glc(β) and 2,400,000 for anti Mannan and setting the criteria for identification of CD as those individuals who are above cut-off levels for either of the antibodies it is possible to achieve 82% sensitivity with 70% specificity. Achieving this sensitivity by each of the antibodies alone would require lower cut off points, but these lower cutoffs would lead to poor specificity (e.g., a specificity of 37% for Glc(β1,3)Glc(β)).


Example 2
Comparative Antiglycan Antibody Levels in the Serum of Crohn's Disease (CD) Colitis Patients and Ulcerative Colitis (UC) Patients

An anti-glycan antibody profile for IgG and IgA in the serum of the patients was obtained using GlycoChip® arrays (Glycominds, Ltd., Lod, Israel, Cat No. 9100). The arrays were constructed using procedures described in Schwarz et. al., Glycobiology 13: 749-54, 2003. Anti-glycan antibody profiles of 6 CD colitis patients and 19 UC patients were compared. All serum samples were collected and tested as described in Example 1.


Tables 7 and 8 show the levels of IgG and IgA type antiglycan antibodies that were detected at significantly different levels between the CD Colitis population and the UC population. The values presented for IgG and IgA are absolute values. Comparison of the average and median values of anti-carbohydrate antibodies in the CD Colitis patients and UC patients populations reveals a significant elevation in most of the anti glycans antibodies in the CD group as compared to the group containing individuals with the other digestive diseases group. All the anti glycans levels that are displayed in Tables 7 and 8 show statistically significant (α=0.05; p<0.05) differences between the CD Colitis group and the UC group, with the exception of anti Mannan (ASCA) IgA and IgG. The most significant difference between the antibodies levels in the IgG class was found in the levels of anti Man(α1,3)Man(α), whereas for the IgA class the most significant difference was found between the levels of anti GlcNAc(β1,4)GlcNAc(β) antibodies. No statistically significant difference between the levels of anti Mannan (IgG or IgA) levels of the CD Colitis patients and UC patients populations was detected in these studies. FIG. 2 is a box plot graph of the difference between CD colitis and UC groups for the levels of some antiglycan IgG and IgA antibodies.


Example 3
A Panel of Serological Antibodies (gASCA, ACCA, ALCA and AMCA) and CARD15 Gene Variations Predict a Complicated Disease Course and Need for Surgery in Some Crohn's Disease Patients

A panel of anti glycan antibodies and CARD15 gene variants were examined to determine if they could improve predictions of a complicated disease course (penetrating, fistulizing or structuring, fibrostenosing disease course, or the need for surgery) in patients with Crohn's disease. Differentiation between patients with complicated disease outcomes and patients with non complicated disease outcomes (i.e., inflammatory type) facilitates selection of the must suitable treatment at an early stage of the disease.


Frozen samples from a total of 913 CD patients (mean age 42.3 years, 58% female) were retrospectively analyzed. Clinical characteristics for complications (strictures or fistulas) and the need for surgery were obtained. The samples were tested for gASCA, ACCA, ALCA, and AMCA by commercially available ELISA-assays (Glycominds Ltd, Israel) in a blinded manner. Briefly, mannan, and p-nitrophenyl derivatives of chitobioside, laminaribioside, and mannobioside (Man(α1,3)Man(α)) were covalently attached to the surface of a clear 96-well microtiter plate via a linker as previously described (Schwarz M et. al., Glycobiology. 2003 November; 13(11):749-54.). Serum samples were diluted 1:100 in 1% BSA/TBST, pH 7.4, dispensed into the wells (50 μL per well) incubated for 30 min at 25° C., then washed with PBST buffer. Bound antibodies were labeled (30 min at 25° C.) with 50 μL of either horseradish peroxidase (HRP)-conjugated goat anti-human IgA (1:12000) for ACCA or IgG (1:25000) type-specific antibody for AMCA, ALCA and gASCA (both antibodies from Jackson, ImmunoResearch Laboratories, West Grove, Pa., USA), washed with PBST buffer, and 50 μL 3,3′,5,5′-tetramethylbenzidine (TMB) was added for detection. The optical density (OD) at 595 nm was read after 15 min for ALCA gASCA and AMCA or 30 minutes for ACCA with a Victor 1420 plate reader (Wallac, Turku, Finland), the enzymatic reaction was stopped with 50 μL 1% sulfuric acid solution and read at 450 nm. Each plate includes a calibrator sample with a defined ELISA Unit (EU) value of 50 units. The final value of Units was calculated by dividing the OD of the test sample with the OD of the calibrator in the same plate and multiplying it by 50. All patients were genotyped for the main variants in CARD15 (R702W, G908R, 1007fs) as described in Vermiare et. al., Gastroenterology 123:106-11, 2002, and the number of CARD15 variants (0-3) were recorded for each patient.


Statistical methods and data analysis: All antibodies data were transformed to square root to obtain a distribution as close as possible to normal. Student's T-test was used to assess significance differences in anti glycan antibodies between groups, and χ2 test was used for non-parametric variables. P-values of less than 0.05 were considered to be statistically significant. ROC curves were calculated using “Analyse-it” software package version 1.17. Regression analysis was performed using SPSS.


Predicting a Fistulizing or Fibrostenosing Disease Course in CD Patients

Significantly higher levels of all anti glycan antibodies (ALCA, ACCA, AMCA, gASCA, p<0.000001 for all) were detected in CD patients with complicated disease course (penetrating, fistulizing or structuring, fibrostenosing) as opposed to CD patients with inflammatory type of disease, see Table 9. The percentage of patients CARD15 variants in the group of CD patients with complicated disease course was higher than non complicated CD group (47.4% vs 34.8%, p=0.01).


Regression analysis considering all variables reveal that ALCA and ACCA are significant predictors as compared to gASCA and CARD15, see Table 10. Although AMCA levels antibodies were significantly higher in CD patients with complicated disease course AMCA did not contribute any additional significance.


The combined levels of ALCA, ACCA, gASCA and number of CARD15 variants, each multiplied by its regression coefficients to create a combined score, were determined. FIG. 3 describes ROC curves comparing the prediction performance of the known predictors gASCA and CARD15 to the combination of ALCA, ACCA, gASCA and number of CARD15. The area under the ROC curve for all markers combination is higher then for combination of gASCA and CARD15 (0.69 vs. 0.64).


Table 11 describes the diagnostic performance of combination of gASCA and CARD15, and the combination of ALCA, ACCA, gASCA and CARD15. It was found that both ALCA and ACCA significantly add to the prediction ability compared to the known ASCA and CARD15 variants. As can be seen in FIG. 3 and Table 11, the combined score identifies 45% of the CD who will have a complicated disease course with above 80% specificity. The combined markers offer clearly superior prediction ability compared the use of gASCA and CARD15 alone.


Predicting the Need for Surgery in CD Patients

Significantly higher levels of all anti glycan antibodies (ALCA, AMCA, p<0.01 and ACCA, gASCA, p<0.00001) were detected in CD patients needing surgery as opposed to CD patients who did not need surgery, see Table 12. The percentage of patients CARD15 variants in the group of CD patients needing surgery was higher than in the non-complicated CD group (46.0% vs 30.8%, p=0.001). Regression analysis considering all variables indicates that only ACCA is a significant predictor relative to the predictive ability of gASCA and CARD15, see Table 13. Although AMCA and ALCA levels antibodies were significantly higher in CD patients needing surgery, they did not add significant predictive ability over gASCA and CARD15.


The levels of ACCA, gASCA and the number of CARD15 variants, each multiplied by its regression coefficients, were added to create a combined score. Table 14 describes the diagnostic performance of combination of gASCA and CARD15, and the combination of ACCA, gASCA and CARD15.


These results demonstrate that ACCA significantly contributes to the prediction ability over the known ASCA and CARD15 variants. As can be seen in Table 14, the combined score identifies 30% of the CD patients with a need for surgery with above 90% specificity versus only 23% that can be identified if using only gASCA and CARD15. The combined performance are clearly better then the use of gASCA and CARD15 alone.


Example 4
Improved Diagnosis of Inflammatory Bowel Disease (IBD) Using a Panel of Serological Antibodies (gASCA, ACCA, ALCA and AMCA) and CARD15 Gene Variations

A panel of anti glycan antibodies and CARD15 gene variants were examined to determine if they could improve the diagnosis of IBD patients by differentiation between patients with IBD and OGD patients as well as normal population.


A total of 1225 IBD patients (913 CD, 272 UC, 40 IC), as well as 200 healthy controls and 113 patients with non-IBD gastrointestinal inflammation (diverticular disease) were tested for gASCA, ALCA, ACCA and AMCA by commercially available ELISA-assays (Glycominds Ltd, Israel) in a blinded manner. Briefly, mannan, and p-nitrophenyl derivatives of chitobioside, laminaribioside, and mannobioside were covalently attached to the surface of a clear 96-well microtiter plate via a linker as previously described (Schwarz et al., Glycobiology 13:749-54, 2003). Serum samples were diluted 1:100 in 1% BSA/TBST, pH 7.4, dispensed into the wells (50 μL per well) incubated for 30 min at 25° C., then washed with PBST buffer. Bound antibodies were labeled (30 min at 25° C.) with 50 μL of either horseradish peroxidase (HRP)-conjugated goat anti-human IgA (1:12000) for ACCA or IgG (1:25000) type-specific antibody for AMCA, ALCA and gASCA (both antibodies from Jackson, ImmunoResearch Laboratories, West Grove, Pa., USA), washed with PBST buffer, and 50 μL 3,3′,5,5′-tetramethylbenzidine (TMB) was added for detection. The optical density (OD) at 595 nm was read after 15 min for ALCA gASCA and AMCA or 30 minutes for ACCA with a Victor 1420 plate reader (Wallac, Turku, Finland). The enzymatic reaction was stopped with 50 μL 1% sulfuric acid solution and read at 450 nm. Each plate included a calibrator sample with a defined ELISA Unit (EU) value of 50 units. The final value of Units was calculated by dividing the OD of the test sample with the OD of the calibrator in the same plate and multiplying it by 50. All patients were genotyped for the main variants in CARD15 (R702W, G908R, 1007fs) as described in Vermiare et. al., Gastroenterology 123:106-11, 2002, and the number of CARD15 variants (0-3) were recorded for each patient.


Statistical methods and data analysis: All antibodies data were transformed to square root to get distribution as close as possible to normal. Student's T-test was used to assess significance differences in anti glycan antibodies between groups, P-values of less than 0.05 were considered to be statistically significant. ROC curves were calculated using “Analyse-it” software package version 1.17. Regression analysis was performed using SPSS.


Significantly higher levels of all anti glycan antibodies (ALCA, AMCA, gASCA, p<0.0001 for all) were observed in IBD patients as opposed to CD patients with inflammatory type of disease, see Table 15. Regression analysis considering all variables have shown that ALCA and AMCA are significant predictors over gASCA and CARD15, see Table 16.


A combined score was determined based on the levels of ALCA, ACCA, AMCA gASCA and number of CARD15 variants, each multiplied by its regression coefficients. FIG. 4 describes ROC curves comparing the diagnosis performance of the known predictors gASCA and CARD15 to the combination of ALCA, ACCA, gASCA and CARD15. The area under the ROC curve for all markers combination is higher then for combination of gASCA and CARD15 (0.830 vs. 0.765).


Table 17 describes the diagnostic performance of a combination of gASCA and CARD15, and the combination of ALCA, ACCA, AMCA, gASCA and CARD15. ALCA, ACCA and AMCA were found to significantly contribute to the prediction ability over the known ASCA and CARD15 variants. As can be seen in FIG. 4 and Table 17, the combined score identified IBD in 73% of subjects with above 80% specificity. The combined performance of ALCA, ACCA, gASCA, AMCA, and CARD15 were clearly superior than the use of gASCA and CARD15 alone.


Example 5
Anti-Laminarin IgG Antibodies Differentiate Between Crohn's Disease and Ulcerative Colitis or Irritable Bowel Syndrome and React in a Pattern that is Distinct from the Pattern Observed to ALCA Antibodies

Anti-laminaribioside (Glc(β1,3)Glc(β)) carbohydrate antibody (ALCA) has been reported to be specific for CD patients, and to enable differentiation between CD and UC. Laminarin is storage polysaccharide of Laminaria and other brown algae; made up of (β1,3)-glucan with some (β1,6) linkages and branches. Here it is demonstrated that the reactivity of CD and UC patients towards anti-laminarin IgG and ALCA IgG are different. However, both can be used for differentiating between CD, and UC or IBS.


Frozen samples from CD (n=133), UC (n=75), and IBS (n=22) patients, diagnosed by standard clinical practice, were retrospectively analyzed. The samples were tested for anti-laminarin IgG antibodies using ELISA-assays. Briefly, laminarin (CAS Number 9008-22-4, Sigma L9634) and p-nitrophenyl derivative of Glc(β1,3)Glc(β) were covalently attached to the surface of a clear 96-well microtiter plate as previously described (Schwarz et al., Glycobiology 13:749-54, 2003). Serum samples were diluted 1:100 in 1% BSA/TBST, pH 7.4, dispensed into the wells (50 μL per well) incubated for 30 min at 25° C., then washed with PBST buffer. Bound antibodies were labeled (30 min at 25° C.) with 50 μL of either horseradish peroxidase (HRP)-conjugated goat anti-human IgG (1:25000) type-specific antibody (Jackson, ImmunoResearch Laboratories, West Grove, Pa., USA), washed with PBST buffer, and 50 μL 3,3′,5,5′-tetramethylbenzidine (TMB) was added for detection. The optical density (OD) at 595 nm was read after 15 min with a Victor 1420 plate reader (Wallac, Turku, Finland), the enzymatic reaction was stopped with 50 μL 1% sulfuric acid solution and read at 450 nm. T-test was used to calculate significant difference between groups.


Significantly higher levels of anti-laminarin IgG were detected in CD patients vs UC, (p<0.001), and in CD vs IBS (p=0.01) see FIG. 5. Both ALCA and anti-laminarin differentiate between UC and CD patients. Using a Receiver Operator Characteristic (ROC) curve for differentiation between CD and UC (see FIG. 6), cut off values of 1.25 OD for anti-laminarin, and 0.57 OD for ALCA were chosen. This cutoff allowed for differentiation between CD and UC patients for anti-laminarin with 50.4% sensitivity, 90.7% specificity, 90.5% Positive predictive value, and 64.9% negative predictive value, and for ALCA, with 38.3% sensitivity, 90.7% specificity, 87.9% Positive predictive value, and 45.3% negative predictive value. FIG. 7 demonstrates that there is a subgroup of CD (n=25) and UC (n=5) patients that are negative for ALCA (below cutoff) but positive (above cut off) for anti-laminarin IgG antibodies. There is in addition a subgroup of CD (n=14) and UC (n=5) patients that are positive for ALCA (above cutoff) but negative (below cut off) for anti-laminarin IgG. Although laminaribioside and laminarin have common structural element in (Glc(β1,3)Glc(β)), laminarins nevertheless have a distinct structural fragments of (Glc(β1,6)Glc(β)) and Glc(β1,6)[Glc(β1,3)]Glc(β) branches. This reflects the different reactivities of CD and UC patients towards anti-laminarin IgG and ALCA IgG. However, (Glc(β1,6)Glc(β)), (Glc(β1,3)Glc(β)), Glc(β1,6)[Glc(β1,3)]Glc(β) or laminarin can be used for differentiating CD, and UC or IBS.


The descriptions given are intended to exemplify, but not limit, the scope of the invention. Additional embodiments are within the claims.









TABLE 1







Saccharides displayed on the glycan array










Glycan No.
IUPAC
LINEARCODE ®
Common Name













0
p-Nitronhenol
pNP-0



1
α-Gal
Aa



2
β-Gal
Ab



3
Gal(β1,3)GalNAc(α)
Ab3ANa



4
Gal(β1,3)GlcNAc(β)
Ab3GNb



5
Gal(β1,4)Glc(β)
Ab4Gb
Lactose


6
Gal(β1,6)Gal(β)
Ab6Ab



7
α-GalNAc
ANa



8
β-GalNAc
ANb



9
α-Fuc
Fa



10
β-Fuc
Fb



11
α-Glc
Ga



12
Glc(α1.4)Glc(α)
Ga4Ga
Maltose


13
Glc(α1,4)Glc(β)
Ga4Gb



14
β-Glc
Gb



15
Glc(β1,4)Glc(β)
Gb4Gb
Cellobiose


16
Glc(β1,4)Glc(β1,4)Glc(β)
Gb4Gb4Gb
Cellotriose


17
α-GlcNAc( )
GNa



18
β-GlcNAc
GNb



19
GlcNAc(β1,3)GalNAc(α)
GNb3ANa



20
GlcNAc(β1,4)GlcNAc(β)
GNb4GNb
Chitobiose


21
α-Rha
Ha



22
β-GalA
Lb



23
α-Man
Ma



24
β-Man
Mb



25
α-Neu5Ac
NNa



26
α-L-Araf
Ra



27
β-GlcA
Ub



28
α-Xyl
Xa



29
β-Xyl
Xb



30
Gal(β1,3)[GlcNAc(β1,6)]GalNAc(α)
Ab3(GNb6)ANa



31
Gal(β1,4)GlcNAc(α)
Ab4GNa



32
Gal(α1,3)Gal(β1,4)GlcNAc(β)
Aa3Ab4GNb
Linear B-2


33
Gal(β1,3)Gal(β1,4)GalNAc(β)
Ab4GNb



34
Man(β1,4)GlcNAc(β)
Mb4Gb



35
GlcNAc(β1,6)GalNAc(α)
GNb6ANa



36
Fuc(α1,2)Gal(β)
Fa2Ab



37
Man(α1,3)Man(α)
Ma3Ma



38
β-GlcNAc 6-sulfate
GN[6S]b



39
Glc(β1,3)Glc(β)
Gb3Gb



40
β-Gal 3-sulfate
A[3S]b



41
Man(α1,3)[Man(α1,6)]Man(β)
Ma3(Ma6)Mb



42
GlcNAc(β1,3)Gal(α1,4)Glc(β)
GNb3Ab4Gb
Lacto-3


43
Gal(α1,4)Gal(β1,4)Glc(β)
Aa4Ab4Gb
Pk antigen


44
Man(α1,6)Man(α)
Ma6Ma



45
Man(α1,2)Man(α)
Ma2Ma



46
Dextran

Dextran


47
Mannam

Mannam


48
Xylan

Xylan
















TABLE 2





Fluorescent signals from binding of IgG antibodies to different glycans in CD


patients and non CD patients. Glycans are presented in LINEARCODE ®.

























Patient No.
Clinical condition
IgG Gb
IgG Gb3Gb
IgG Gb4Gb
IgG GN[6S]b
IgG Ma
IgG Ma3(Ma6)Mb
IgG Ma3Ma
IgG Mannan
IgG Xylan





10,001
Crohn's disease
1,360,254
1,977,964
1,338,648
1,027,193
1,410,642
1,144,296
1,583,677
7,628,072
5,577,215


10,004
Crohn's disease
3,663,580
5,704,570
5,099,956
2,099,879
2,164,970
1,466,706
3,207,783
7,476,981
4,596,345


10,005
Crohn's disease
1,526,204
1,871,425
1,454,552
1,697,361
1,335,277
921,447
991,861
5,827,429
4,982,760


10,006
Crohn's disease
774,615
281,544
488,393
297,446
261,425
153,551
267,094
1,310,353
543,373


10,007
Crohn's disease
1,183,143
1,474,083
1,010,984
1,337,825
1,522,187
957,160
1,102,706
3,891,170
2,264,442


10,008
Crohn's disease
1,047,535
3,935,252
1,173,449
656,185
610,749
487,133
508,943
7,900,531
2,858,992


10,009
Crohn's disease
1,120,092
1,061,053
913,803
773,633
434,718
653,203
735,213
3,625,333
860,059


10,011
Crohn's disease
1,555,366
3,915,250
1,263,015
1,514,790
1,319,000
600,433
695,166
6,044,060
2,016,766


10,012
Crohn's disease
738,615
997,829
828,833
710,883
815,777
512,116
449,986
1,016,305
509,887


10,013
Crohn's disease
491,219
494,196
487,233
405,409
550,041
369,100
360,682
975,473
858,010


10,015
Crohn's disease
2,507,309
3,287,329
3,150,129
1,752,931
1,210,172
1,280,894
1,706,919
8,298,001
6,144,885


10,016
Crohn's disease
1,695,721
2,983,993
2,389,536
1,363,739
1,073,805
1,019,572
933,689
8,176,923
3,474,025


10,018
Crohn's disease
2,349,612
1,749,025
1,975,697
1,316,616
1,642,423
857,701
1,424,193
2,438,472
1,837,913


10,021
Crohn's disease
936,577
2,010,561
1,238,079
736,454
647,085
580,544
668,362
4,677,824
1,836,902


10,025
Crohn's disease
1,125,348
7,400,065
1,364,422
873,065
696,782
618,026
961,392
7,750,817
610,583


10,026
Crohn's disease
584,311
2,397,273
1,007,841
570,786
396,704
366,620
600,604
4,427,669
409,875


10,027
Crohn's disease
331,704
3,884,268
1,013,711
391,803
323,622
409,228
549,358
4,184,600
1,477,393


10,028
Crohn's disease
527,070
2,540,157
776,682
842,969
471,600
371,962
644,191
1,133,383
580,308


10,031
Crohn's disease
1,160,637
1,403,953
1,163,714
903,043
1,090,200
922,033
1,360,531
6,070,889
6,267,773


10,033
Crohn's disease
1,658,517
1,171,191
795,746
1,166,575
845,487
628,923
860,940
8,668,310
1,372,493


10,034
Crohn's disease
487,703
454,402
1,030,665
343,963
377,012
317,412
402,687
4,878,747
873,284


10,036
Crohn's disease
1,669,205
2,969,747
1,661,164
1,729,819
2,023,690
1,699,947
1,824,104
7,240,661
3,315,784


10,041
Crohn's disease
2,099,634
8,111,207
1,506,594
1,366,204
2,194,579
1,943,357
1,877,528
6,166,731
1,716,244


10,042
Crohn's disease
3,414,756
6,232,427
4,724,789
3,236,890
2,752,951
2,886,293
3,805,675
4,966,270
2,207,087


10,043
Crohn's disease
2,375,664
8,432,547
5,565,720
1,826,113
2,179,476
2,694,502
4,144,108
7,766,334
1,594,568


10,047
Crohn's disease
936,002
6,541,240
736,485
1,344,797
1,007,696
870,673
1,011,207
1,929,720
510,038


10,058
Crohn's disease
1,229,222
3,933,918
1,268,315
1,097,145
1,122,154
1,202,918
1,158,350
1,060,988
3,370,770


10,060
Crohn's disease
3,776,848
7,519,448
3,738,773
3,273,535
2,478,007
3,298,731
2,075,262
6,622,444
2,830,021


10,061
Crohn's disease
377,655
7,004,834
426,579
359,296
413,067
380,756
309,119
1,440,898
277,672


10,062
Crohn's disease
2,157,588
3,580,257
2,335,797
2,291,757
2,178,945
1,790,623
1,986,588
5,928,994
4,135,199


10,064
Crohn's disease
1,201,946
2,571,544
2,116,543
1,307,836
2,149,447
3,229,183
2,010,487
7,015,353
4,157,443


10,067
Crohn's disease
1,662,361
4,367,868
1,723,425
1,379,202
1,863,573
2,466,987
2,121,119
4,103,563
1,406,894


10,068
Crohn's disease
646,782
805,864
612,996
820,938
1,066,384
2,089,715
1,626,952
856,926
620,606


10,071
Crohn's disease
1,759,894
4,847,180
1,435,670
1,215,684
1,677,667
1,557,477
2,457,616
6,460,883
3,745,128


10,073
Crohn's disease
842,124
3,215,453
1,223,370
957,636
1,823,465
2,274,968
1,845,219
7,159,301
6,675,699


10,074
Crohn's disease
1,490,333
2,253,024
627,434
697,763
1,567,676
1,854,560
1,499,634
5,758,566
998,526


10,075
Crohn's disease
5,537,343
9,220,529
4,909,831
2,091,679
3,060,118
2,760,344
4,585,798
7,712,384
6,780,460


10,077
Crohn's disease
804,027
1,800,557
827,615
1,099,475
844,037
632,785
1,010,415
1,238,077
908,558


10,078
Crohn's disease
1,129,868
3,107,666
2,487,836
1,523,754
1,578,420
1,459,959
1,509,299
7,284,452
2,493,059


10,081
Crohn's disease
1,416,365
2,436,837
1,243,841
933,009
1,418,666
692,890
1,391,276
5,617,906
4,927,776


10,089
Crohn's disease
3,140,987
2,809,714
3,881,344
1,459,563
1,732,146
612,187
1,751,178
1,948,648
1,671,266


10,090
Crohn's disease
1,142,664
6,465,008
6,126,851
1,040,285
1,733,530
947,788
1,075,332
7,029,051
1,226,773


10,094
Crohn's disease
2,581,852
3,002,260
2,533,016
1,828,766
2,171,645
1,864,642
1,426,014
3,755,208
1,359,423


10,095
Crohn's disease
4,307,357
5,194,520
2,939,889
1,440,026
1,664,132
1,246,967
1,260,260
5,473,997
1,284,127


10,102
Crohn's disease
602,214
902,531
797,794
684,982
768,939
650,448
612,321
779,631
515,705


10,051
No digestive disea
2,345,273
2,322,503
1,994,931
2,743,406
1,186,818
1,041,917
1,987,733
3,590,967
1,737,022


10,052
No digestive disea
941,167
597,884
747,644
414,298
385,995
300,723
438,891
736,782
776,440


10,053
No digestive disea
346,709
531,417
276,989
339,655
283,955
275,260
326,337
792,256
625,138


10,054
No digestive disea
692,918
664,121
993,676
680,576
539,916
425,475
213,664
1,280,390
1,600,067


10,059
Anal fissure
931,210
1,033,766
686,670
585,045
482,405
434,125
288,509
2,858,138
726,949


10,066
Proctitis/Psoriasis
977,625
955,662
1,003,683
880,485
698,411
775,253
855,457
1,721,699
1,307,196


10,080
No digestive disea
1,742,919
2,061,316
1,679,459
862,024
678,925
529,711
671,004
1,963,921
1,987,675


10,082
No digestive disea
606,761
2,058,347
951,804
631,202
681,631
500,014
512,486
4,193,860
1,440,782


10,003
Ulcerative colitis
905,251
695,019
504,690
729,287
432,922
336,989
349,315
1,022,364
504,020


10,020
Ulcerative colitis
1,354,222
4,073,378
1,231,701
1,258,840
1,363,896
902,559
705,623
2,556,960
1,911,575


10,022
Ulcerative colitis
971,547
2,471,052
1,617,809
805,585
696,492
656,384
356,351
6,619,844
2,466,668


10,023
Ulcerative colitis
476,805
1,684,016
407,103
335,428
741,738
185,491
265,536
708,233
482,414


10,024
Ulcerative colitis
1,536,705
1,866,888
1,294,792
1,278,711
981,713
422,316
709,227
6,380,359
2,793,937


10,030
Ulcerative colitis
313,802
319,115
370,440
288,801
383,159
267,131
302,649
1,539,392
918,717


10,039
Ulcerative colitis
788,940
1,322,675
2,049,445
579,957
427,353
484,029
500,544
1,614,749
627,274


10,040
Ulcerative colitis
508,502
878,468
506,749
390,383
397,998
417,665
292,485
2,881,788
977,455


10,044
Ulcerative colitis
1,134,152
1,000,922
1,430,170
794,829
1,166,622
749,019
912,335
1,385,640
1,761,062


10,050
Ulcerative colitis
1,307,947
1,067,601
1,111,619
912,013
1,066,915
766,151
951,103
1,829,813
972,519


10,065
Ulcerative colitis
983,243
1,390,482
1,028,795
842,732
666,535
672,182
852,588
1,333,880
1,363,312


10,069
Ulcerative colitis
598,736
708,042
978,417
672,092
969,555
339,385
366,514
1,736,635
1,231,461


10,072
Ulcerative colitis
320,461
473,172
342,039
363,893
455,588
392,522
506,615
3,309,525
471,592


10,079
Ulcerative colitis
405,166
3,763,266
904,868
513,527
425,264
370,064
356,485
1,665,869
576,365


10,084
Ulcerative colitis
703,594
1,982,878
2,259,105
545,266
592,993
431,487
430,193
1,655,824
548,041


10,086
Ulcerative colitis
686,425
808,037
713,774
466,633
402,319
379,369
356,194
2,174,9298
1,547,265


10,087
Ulcerative colitis
615,110
428,332
577,232
386,386
409,432
329,779
512,020
1,319,329
382,061


10,096
Ulcerative colitis
997,504
2,041,057
949,569
673,275
633,246
502,614
613,755
5,289,045
757,079


10,097
Ulcerative colitis
424,300
1,024,601
805,975
458,307
267,456
386,277
295,285
1,478,519
510,925



Avarage



Crohn's disease
1,625,556
3,518,257
1,898,152
1,239,749
1,345,981
1,243,023
1,426,441
4,904,849
2,390,714



No Chrohn's Disea
874,703
1,419,404
1,022,931
719,712
625,491
487,551
552,944
2,356,692
1,148,297



Median



Crohn's disease
1,229,222
2,983,993
1,268,315
1,166,575
1,335,277
947,788
1,260,260
5,473,997
1,716,244



No Chrohn's Disea
788,940
1,033,766
951,804
631,202
539,916
425,475
438,891
1,736,635
972,519



ttest CD vs Non CD
0.0016300.97
4.0972E−05
0.004132072
0.000688569
3.87726E−06
2.11271E−05
3.23203E−05
1.02024E−05
0.00132903




















Patient No.
Clinical condition
IgG Ma2Ma
IgG Aa
IgG Ab
IgG ANa
IgG Ga
IgG ASCA (IU)
pANC







10,001
Crohn's disease
849,550
1,028,505
820,014
466,637
1,258,316



10,004
Crohn's disease
3,150,105
1,853,626
1,851,915
1,134,167
2,304,370



10,005
Crohn's disease
857,537
1,060,156
1,075,287
1,097,821
1,936,815



10,006
Crohn's disease
495,362
161,595
114,468
135,241
302,565



10,007
Crohn's disease
894,460
1,206,075
1,032,927
804,835
1,442,191



10,008
Crohn's disease
918,954
1,143,656
1,918,663
330,682
2,831,482

80 neg



10,009
Crohn's disease
1,786,497
809,917
1,065,462
389,609
834,189



10,011
Crohn's disease
795,378
1,235,678
1,111,199
648,037
2,843,354



10,012
Crohn's disease
974,119
561,052
700,662
589,469
1,559,067



10,013
Crohn's disease
497,863
258,936
289,477
390,232
443,436



10,015
Crohn's disease
1,865,891
2,313,400
1,657,409
1,472,395
1,738,460



10,016
Crohn's disease
1,423,401
4,167,686
1,150,816
837,155
1,754,605



10,018
Crohn's disease
2,114,539
1,282,598
1,116,190
1,304,881
1,556,960



10,021
Crohn's disease
588,760
431,224
417,858
624,273
1,097,281



10,025
Crohn's disease
1,306,723
472,016
407,187
666,244
1,052,914

49 neg



10,026
Crohn's disease
754,569
614,529
575,940
804,015
794,465



10,027
Crohn's disease
409,405
1,011,807
325,270
225,780
860,654



10,028
Crohn's disease
388,120
400,412
374,748
565,621
933,864



10,031
Crohn's disease
1,024,636
614,602
645,633
434,719
1,029,243



10,033
Crohn's disease
999,469
487,495
699,125
710,940
1,311,185

108 neg 



10,034
Crohn's disease
317,845
130,726
240,504
254,960
353,496



10,036
Crohn's disease
1,815,367
1,312,161
847,504
1,148,197
2,764,778



10,041
Crohn's disease
1,666,462
1,002,663
944,926
614,258
1,790,996



10,042
Crohn's disease
1,975,431
2,453,713
1,169,199
1,491,661
2,608,430



10,043
Crohn's disease
6,234,204
1,533,054
850,045
857,270
4,438,841



10,047
Crohn's disease
1,276,888
609,950
611,659
498,004
1,408,015



10,058
Crohn's disease
1,097,275
739,330
352,629
525,407
1,349,540

 9 neg



10,060
Crohn's disease
2,587,250
2,051,391
1,446,321
1,320,361
3,268,250



10,061
Crohn's disease
1,125,410
264,741
171,150
196,852
711,761



10,062
Crohn's disease
1,725,643
1,300,507
939,781
1,000,803
1,809,051



10,064
Crohn's disease
1,546,371
3,778,662
696,314
536,893
1,212,355



10,067
Crohn's disease
3,016,091
1,374,889
342,454
509,186
2,469,775



10,068
Crohn's disease
1,364,668
236,510
358,229
488,415
1,037,834



10,071
Crohn's disease
1,980,052
1,109,196
1,555,029
698,647
1,691,995



10,073
Crohn's disease
2,240,331
421,833
391,254
494,614
1,551,800

72 neg



10,074
Crohn's disease
1,155,521
385,865
620,552
291,814
637,642

43 neg



10,075
Crohn's disease
4,835,416
1,560,441
1,816,357
994,508
2,812,624



10,077
Crohn's disease
726,513
1,221,596
352,019
371,924
1,047,431

15 neg



10,078
Crohn's disease
1,974,718
485,474
430,568
587,379
1,318,049

89 neg



10,081
Crohn's disease
1,038,228
799,172
688,082
440,606
759,311

39 neg



10,089
Crohn's disease
1,975,468
6,235,212
1,056,023
879,862
1,561,838

12 neg



10,090
Crohn's disease
996,138
616,609
527,011
612,911
1,024,901



10,094
Crohn's disease
1,889,334
603,455
449,558
730,609
1,321,795



10,095
Crohn's disease
1,587,782
704,930
541,730
441,276
2,730,801



10,102
Crohn's disease
999,742
425,568
257,965
402,233
1,119,216



10,051
No digestive disea
1,601,098
325,091
277,928
291,398
765,670



10,052
No digestive disea
345,938
791,714
924,915
549,282
3,092,123



10,053
No digestive disea
314,716
226,043
634,923
193,641
1,110,574



10,054
No digestive disea
484,686
194,929
147,713
136,850
665,259



10,059
Anal fissure
411,652
491,013
482,992
344,004
798,813



10,066
Proctitis/Psoriasis
878,148
532,501
611,229
555,691
889,849



10,080
No digestive disea
556,509
544,141
349,525
358,554
729,190



10,082
No digestive disea
616,439
736,553
722,306
386,966
1,006,755



10,003
Ulcerative colitis
640,303
187,886
165,987
257,702
659,133



10,020
Ulcerative colitis
641,831
1,107,251
1,067,519
758,804
1,289,501



10,022
Ulcerative colitis
689,170
612,362
645,057
377,726
1,467,537

40 neg



10,023
Ulcerative colitis
524,736
230,640
167,922
159,075
693,800



10,024
Ulcerative colitis
1,501,433
984,301
963,564
803,682
1,278,165



10,030
Ulcerative colitis
465,098
218,405
486,030
131,947
660,381



10,039
Ulcerative colitis
962,879
535,526
415,798
335,651
694,135



10,040
Ulcerative colitis
1,617,762
364,266
487,974
236,382
487,736



10,044
Ulcerative colitis
830,609
702,427
721,510
678,997
1,026,423



10,050
Ulcerative colitis
1,200,920
416,618
518,265
637,011
992,490



10,065
Ulcerative colitis
1,165,936
433,662
723,424
593,461
953,378



10,069
Ulcerative colitis
599,938
205,729
474,181
329,163
1,215,250

 8 neg



10,072
Ulcerative colitis
482,991
192,196
198,520
131,397
1,015,614



10,079
Ulcerative colitis
293,343
150,330
173,270
460,674
983,715



10,084
Ulcerative colitis
509,652
438,643
376,558
448,064
735,412



10,086
Ulcerative colitis
476,815
203,077
107,695
323,692
877,230



10,087
Ulcerative colitis
380,169
254,434
239,993
338,760
578,501

 6 neg



10,096
Ulcerative colitis
685,412
384,127
475,422
459,440
1,205,875



10,097
Ulcerative colitis
422,520
174,679
275,494
344,389
751,112




Avarage




Crohn's disease
1,542,963
1,168,009
775,738
666,031
1,570,527




No Chrohn's Disea
714,840
431,083
476,137
397,133
985,390




Median




Crohn's disease
1,276,888
814,529
688,082
589,469
1,349,540




No Chrohn's Disea
599,938
384,127
475,422
344,389
889,848




ttest CD vs Non CD
0.000372938
0.00157261
0.00367082
0.000291031
0.001831333

















TABLE 3





Fluorescent signals from binding of IgA and IgM antibodies to different glycans


in CD patients and non CD patients. Glycans are presented in LINEARCODE ®.





















Patient No.
Clinical Condition
IgA ASCA (IU)
IgA GNb3ANa
IgA GNb4GNb
IgA Ma5Ma
IgA Mannan





10,001
Crohn's disease

234,038
217,568
282,269
2,901,044


10,004
Crohn's disease

756,739
769,776
665,102
8,412,607


10,005
Crohn's disease

380,334
743,508
591,533
1,821,783


10,006
Crohn's disease

255,036
243,466
308,555
1,177,812


10,007
Crohn's disease

266,542
363,415
367,037
1,361,741


10,008
Crohn's disease
33
674,715
769,785
779,172
2,027,609


10,009
Crohn's disease

649,639
641,504
669,796
1,044,123


10,011
Crohn's disease

533,187
774,440
814,480
3,353,356


10,012
Crohn's disease

448,590
617,530
434,796
927,252


10,013
Crohn's disease

1,120,824
1,219,712
1,119,489
1,197,765


10,015
Crohn's disease

973,774
1,365,559
988,046
1,685,774


10,016
Crohn's disease

993,380
832,750
816,158
3,390,170


10,018
Crohn's disease

872,212
826,559
884,411
1,355,268


10,021
Crohn's disease

332,912
318,413
283,699
652,771


10,025
Crohn's disease
54
798,846
525,004
575,726
1,857,147


10,026
Crohn's disease

752,315
660,677
693,119
887,797


10,027
Crohn's disease

289,687
220,786
273,054
912,829


10,028
Crohn's disease

153,168
355,502
107,442
861,641


10,031
Crohn's disease

314,983
339,395
450,527
1,322,991


10,033
Crohn's disease
43
549,648
505,120
641,307
3,306,701


10,034
Crohn's disease

245,321
299,225
183,931
1,010,743


10,036
Crohn's disease

722,490
1,092,178
888,276
1,469,569


10,041
Crohn's disease

342,492
461,173
317,150
1,410,747


10,042
Crohn's disease

618,649
804,299
660,287
1,012,221


10,043
Crohn's disease

1,052,988
1,108,655
790,738
2,747,565


10,047
Crohn's disease

610,743
304,354
747,408
3,723,514


10,058
Crohn's disease
18
440,772
433,871
459,197
1,080,842


10,060
Crohn's disease

979,471
656,668
2,481,088
5,456,752


10,061
Crohn's disease

1,409,783
1,785,954
1,864,605
3,090,000


10,062
Crohn's disease

973,871
1,265,139
1,048,774
7,127,363


10,064
Crohn's disease

727,884
1,126,501
745,449
7,702,531


10,067
Crohn's disease

241,286
289,944
334,231
1,120,597


10,068
Crohn's disease

860,717
920,038
812,376
1,306,235


10,071
Crohn's disease

1,047,039
798,301
995,826
2,852,441


10,073
Crohn's disease
113
1,181,172
1,345,794
844,175
5,292,942


10,074
Crohn's disease
18
620,845
648,591
563,327
3,405,349


10,075
Crohn's disease

264,428
296,290
295,247
3,304,817


10,077
Crohn's disease
5
440,662
316,162
186,000
647,541


10,078
Crohn's disease
104
704,473
636,347
1,356,702
2,979,296


10,081
Crohn's disease
17
509,535
360,565
260,050
1,558,484


10,089
Crohn's disease
29
1,030,030
1,025,812
692,547
930,450


10,090
Crohn's disease

405,004
376,014
275,862
2,584,137


10,094
Crohn's disease

881,860
584,765
435,724
826,038


10,095
Crohn's disease

38,087
41,257
14,441
540,612


10,102
Crohn's disease

482,397
457,212
428,631
899,291


10,051
No digestive disease

774,286
1,543,419
674,603
1,290,323


10,052
No digestive disease

393,022
425,926
368,686
881,150


10,053
No digestive disease

878,508
1,064,617
748,198
1,055,576


10,054
No digestive disease

441,376
439,396
439,527
1,086,886


10,059
Anal fissure

293,422
265,604
410,485
1,062,125


10,066
Proctitis/Psoriasis

986,215
915,090
363,621
1,950,182


10,080
No digestive disease

707,800
741,718
472,696
1,882,808


10,082
No digestive disease

997,253
194,653
179,355
994,997


10,003
Ulcerative colitis

150,201
168,212
117,909
941,586


10,020
Ulcerative colitis

141,658
182,637
483,747
1,227,006


10,022
Ulcerative colitis
18
206,741
242,903
361,417
1,276,258


10,023
Ulcerative colitis

533,213
250,089
229,484
963,955


10,024
Ulcerative colitis

338,631
355,952
420,148
1,035,057


10,030
Ulcerative colitis

206,757
302,015
432,372
1,372,125


10,039
Ulcerative colitis

809,397
475,750
340,776
1,239,784


10,040
Ulcerative colitis

169,128
226,449
177,048
1,052,267


10,044
Ulcerative colitis

333,466
446,973
337,007
731,340


10,050
Ulcerative colitis

293,205
249,396
280,097
665,569


10,066
Ulcerative colitis

297,672
356,560
285,878
777,227


10,069
Ulcerative colitis
8
248,549
230,391
330,608
711,540


10,072
Ulcerative colitis

263,715
210,346
256,584
1,240,896


10,079
Ulcerative colitis

366,346
516,296
425,728
993,085


10,084
Ulcerative colitis

203,365
235,662
248,564
702,479


10,086
Ulcerative colitis

563,803
342,868
106,336
722,441


10,087
Ulcerative colitis
19
517,514
190,637
266,757
1,128,041


10,096
Ulcerative colitis

536,802
460,213
594,745
910,216


10,097
Ulcerative colitis

305,982
324,637
379,409
910,626



Avarage



Crohn's disease

626,280
661,007
654,844
2,320,850



No Crohn's Disease

442,890
421,422
360,447
1,067,616



Median



Crohn's disease

618,649
636,347
641,307
1,469,569



No Crohn's Disease

338,631
324,637
361,417
1,035,057



ttest CD vs Non CD

0.014066493
0.006955663
0.00158187
0.001111753

















Patient No.
Clinical Condition
IgA Ab
IgA Ab6Ab
IgA GNb6ANa
IgA Aa3Ab4GNb3Ab4Gb







10,001
Crohn's disease
162,963
222,014
457,637
160,609



10,004
Crohn's disease
336,469
723,124
704,572
312,718



10,005
Crohn's disease
376,168
376,729
481,419
479,168



10,006
Crohn's disease
181,747
301,883
397,316
147,591



10,007
Crohn's disease
145,443
267,124
156,536
175,515



10,008
Crohn's disease
357,896
656,873
690,791
405,779



10,009
Crohn's disease
531,803
459,344
760,867
505,990



10,011
Crohn's disease
399,677
384,850
732,815
451,006



10,012
Crohn's disease
793,281
351,295
733,115
258,768



10,013
Crohn's disease
666,523
921,613
1,574,544
755,187



10,015
Crohn's disease
671,617
644,176
1,884,674
823,921



10,016
Crohn's disease
788,283
953,482
960,341
1,035,719



10,018
Crohn's disease
905,785
944,644
1,114,615
1,120,640



10,021
Crohn's disease
253,534
238,664
367,215
291,684



10,025
Crohn's disease
365,034
421,319
614,655
422,498



10,026
Crohn's disease
341,464
350,620
1,150,207
365,731



10,027
Crohn's disease
153,556
230,660
349,796
162,963



10,028
Crohn's disease
54,145
99,647
194,085
70,783



10,031
Crohn's disease
160,146
222,400
447,640
165,475



10,033
Crohn's disease
273,900
429,171
778,721
370,672



10,034
Crohn's disease
171,098
122,238
369,875
243,404



10,036
Crohn's disease
374,533
610,588
643,454
439,899



10,041
Crohn's disease
199,838
291,742
205,720
181,180



10,042
Crohn's disease
420,518
458,300
1,391,126
529,478



10,043
Crohn's disease
605,571
542,596
569,482
628,435



10,047
Crohn's disease
392,383
327,753
458,138
446,556



10,058
Crohn's disease
319,531
471,263
326,815
334,876



10,060
Crohn's disease
644,454
689,063
709,019
664,299



10,061
Crohn's disease
1,206,122
1,066,288
1,343,921
1,252,570



10,062
Crohn's disease
1,022,422
795,474
886,127
648,731



10,064
Crohn's disease
276,204
387,207
429,791
361,165



10,067
Crohn's disease
212,729
275,459
299,711
163,918



10,068
Crohn's disease
323,221
314,013
563,963
485,132



10,071
Crohn's disease
641,204
545,489
738,740
519,438



10,073
Crohn's disease
947,978
502,913
549,025
1,734,370



10,074
Crohn's disease
457,612
527,719
487,532
484,359



10,075
Crohn's disease
194,980
259,283
247,300
225,781



10,077
Crohn's disease
157,701
285,013
251,925
125,116



10,078
Crohn's disease
303,071
458,245
551,350
354,403



10,081
Crohn's disease
186,390
227,023
326,164
197,405



10,089
Crohn's disease
347,786
456,655
544,660
386,430



10,090
Crohn's disease
412,253
337,503
306,485
305,576



10,094
Crohn's disease
256,814
320,654
593,541
406,523



10,095
Crohn's disease
45,568
76,182
27,736
37,539



10,102
Crohn's disease
206,488
236,594
325,721
249,229



10,051
No digestive disease
288,495
266,679
968,229
284,006



10,052
No digestive disease
135,704
180,348
303,864
112,295



10,053
No digestive disease
372,457
545,551
640,635
295,387



10,054
No digestive disease
246,375
279,630
318,118
198,859



10,059
Anal fissure
218,307
224,109
317,736
179,601



10,066
Proctitis/Psoriasis
495,388
657,131
736,683
485,492



10,080
No digestive disease
308,624
445,061
649,226
299,570



10,082
No digestive disease
96,297
150,924
193,102
88,789



10,003
Ulcerative colitis
76,240
126,755
143,652
78,004



10,020
Ulcerative colitis
319,940
583,244
178,132
321,496



10,022
Ulcerative colitis
188,916
399,670
208,178
182,508



10,023
Ulcerative colitis
118,896
136,478
201,303
131,550



10,024
Ulcerative colitis
139,853
233,051
359,658
170,812



10,030
Ulcerative colitis
127,271
136,718
323,945
126,499



10,039
Ulcerative colitis
183,846
235,006
449,717
181,355



10,040
Ulcerative colitis
113,511
176,403
249,464
117,935



10,044
Ulcerative colitis
194,884
169,474
449,998
213,189



10,050
Ulcerative colitis
239,071
305,609
324,797
312,988



10,066
Ulcerative colitis
255,302
270,165
568,720
250,785



10,069
Ulcerative colitis
204,935
197,255
419,431
198,088



10,072
Ulcerative colitis
286,381
174,449
263,180
169,568



10,079
Ulcerative colitis
569,214
361,508
887,360
422,569



10,084
Ulcerative colitis
442,837
206,449
182,069
254,076



10,086
Ulcerative colitis
137,226
98,580
117,532
134,968



10,087
Ulcerative colitis
194,669
142,531
298,763
196,730



10,096
Ulcerative colitis
398,374
513,371
588,895
405,529



10,097
Ulcerative colitis
245,148
235,651
467,802
285,631




Avarage




Crohn's disease
405,469
439,668
622,644
444,187




No Crohn's Disease
244,372
276,066
400,377
225,862




Median




Crohn's disease
341,464
384,850
549,025
370,672




No Crohn's Disease
218,307
233,051
323,945
198,088




ttest CD vs Non CD
0.004639777
0.001853597
0.007398896
0.001413793

















TABLE 4





Fluorescent signals from binding of IgM antibodies to different glycans in CD patients


and non CD patients. Glycans are presented in LINEARCODE ®.





















Patient








No.
Clinical condition
IgM A[3S]b
IgM Aa
IgM Aa3Ab4GNb
IgM Aa4Ab4Gb
IgM Ab3(GNb6)ANa





10,001
Crohn's disease
0
0
0
0
0


10,004
Crohn's disease
0
0
0
0
0


10,005
Crohn's disease
0
0
0
0
161,405


10,006
Crohn's disease
0
68,568
0
402,561
166,017


10,007
Crohn's disease
0
0
0
0
0


10,008
Crohn's disease
0
0
0
0
0


10,009
Crohn's disease
0
0
0
0
0


10,011
Crohn's disease
0
0
0
0
0


10,012
Crohn's disease
0
0
0
0
0


10,013
Crohn's disease
1,274,136
1,194,896
1,392,444
0
0


10,015
Crohn's disease
367,307
390,644
325,647
0
0


10,016
Crohn's disease
260,897
0
14,251
0
0


10,018
Crohn's disease
248,996
226,314
158,547
0
0


10,021
Crohn's disease
762,735
852,490
700,041
0
327,738


10,025
Crohn's disease
466,121
319,573
565,269
0
0


10,026
Crohn's disease
0
0
0
0
0


10,027
Crohn's disease
151,367
437,186
547,822
0
0


10,028
Crohn's disease
510,204
540,836
723,234
0
81,777


10,031
Crohn's disease
165,011
242,183
199,166
0
15,958


10,033
Crohn's disease
14,440
0
1,113,845
0
0


10,034
Crohn's disease
770,101
695,338
641,641
0
121,757


10,036
Crohn's disease
163,646
642,487
2,180,044
0
0


10,041
Crohn's disease
123,889
89,104
151,581
0
0


10,042
Crohn's disease
0
1,345,482
1,158,234
0
0


10,043
Crohn's disease
0
0
0
0
0


10,047
Crohn's disease
831,510
857,115
1,076,947

465,551


10,058
Crohn's disease
128,555
220,493
428,347




10,060
Crohn's disease
363,862
1,284,367
474,206

19,714


10,061
Crohn's disease
690,511
1,095,509
1,128,863

621,675


10,062
Crohn's disease
715,200
1,485,943
2,464,680

220,921


10,064
Crohn's disease
245,487
664,556
1,633,864

635,144


10,067
Crohn's disease
222,329
141,266
75,592




10,068
Crohn's disease
0
0
0
0
0


10,071
Crohn's disease
67,858
77,830
88,393
0
272,031


10,073
Crohn's disease
0
0
147,447
30,339
184,079


10,074
Crohn's disease
0
0
0
0
0


10,075
Crohn's disease
65,267
34,147
241,365
0
65,722


10,077
Crohn's disease
0
214,916
88,848
0
321,513


10,078
Crohn's disease
0
0
0
0
0


10,081
Crohn's disease
0
0
0
0
0


10,089
Crohn's disease
0
0
0
0
0


10,090
Crohn's disease
0
0
0
0
6,781


10,094
Crohn's disease
68,165
118,072
97,315
93,394
70,477


10,095
Crohn's disease
0
0
0
0
0


10,102
Crohn's disease
0
0
0
0
0


10,051
No digestive disease
0
0
0
0
0


10,052
No digestive disease
0
0
0
0
0


10,053
No digestive disease
0
803,031
314,948
0
0


10,054
No digestive disease
0
0
33,896
86,151
118,374


10,059
Anal fissure
0
0
0
47,80
0


10,066
Proctitis/Psoriasis
255,614
613,172
366,386
711,585
672,896


10,080
No digestive disease

142,813
1,437,670
367,136
255,635


10,082
No digestive disease



361,634
266,794


10,003
Ulcerative colitis







10,020
Ulcerative colitis







10,022
Ulcerative colitis
0
0
230,936
5,354
0


10,023
Ulcerative colitis
0
0
0
538,071
0


10,024
Ulcerative colitis
0
0
0
119,591
2,544,871


10,030
Ulcerative colitis
0
0
0
0
79,886


10,039
Ulcerative colitis
0
0
0
0
26,754


10,040
Ulcerative colitis
0
0
0
0
0


10,044
Ulcerative colitis
7,575
99,214
210,443
53,421
548,458


10,050
Ulcerative colitis
0
0
0
0
0


10,065
Ulcerative colitis
646,009
651,393
679,823
669,033
381,610


10,069
Ulcerative colitis
0
0
0
0
0


10,072
Ulcerative colitis
0
0
0
0
375,381


10,079
Ulcerative colitis
0
79,891
36,805
512,305
182,972


10,084
Ulcerative colitis
0
0
0
0
0


10,086
Ulcerative colitis
16,235
221,934
0
293,278
0


10,087
Ulcerative colitis
175,021
175,678
321,514
145,748
337,665


10,096
Ulcerative colitis







10,097
Ulcerative colitis




1,022,582



Avarage



Crohn's disease
193,725
294,251
395,947
11,695
83,517



No Crohn's Disease
40,765
103,227
134,534
144,481
252,329



Median



Crohn's disease
14,440
68,568
88,848





No Crohn's Disease








ttest CD vs Non CD
0.014433781
0.036400897
0.041051138
0.000390828
0.047775166


















Patient









No.
Clinical condition
IgM Ab3ANa
IgM GNb3Ab4Gb
IgM GNb3ANa
IgM Dextran
IgM Mannan







10,001
Crohn's disease
0
608,457
657,592
230,160
2,084,216



10,004
Crohn's disease
0
542,436
730,879
360,390
722,969



10,005
Crohn's disease
0
1,375,070
2,933,445
388,048
117,931



10,006
Crohn's disease
0
1,695,894
1,963,416
3,110,617
810,502



10,007
Crohn's disease
0
1,178,646
993,402
969,884
612,220



10,008
Crohn's disease
0
735,201
1,372,932
468,089
796,727



10,009
Crohn's disease
0
322,451
680,970
59,317
0



10,011
Crohn's disease
0
205,150
1,039,057
494,848
0



10,012
Crohn's disease
0
972,528
1,688,071
1,221,314
1,490,590



10,013
Crohn's disease
0
1,174,565
2,419,276
2,049,830
2,586,785



10,015
Crohn's disease
0
1,054,492
1,546,327
2,107,182
1,416,006



10,016
Crohn's disease
0
1,328,058
3,127,245
1,667,531
70,238



10,018
Crohn's disease
0
1,430,548
1,912,812
2,166,938
1,971,045



10,021
Crohn's disease
4,353
1,469,658
2,142,999
2,094,545
1,285,376



10,025
Crohn's disease
0
2,975,994
3,777,466
2,312,303
2,435,341



10,026
Crohn's disease
0
745,061
3,384,432
3,509,606
409,591



10,027
Crohn's disease
0
1,779,829
3,426,917
1,720,479
3,144,526



10,028
Crohn's disease
46,616
1,562,488
2,857,289
2,236,531
3,049,138



10,031
Crohn's disease
0
578,140
849,394
973,540
910,393



10,033
Crohn's disease
0
879,981
1,786,910
822,422
587,545



10,034
Crohn's disease
76,717
1,117,458
1,646,989
1,616,572
1,320,077



10,036
Crohn's disease
0
2,573,605
2,518,175
2,570,459
1,552,108



10,041
Crohn's disease
0
781,745
1,733,620
929,763
1,789,860



10,042
Crohn's disease
0
2,298,533
3,652,328
4,851,471
1,342,805



10,043
Crohn's disease
0
943,254
3,801,228
349,534
628,039



10,047
Crohn's disease
147,112
1,854,934
3,495,774
3,223,236
1,936,982



10,058
Crohn's disease

897,206
1,775,488
766,028
983,376



10,060
Crohn's disease

926,098
2,910,549
1,296,914
859,571



10,061
Crohn's disease
149,877
2,612,378
3,589,958
2,379,098
4,605,631



10,062
Crohn's disease
180,832
1,464,405
2,716,333
1,256,919
1,245,680



10,064
Crohn's disease

1,893,522
3,343,233
2,212,175
2,923,034



10,067
Crohn's disease

631,443
1,765,852
1,280,499
1,011,954



10,068
Crohn's disease
0
0
829,715
0
0



10,071
Crohn's disease
0
669,203
1,023,200
302,307
2,573,082



10,073
Crohn's disease
5,781
693,896
1,80,873
1,506,812
2,148,575



10,074
Crohn's disease
0
1,549,121
2,082,886
1,385,468
531,246



10,075
Crohn's disease
0
839,403
1,814,627
1,571,440
582,384



10,077
Crohn's disease
0
576,897
1,309,189
1,059,111
369,244



10,078
Crohn's disease
0
43,955
952,620
464,210
791,441



10,081
Crohn's disease
0
28,386
907,289
0
93,410



10,089
Crohn's disease
0
0
319,608
308,448
0



10,090
Crohn's disease
0
326,922
551,737
253,387
635,071



10,094
Crohn's disease
4,567
427,222
634,599
741,918
1,331,605



10,095
Crohn's disease
0
331,811
1,357,109
7,11,417
2,803,494



10,102
Crohn's disease
0
0
78,782
0
860,022



10,051
No digestive disease
0
0
0
70,898
0



10,052
No digestive disease
0
0
0
0
0



10,053
No digestive disease
0
909,819
1,957,899
2,93,154
160,549



10,054
No digestive disease
0
1,417,516
2,034,745
1,190,821
0



10,059
Anal fissure
0
621,074
860,869
553,501
0



10,066
Proctitis/Psoriasis
648,481
1,399,015
2,112,942
2,036,326
2,861,646



10,080
No digestive disease
13,016
682,951
1,763,399
466,996
226,598



10,082
No digestive disease
58,052
1,059,304
3,803,965
460,919




10,003
Ulcerative colitis








10,020
Ulcerative colitis








10,022
Ulcerative colitis
0
530,365
1,220,301
910,810
0



10,023
Ulcerative colitis
0
345,812
630,728
401,625
109,462



10,024
Ulcerative colitis
64,642
1,271,762
2,775,365
877,756
1,161,681



10,030
Ulcerative colitis
60,684
606,210
622,605
1,558,797
0



10,039
Ulcerative colitis
32,355
732,277
910,699
542,797
51,325



10,040
Ulcerative colitis
0
798,350
1,289,960
751,879
156,868



10,044
Ulcerative colitis
59,039
402,433
873,504
961,761
697,203



10,050
Ulcerative colitis
0
445,848
728,257
737,999
134,037



10,065
Ulcerative colitis
201,783
1,203,436
1,975,174
1,363,891
1,042,471



10,069
Ulcerative colitis
0
1,127,666
1,331,796
0
313,657



10,072
Ulcerative colitis
0
825,856
1,084,765
2,081,853
566,681



10,079
Ulcerative colitis
79,189
828,413
1,477,648
992,691
696,436



10,084
Ulcerative colitis
0
650,663
1,075,158
309,983
489,824



10,086
Ulcerative colitis
0
835,147
1,931,046
1,405,512
824,630



10,087
Ulcerative colitis
220,927
592,753
1,540,709
897,343
1,016,698



10,096
Ulcerative colitis

331,000
441,228
452,374
582,057



10,097
Ulcerative colitis
33,778
854,116
2,517,741
913,480
517,995




Avarage




Crohn's disease
13,908
1,024,356
1,895,124
1,333,594
1,277,643




No Crohn's Disease
54,516
684,140
1,294,463
838,279
429,258




Median




Crohn's disease

897,206
1,765,852
1,221,314
983,376




No Crohn's Disease

662,951
1,220,301
751,679
160,549




ttest CD vs Non CD
0.059924749
0.029702213
0.17590683
0.034573847
0.000253081

















TABLE 5







Specificity and sensitivity of the different IgG anti glycans for differentiation between


CD and other digestive diseases using different cut-off values. The cutoff values for each glycans


where set as the 89 percentiles of the other digestive disease group. Glycans are presented in


LINEARCODE ®.









Anti Glycan IgG antibodies


















Cut-off level

Gb
Gb3Gb
Gb4Gb
GGN[6S]b
MMa
Ma3(Ma6)Mb
MMa3Ma
MMannan
XXylan
MMa2Ma





65 percentile of
Sensitivity for CD %
76
73
62
62
58
60
71
78
58
71


non CD



Specificity for CD %
70
63
67
70
67
78
70
67
63
67


75 percentile of
Sensitivity for CD %
62
71
58
60
71
60
64
73
62
71


non CD



Specificity for CD %
74
74
78
78
52
78
78
74
74
78


85 percentile of
Sensitivity for CD %
56
64
51
49
49
56
62
67
40
62


non CD



Specificity for CD %
81
81
81
81
85
85
81
81
81
85


90 percentile of
Sensitivity for CD %
49
62
33
42
44
56
60
47
36
40


non CD



Specificity for CD %
89
89
89
89
89
93
89
89
89
89
















TABLE 6







The sensitivity, specificity, True Positives (TP), True Negative (TN), False


Positives (FP), and False Negatives (FN), and Positive Predictive Value


(PPV) in different cut-of values for differentiation between CD and other


digestive disease according to the level of Anti-Glc (β1,3) Glc (β) IgG.














IgG Gb3Gb









(abnormals


above cut-off)
Sensitivity
Specificity
TP
TN
FP
FN
PPV


















100.0%
0.0%
45
0
27
0
62.5


0
95.6%
0.0%
43
0
27
2
61.43


6,963
95.6%
3.7%
43
1
26
2
62.32


27,235
93.3%
3.7%
42
1
26
3
61.76


27,402
91.1%
3.7%
41
1
26
4
61.19


62,662
88.9%
3.7%
40
1
26
5
60.61


78,554
88.9%
7.4%
40
2
25
5
61.54


86,949
88.9%
11.1%
40
3
24
5
62.5


87,267
86.7%
11.1%
39
3
24
6
61.9


108,535
86.7%
14.8%
39
4
23
6
62.9


133,683
86.7%
18.5%
39
5
22
6
63.93


156,547
86.7%
22.2%
39
6
21
6
65


174,695
86.7%
25.9%
39
7
20
6
66.1


241,622
84.4%
25.9%
38
7
20
7
65.52


242,565
84.4%
29.6%
38
8
19
7
66.67


312,940
84.4%
33.3%
38
9
18
7
67.86


317,476
84.4%
37.0%
38
10
17
7
69.09


344,750
82.2%
37.0%
37
10
17
8
68.52


371,507
80.0%
37.0%
36
10
17
9
67.92


371,648
80.0%
40.7%
36
11
16
9
69.23


378,722
77.8%
40.7%
35
11
16
10
68.83


379,003
77.8%
44.4%
35
12
15
10
70


430,129
77.8%
48.1%
35
13
14
10
71.43


441,239
77.8%
51.9%
35
14
13
10
72.92


454,736
75.6%
51.9%
34
14
13
11
72.34


489,733
75.6%
55.6%
34
15
12
11
73.91


525,203
73.3%
55.6%
33
15
12
12
73.33


526,443
73.3%
59.3%
33
16
11
12
75


546,432
73.3%
63.0%
33
17
10
12
76.74


612,367
73.3%
66.7%
33
18
9
12
78.57


851,962
73.3%
70.4%
33
19
8
12
80.49


979,509
71.1%
70.4%
32
19
8
13
80


1,209,892
71.1%
74.1%
32
20
7
13
82.05


1,266,954
71.1%
77.8%
32
21
6
13
84.21


1,317,083
68.9%
77.8%
31
21
6
14
83.78


1,376,957
66.7%
77.8%
30
21
6
15
83.33


1,379,223
66.7%
81.5%
30
22
5
15
85.71


1,425,185
64.4%
81.5%
29
22
5
16
85.29


1,461,919
64.4%
85.2%
29
23
4
16
87.88


1,560,904
62.2%
85.2%
28
23
4
17
87.5


1,574,353
62.2%
88.9%
28
24
3
17
90.32


1,705,604
60.0%
88.9%
27
24
3
18
90


1,722,429
57.8%
88.9%
26
24
3
19
89.66


1,732,725
57.8%
92.6%
26
25
2
19
92.86


1,817,947
55.6%
92.6%
25
25
2
20
92.59


1,825,768
53.3%
92.6%
24
25
2
21
92.31


1,869,774
51.1%
92.6%
23
25
2
22
92


1,880,984
48.9%
92.6%
22
25
2
23
91.67


1,994,899
46.7%
92.6%
21
25
2
24
91.3


2,067,775
44.4%
92.6%
20
25
2
25
90.91


2,154,178
42.2%
92.6%
19
25
2
26
90.48


2,324,221
40.0%
92.6%
18
25
2
27
90


2,467,429
37.8%
92.6%
17
25
2
28
89.47


2,551,776
35.6%
92.6%
16
25
2
29
88.89


2,703,085
35.6%
96.3%
16
26
1
29
94.12


2,850,072
33.3%
96.3%
15
26
1
30
93.75


3,096,078
31.1%
96.3%
14
26
1
31
93.33


3,186,273
28.9%
96.3%
13
26
1
32
92.86


3,441,678
28.9%
100.0%
13
27
0
32
100


3,511,076
26.7%
100.0%
12
27
0
33
100


3,559,430
24.4%
100.0%
11
27
0
34
100


3,576,889
22.2%
100.0%
10
27
0
35
100


4,137,076
20.0%
100.0%
9
27
0
36
100


4,327,530
17.8%
100.0%
8
27
0
37
100


5,107,549
15.6%
100.0%
7
27
0
38
100


5,545,432
13.3%
100.0%
6
27
0
39
100


5,640,050
11.1%
100.0%
5
27
0
40
100


5,724,798
8.9%
100.0%
4
27
0
41
100


6,708,583
6.7%
100.0%
3
27
0
42
100


6,891,638
4.4%
100.0%
2
27
0
43
100


7,209,245
2.2%
100.0%
1
27
0
44
100


7,299,442
0.0%
100.0%
0
27
0
45
#####
















TABLE 7







Part I. Fluorescent signals from binding of IgG antibodies to different glycans in CD Colitis patients and UC patients. Glycans are presented in


LINEARCODE ®.















Patient No.
Patient No. Clinical condition
IgG_Aa
IgG_Ab4GNa
IgG_Ab4GNb
IgG_Ana
IgG_Ga
IgG_Gb
IgG_GN(6S)b





10015
Crohn's disease
2313399.5
635468
690377.5
1472394.5
1738460.25
2507309.25
1752931


10018
Crohn's disease
1282598
1535296.5
773145
1304881
1556959.75
2349611.5
1316616


10028
Crohn's disease
400412
2027543.5
276464.5
565620.5
933864
527070
842969


10068
Crohn's disease
236509.5
326480.5
365799.5
468415
1037833.75
646782.25
820937.5


10089
Crohn's disease
6235212
873746.5
828641.5
879861.5
1551637.75
3140987
1459563


10102
Crohn's disease
425568
1252680.5
275934.5
402232.5
1119215.5
602214.25
684982


10105
Crohn's disease





208854.5


10003
Ulcerative colitis
187885.5
377841
259127
257702
659132.75
905251.25
729287


10020
Ulcerative colitis
1107251
1374336.5
775070.5
758803.5
1269500.5
1354221.5
1258840


10022
Ulcerative colitis
612362
549887
517309
377725.5
1467537
971547.25
805564.5


10023
Ulcerative colitis
230639.5
287362
216928.5
159075
693799.5
476804.75
335428


10024
Ulcerative colitis
984300.5
860812.5
654889
803682
1278164.75
1536704.5
1278711


10030
Ulcerative colitis
218405
948666.5
148121.5
131947
660381
313801.5
288801


10039
Ulcerative colitis
535525.5
355678.5
308129
335650.5
694135
788940
579956.5


10040
Ulcerative colitis
364266
313945
301998.5
236382
487735.75
508502.25
390982.5


10044
Ulcerative colitis
702426.5
809831
486338
678997
1026423.25
1134152
794829


10050
Ulcerative colitis
416618
1388773
491837
637010.5
992490
1307946.75
912013


10065
Ulcerative colitis
433662
500898.5
456155
593461
953378.25
983242.75
842731.5


10069
Ulcerative colitis
205728.5
714726
259398.5
329163
1215249.5
598735.5
672092


10072
Ulcerative colitis
192896
194102.5
182286
231396.5
1015614.25
320461
363892.5


10079
Ulcerative colitis
150330
519316
199636
460673.5
983715.25
405166
513526.5


10084
Ulcerative colitis
438643
696196
312418
448064
735412.25
703594
545286


10086
Ulcerative colitis
203076.5
203979
127167.5
323691.5
877230.25
686424.75
465633


10087
Ulcerative colitis
254433.5
421656
304673.5
338759.5
578500.5
615110
386385.5


10096
Ulcerative colitis
384127
1044393
244746
459440
1205875.25
997504
673275


10097
Ulcerative colitis
174679
267596.5
167481.5
344388.5
751111.75
424300.25
458307


10029
Ulcerative colitis





1024750


Average
Crohn's disease colitis
1,815,617
1,108,536
535,060
848,901
1,322,995
1,628,996
1,146,333



Ulcerative colitis
410,382
622,631
337,564
416,106
923,441
791,179
647,134


Med
Crohn's disease colitis
854,083
1,063,214
528,089
722,741
1,335,427
1,498,197
1,079,793



Ulcerative colitis
364,266
519,316
301,999
344,389
953,378
703,594
579,957



ttest
0.012022185
0.026037602
0.044509262
0.002568067
0.006995736
0.009487981
0.003042923










Part II.












Patient No.
Patient No. Clinical condition
IgG_GNb
IgG_GNb6ANa
IgG_Ma
IgG_Ma2Ma





10015
Crohn's disease
2155136.5
2105251
1210171.5
1865891


10018
Crohn's disease
1853996.5
1063920.5
1642422.5
2114538.5


10028
Crohn's disease
815951
1646003
471600
388120


10068
Crohn's disease
995101.5
1045720
1065364
1364558


10089
Crohn's disease
6756773.5
2984861.5
1732145.5
1975468


10102
Crohn's disease
984931
788111
768939
999741.5


10105
Crohn's disease


10003
Ulcerative colitis
575919
821537.5
432922
640303


10020
Ulcerative colitis
1372903
1524422.5
1363896
641830.5


10022
Ulcerative colitis
892125
2107553
696491.5
689169.5


10023
Ulcerative colitis
380898.5
412904.5
741737.5
524735.5


10024
Ulcerative colitis
1293243.5
1428660.5
981713
1501423


10030
Ulcerative colitis
368437.5
1521634
383159
465097.5


10039
Ulcerative colitis
603719
900021.5
427352.5
962878.5


10040
Ulcerative colitis
943099.5
1502139
387998
1617762


10044
Ulcerative colitis
1069004
740931
1166622
830608.5


10050
Ulcerative colitis
1120248
836121
1056914.5
1200920


10065
Ulcerative colitis
2518317
610962.5
666534.5
1165935.5


10069
Ulcerative colitis
899127
584783.5
359555
599937.5


10072
Ulcerative colitis
423833
310437.5
455587.5
482990.5


10079
Ulcerative colitis
508108
411685.5
425263.5
293342.5


10084
Ulcerative colitis
826299.5
552446.5
592992.5
509651.5


10086
Ulcerative colitis
744875
321304
402319
476814.5


10087
Ulcerative colitis
353199
256942.5
409432
380168.5


10096
Ulcerative colitis
910091.5
558828.5
633246
685412


10097
Ulcerative colitis
1859201.5
433687
267456
422519.5


10029
Ulcerative colitis


Average
Crohn's disease colitis
2,260,315
1,605,645
1,148,440
1,451,386



Ulcerative colitis
929,613
833,526
623,747
741,658


Med
Crohn's disease colitis
1,424,549
1,354,962
1,137,768
1,615,225



Ulcerative colitis
892,125
610,963
455,588
640,303



ttest
0.022705775
0.012278151
0.004574538
0.003038408
















TABLE 8







Part I. Fluorescent signals from binding of IgA antibodies to different glycans in CD Colitis patients and UC patients. Glycans are presented in


LINEARCODE ®.















Patient No.
Clinical condition
IgA_Aa3Ab4GNb3Ab4Gb
IgA_Aa4Ab4Gb
IgA_Ab
IgA_Ab3(GNb6)ANa
IgA_Ab3GNb
IgA_Ab6Ab
IgA_ANa





10015
Crohn's disease
823920.5
642431
671617
582327.5
1250743.5
644176
712552.5


10018
Crohn's disease
1120640
692655.5
905785
806576
555300
944644
509272.5


10028
Crohn's disease
70782.5
65409
54145
50555
64293
99647
102094.5


10068
Crohn's disease
485132
423765
323220.5
300755
278180.5
314013
335295


10089
Crohn's disease
386429.5
475156
347788
300281.5
396131
456654.5
426221.5


10102
Crohn's disease
249229
289752.5
206488
157775.5
189939
236594
224709.5


10105
Crohn's disease


10003
Ulcerative colitis
78003.5
74646.5
76239.5
77832.5
76386
128755
99557


10020
Ulcerative colitis
321496
286915
319939.5
316325
358795.5
583244
550607


10022
Ulcerative colitis
182507.5
253611.5
188916
269222.5
230976.5
399670
278082.5


10023
Ulcerative colitis
131549.5
113203.5
118895.5
106896
121660.5
136477.5
183293.5


10024
Ulcerative colitis
170812
191188.5
139852.5
313233
141818.5
233050.5
146876


10030
Ulcerative colitis
126498.5
114379.5
127270.5
101520.5
93169.5
136717.5
136593.5


10039
Ulcerative colitis
181355
168185
183845.5
185994.5
165022.5
235006
180943


10040
Ulcerative colitis
117934.5
122886.5
113510.5
116982.5
110072.5
176402.5
148789


10044
Ulcerative colitis
213188.5
235379.5
194883.5
299006
282039.5
169473.5
153085.5


10050
Ulcerative colitis
312988
253641
239070.5
233244.5
213519.5
305608.5
264615.5


10065
Ulcerative colitis
250784.5
555877.5
255301.5
267297.5
174792
270164.5
251877.5


10069
Ulcerative colitis
198087.5
171640.5
204934.5
161723.5
230896.5
197254.5
183682


10072
Ulcerative colitis
169567.5
230948
286381
174653
174006
174449
167844


10079
Ulcerative colitis
422569
430651.5
569214
337161
328102
361507.5
352796.5


10084
Ulcerative colitis
254076
234589
442836.5
212473
202150.5
206448.5
192001


10086
Ulcerative colitis
134968
117207
137226
73241.5
78799.5
98580
67717


10087
Ulcerative colitis
196730
404271.5
194668.5
134105.5
164685
142530.5
145004


10096
Ulcerative colitis
405,529
392063.5
398373.5
352667
365977.5
513370.5
391423


10097
Ulcerative colitis
285630.5
280728
245147.5
193135
199541
235651
203575.5


10029
Ulcerative colitis


Average
Crohns
522,689
431,528
418,174
366,378
455,765
449,288
385,024



UC
218,646
243,790
233,500
206,669
195,390
247,598
215,703


Med
Crohns
435,781
449,461
335,504
300,518
337,156
385,334
380,758



UC
196,730
234,589
194,884
193,135
174,792
206,449
183,294



ttest
0.003432508
0.017087855
0.042789261
0.036632153
0.015545789
0.028930448
0.018529045










Part II















Patient No.
Clinical condition
IgA_ANb
IgA_Gb
IgA_Gb3Gb
IgA_GNb
IgAGNb3Ab4Gb
IgA_GNb3Ana
IgA_GNb4GNb





10015
Crohn's disease
782432
2352257.5
3792549.5
1848069.5
957892.25
973773.5
1365558.5


10018
Crohn's disease
534881
1744966.5
1050178.5
1108481.5
809108
872211.5
826559


10028
Crohn's disease
100331.5
193866.5
186673.5
226701.5
144574
153168.25
355502


10068
Crohn's disease
303011.5
1012507
628503
691170.5
1218454
860716.75
920038.25


10089
Crohn's disease
420382.5
993118
1402344.5
975042.5
2982001.5
1030029.75
1025812.25


10102
Crohn's disease
254464
625656
628931.5
317767
288563.75
482396.5
457211.75


10105
Crohn's disease




313559
376495
459207.5


10003
Ulcerative colitis
98065.5
143964
141554.5
200912.5
116158.75
150200.75
168212.25


10020
Ulcerative colitis
531219.5
748577
786919.5
923043.5
146937.5
141658
182637


10022
Ulcerative colitis
323070.5
676825
455035
491029.5
218443.5
206741
242902.75


10023
Ulcerative colitis
145928.5
314442
284436.5
275060.5
238630.25
533213
250089


10024
Ulcerative colitis
189008.5
832661.5
442657
479785.5
288009
338630.5
355951.5


10030
Ulcerative colitis
231126
409200
284786.5
408023.5
236637.5
206756.5
302015


10039
Ulcerative colitis
168373
491547
517175.5
392005
786417
809396.5
475749.5


10040
Ulcerative colitis
177785.5
279361
218811.5
280689.5
205950.75
169128.25
226448.5


10044
Ulcerative colitis
161501
753256
473594.5
555971
392169.25
333466.25
446973.25


10050
Ulcerative colitis
271901
695130
382399.5
526927.5
383543.5
293205.25
249395.5


10065
Ulcerative colitis
203122.5
697130.5
670787.5
457057
291427.75
297671.75
356560.25


10069
Ulcerative colitis
212249.5
635934
527218.5
363936.5
194509.5
248548.5
230391


10072
Ulcerative colitis
185039.5
365880.5
357007
390922.5
288597
263714.5
210346.25


10079
Ulcerative colitis
366925
554240.5
2257419.5
1048892.5
406795.25
366346
516296.25


10084
Ulcerative colitis
206100.5
581235.5
434302.5
414222
179011.25
203365.25
235661.5


10086
Ulcerative colitis
101404
197886.5
207273
193242
433317.5
563802.75
342868


10087
Ulcerative colitis
171203
483024
475046
343527
203492.5
517514
190636.5


10096
Ulcerative colitis
433166
869958.5
824120.5
833330.5
445703.25
536801.5
460213


10097
Ulcerative colitis
229678
553467
738068.5
484123
299604.5
305982.25
324637


10029
Ulcerative colitis


Average
Crohns
399,250
1,153,729
1,281,530
861,205
1,066,766
728,716
825,114



UC
231,940
541,248
551,506
477,300
302,913
341,376
303,578


Med
Crohns
361,697
1,002,813
839,555
833,107
883,500
866,464
873,299



UC
203,123
554,241
455,035
414,222
288,009
297,672
250,089



ttest
0.024586727
0.003969787
0.042899427
0.02591308
0.003184372
0.001126656
1.02649E−05










Part III













Patient No.
Clinical condition
IgA_GNb6ANa
IgA_Ma
IgA_Ma2Ma
IgA_Ma3(Ma6)Mb
IgA_Ma3Ma





10015
Crohn's disease
1884673.5
793071.5
3415595
746825.5
999203.5


10018
Crohn's disease
1114615
961742.5
2917815.5
727784
717096


10028
Crohn's disease
194085
94336.5
256032
87390
103552


10068
Crohn's disease
563962.5
524544
807816.5
435971
503945.5


10089
Crohn's disease
544660
556490
819048.5
379526.5
459454


10102
Crohn's disease
325721
261633.5
729964
231998.5
316389


10105
Crohn's disease


10003
Ulcerative colitis
143651.5
115658.5
287171.5
95305
105407.5


10020
Ulcerative colitis
178131.5
256154
1079174.5
192167
234420


10022
Ulcerative colitis
208178
324237.5
656144
211938
215720.5


10023
Ulcerative colitis
201303
227006.5
637593
207601.5
240763.5


10024
Ulcerative colitis
359657.5
338794
1125587.5
262327
295575.5


10030
Ulcerative colitis
323944.5
272317.5
856355.5
201701
229526.5


10039
Ulcerative colitis
449716.5
387887.5
710761
276315.5
280618


10040
Ulcerative colitis
249464
164073.5
312896.5
135720
121149.5


10044
Ulcerative colitis
449997.5
326666.5
748596
239592.5
308066


10050
Ulcerative colitis
324796.5
314891.5
547079
281154
196723


10065
Ulcerative colitis
568719.5
316328.5
847658
287586.5
286285.5


10069
Ulcerative colitis
419430.5
389266
724998.5
354004
439389


10072
Ulcerative colitis
263180
229358.5
817809
179841
253729.5


10079
Ulcerative colitis
887360
514181.5
1012361
612803
859776.5


10084
Ulcerative colitis
182069
194750.5
1041362.5
178116
217626


10086
Ulcerative colitis
117532
95669.5
191239
121532
100620.5


10087
Ulcerative colitis
298763
303731
700059.5
248842.5
264208.5


10096
Ulcerative colitis
588895
564102
1394898
522042.5
499770


10097
Ulcerative colitis
467802
289141
737150
276116
236299


10029
Ulcerative colitis


Average
Crohns
771,286
531,970
1,491,045
434,916
516,607



UC
351,715
296,011
759,415
257,090
283,457


Med
Crohns
554,311
540,517
813,433
407,749
481,700



UC
323,945
303,731
737,150
239,593
240,764



ttest
0.014389095
0.0113452
0.029286279
0.032460361
0.026205708
















TABLE 9







Anti-glycan antibody levels in CD patients with complicated


disease (fistulizing or fibrostensoing) versus CD patients with


non complicated disease (inflammatory).










Anti glycan antibodies levels,




(EU)0.5




Mean (SD)













Complicated
Non complicated




disease
disease



Antibodies
(n = 264)
(n = 474)






ALCA
6.6 (2.0)**
5.8 (2.0)



ACCA
7.8 (3.4)**
6.4 (2.9)



AMCA
9.0 (2.3)**
8.1 (2.2)



gASCA
8.3 (3.7)**
6.4 (3.7)





**p < 0.00001 versus Non-complicated disease course













TABLE 10







Regression analysis: significance of different marker for


differentiation between CD patients with complicated


disease vs. patients with non-complicated disease











Variable
Coefficient
p














gASCA
0.0231
<0.0001



ACCA
0.0210
<0.0001



ALCA
0.0203
0.0239



CARD15 total number of
0.0595
0.0246



variants













AMCA

Non significant
















TABLE 11







Diagnostics performance for differentiation between CD patients with complicated


diseases and CD patients non-complicated disease course according to combination of gASCA


and CARD15 variants and according to combination of gASCA, ACCA, ALCA and CARD15


variants















Positive
Negative
Overall



Sensitivity
Specificity
predictive
predictive
agreement



(%)
(%)
value (%)
Value (%)
(%)
















Combination of gASCA, ALCA,
44.8
80.1
79.1
47.1
57.9


ACCA, and CARD15 (cutoff = 0.54)


Combination of gASCA, and CARD15
34.7
80.3
74.9
42.1
51.6


(cutoff = 7.1)
















TABLE 12







Anti-glycan antibody levels in CD patients with need for surgery


versus CD patients who do not need surgery.










Anti glycan antibodies levels,




(EU)0.5




Mean (SD)













Need for surgery
No need for surgery



Antibodies
(n = 422)
(n = 333)






ALCA
6.5 (2.0)* 
6.0 (2.0)



ACCA
7.8 (3.4)**
6.8 (3.1)



AMCA
8.9 (2.3)* 
8.3 (2.1)



gASCA
8.3 (3.6)**
6.7 (3.9)





**p < 0.00001 versus No need for surgery


*p < 0.01 versus No need for surgery













TABLE 13







Regression analysis: significance of different marker for


differentiation between CD patients who need surgery


vs. patients without need for surgery.











Variable
Coefficient
p














gASCA
0.0331
<0.0001



ACCA
0.0156
0.0012











ALCA

Non significant











CARD15 total number of
0.089 
0.0246



variants













AMCA

Non significant
















TABLE 14







Diagnostics performance for differentiation between CD patients with need for


surgery and CD patients without need for surgery according to a combination of gASCA and


CARD15 variants and according to combination of gASCA, ACCA and CARD15 variants















Positive
Negative
Overall



Sensitivity
Specificity
predictive
predictive
agreement



(%)
(%)
value (%)
Value (%)
(%)
















Combination of gASCA, ACCA, and
30.7
90.0
71.9
59.5
60.2


CARD15 (cutoff = 0.52)


Combination of gASCA, and CARD15
23.4
90.6
68.6
57.4
59.2


(cutoff = 0.44)
















TABLE 16







Regression analysis: significance of different marker for


differentiation between IBD patients and non-IBD patients.











Variable
Coefficient
p














gASCA
0.0262
<0.0001



ACCA
−0.0054
0.1081



ALCA
0.0420
<0.0001



CARD15 total number of
0.0390
0.0177



variants





AMCA
0.0139
0.0089
















TABLE 15







Anti-glycan antibody levels in IBD patients versus non-IBD pateints










Anti glycan




antibodies levels,




(EU)0.5




Mean (SD)













IBD
Non-IBD



Antibodies
(n = 1225)
(n = 313)






ALCA
5.9 (2.1)**
4.1 (1.4)



ACCA
6.9 (3.3) 
6.8 (2.6)



AMCA
8.2 (2.3)**
7.0 (1.8)



gASCA
6.6 (3.9)**
3.0 (1.4)





**p < 0.00001 versus Non-IBD













TABLE 17







Diagnostic performance for differentiation between IBD patients with and non-IBD


according to combination of gASCA versus combination of gASCA, ACCA, AMCA, ALCA and


CARD15 variants















Positive
Negative
Overall



Sensitivity
Specificity
predictive
predictive
agreement



(%)
(%)
value (%)
Value (%)
(%)
















Combination of gASCA, ACCA,
72.7
80.5
93.4
42.7
74.1


ALCA, AMCA and CARD15 (cutoff =


0.38)


Combination of gASCA and CARD15
66.4
80.5
93.0
38.0
69.2


(cutoff = 4.0)








Claims
  • 1. A method for diagnosing severe Crohn's disease in a subject, the method comprising, providing a test sample from a subject with symptoms of Crohn's disease; anddetermining whether said sample includes an antibody selected from an antibody selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody,wherein the presence of said antibodies in said test sample indicates the subject has severe Crohn's disease.
  • 2. The method of claim 2, wherein said method includes determining whether said sample includes two antibodies selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody.
  • 3. The method of claim 2, wherein said method includes determining whether said sample includes three antibodies selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody.
  • 4. The method of claim 2, wherein said method includes determining whether said sample includes four antibodies selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody.
  • 5. The method of claim 2, wherein said method includes determining whether said sample includes five antibodies selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody.
  • 6. The method of claim 2, wherein said method includes determining whether said sample includes an anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody.
  • 7. The method of claim 1, further comprising determining whether said sample includes an antibody selected from the group consisting of an anti mannan antibody (gASCA) and an anti-Man(α1,3)Man(α) antibody (AMCA), an anti-Man(α1,6)Man(α) antibody (AMBA), an anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA).
  • 8. The method of claim 7, wherein said method comprises determining whether said sample includes two antibodies selected from the group consisting of an anti mannan antibody (gASCA) and an anti-Man(α1,3)Man(α) antibody (AMCA), an anti-Man(α1,6)Man(α) antibody (AMBA), an anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA).
  • 9. The method of claim 7, wherein said method comprises determining whether said sample includes three antibodies selected from the group consisting of an anti mannan antibody (gASCA) and an anti-Man(α1,3)Man(α) antibody (AMCA), an anti-Man(α1,6)Man(α) antibody (AMBA), an anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA).
  • 10. The method of claim 7, wherein said method comprises determining whether said sample includes four antibodies selected from the group consisting of an anti mannan antibody (gASCA), an anti-Man(α1,3)Man(α) antibody (AMCA), an anti-Man(α1,6)Man(α) antibody (AMBA), an anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA).
  • 11. The method of claim 7, wherein said method comprises determining whether said sample includes an anti mannan antibody (gASCA), an anti-Man(α1,3)Man(α) antibody (AMCA), an anti-Man(α1,6)Man(α) antibody (AMBA), an anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA).
  • 12. The method of claim 7, further comprising determining whether said sample includes an anti-neutrophil cytoplasmic antibody (ANCA).
  • 13. The method of claim 1, further comprising determining whether said subject has a CARD15 allele associated with Crohn's disease.
  • 14. The method of claim 7, wherein said method comprises determining whether said subject has the R702W, G908R, or 1007fs CARD15 allele.
  • 15. The method of claim 7, further comprising determining whether said subject with severe Crohn's disease has strictures or fistulas.
  • 16. The method of claim 5, further comprising treating said subject with said antibodies for symptoms associated with severe Crohn's disease.
  • 17. The method of claim 5, wherein said treatment is surgery.
  • 18. The method of claim 5, wherein said anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, said anti-α-GalNAc antibody (AGCA), and said anti-laminarin antibody are IgG antibodies and said anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA) and said anti-β-GalNAc antibodies are IgA antibodies.
  • 19. The method of claim 7, wherein said (gASCA) antibody, anti-Man(α1,3)Man(α) antibody (AMCA) antibody, anti-Man(α1,6)Man(α) antibody (AMBA), anti-Man(α1,2)Man(α) antibody (AMNA), and anti-α-Man antibody (AMA) are IgG antibodies.
  • 20. The method of 19, the anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, the anti-α-GalNAc antibody (AGCA), the anti-β-GalNAc, and the anti-laminarin antibody are IgG antibodies and the anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA) and the anti-β-GalNAc antibody are IgA antibodies
  • 21. The method of claim 1, wherein said test sample is serum.
  • 22. The method of claim 1, wherein the presence of antibodies in said sample are determined using an enzyme-linked immunosorbent assay (ELISA).
  • 23. The method of claim 4, wherein said subject is determined to have severe Crohn's disease if when said anti-β-GalNAc is above S, said anti-Glc(β1,6)Glc(β) antibody is above T, said ALCA level is above W, said AGCA is above X, said anti-laminarin antibody is above Y, and said ACCA level is above Z, wherein S, T, W, X, Y, and Z are independently selected to achieve an optimized clinical parameter selected from the group consisting of: sensitivity, specificity, negative predictive value, positive predictive value and overall agreement.
  • 24. The method of claim 6, wherein said subject is determined to have severe Crohn's disease, if when said gASCA level is above U, and said AMCA is above V, wherein U and V are independently selected to achieve an optimized clinical parameter selected from the group consisting of: sensitivity, specificity, negative predictive value, positive predictive value and overall agreement.
  • 25. The method of claim 4, wherein said method comprises determining the aggregate amount of ALCA, anti-Glc(β1,6)Glc(β) antibody, AGCA, anti-β-GalNAc anti-laminarin antibodies and ACCA, wherein the subject is determined to have severe Crohn's disease if the aggregate amount of said antibodies is greater than R.
  • 26. The method of claim 11, wherein said method comprises determining the aggregate amount of ALCA, anti-Glc(β1,6)Glc(β) antibody, AGCA, anti-β-GalNAc anti-laminarin antibodies and ACCA, wherein the subject is determined to have severe Crohn's disease if the aggregate amount of said antibodies is greater than R.
  • 27. The method of claim 25, wherein said method further comprises determining the aggregate amount of gASCA, AMCA, AMBA, AMNA and AMA antibodies, and said subject is determined to have severe Crohn's disease if the aggregate amount of said antibodies is greater than R.
  • 28. A method for assessing the prognosis of Crohn's disease complications in a subject, the method comprising providing a test sample from a subject with symptoms of Crohn's disease; anddetermining whether said sample includes an antibody selected from an antibody selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, an anti-Glc(α1,6)Glc(α) antibody, and an anti-laminarin antibody,wherein the presence of said antibodies in said test sample indicates a severe Crohn's disease prognosis for said subject.
  • 29. A method for assessing the prognosis of Crohn's disease complications in a subject, the method comprising providing a test sample from a subject with symptoms of Crohn's disease; anddetermining whether said sample includes an anti-Glc(β1,3)Glc(β) antibody (ALCA), an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-Man(α1,3)Man(α) antibody (AMBA), and an anti-Mannan antibody,wherein the presence of said antibodies in said test sample indicates a severe Crohn's disease prognosis for said subject.
  • 30. A method for differentiating inflammatory bowel disease (IBD) from a disease other than IBD in subject, the method comprising providing a test sample from a subject with symptoms of IBD; anddetermining whether said sample includes determining whether said sample includes an antibody selected from an antibody selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), an anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody,wherein the presence of said antibodies in said test sample indicates the subject has inflammatory bowel disease.
  • 31. The method of claim 30, wherein said method includes determining whether said sample includes two antibodies selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), an anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody.
  • 32. The method of claim 30, wherein said method includes determining whether said sample includes three antibodies selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), an anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody.
  • 33. The method of claim 30, wherein said method includes determining whether said sample includes four antibodies selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), an anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody.
  • 34. The method of claim 30, wherein said method includes determining whether said sample includes five antibodies selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), an anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody.
  • 35. The method of claim 30, wherein said method includes determining whether said sample includes an anti-Glc(β1,3)Glc(β) antibody (ALCA), an anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody.
  • 36. The method of claim 30, further comprising determining whether said sample includes an antibody selected from the group consisting of an anti mannan antibody (gASCA), an anti-Man(α1,3)Man(α) antibody (AMCA), an anti-Man(α1,6)Man(α) antibody (AMBA), anti-Man(α1,2)Man(α) antibody (AMNA), and anti-α-Man antibody (AMA).
  • 37. The method of claim 36, wherein said method comprises determining whether said sample includes two antibodies selected from the group consisting of an anti mannan antibody (gASCA), an anti-Man(α1,3)Man(α) antibody (AMCA) antibody, an anti-Man(α1,6)Man(α) antibody (AMBA), an anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA).
  • 38. The method of claim 36, wherein said method comprises determining whether said sample includes three antibodies selected from the group consisting of an anti mannan antibody (gASCA) and an anti-Man(α1,3)Man(α) antibody (AMCA) antibody, anti-Man(α1,6)Man(α) antibody (AMBA), anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA).
  • 39. The method of claim 36, wherein said method comprises determining whether said sample includes four antibodies selected from the group consisting of an anti mannan antibody (gASCA), an anti-Man(α1,3)Man(α) antibody (AMCA) antibody, anti-Man(α1,6)Man(α) antibody (AMBA), anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA).
  • 40. The method of claim 36, wherein said method comprises determining whether said sample includes an anti mannan antibody (gASCA), an anti-Man(α1,3)Man(α) antibody (AMCA) antibody, anti-Man(α1,6)Man(α) antibody (AMBA), anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA).
  • 41. The method of claim 30, wherein said method further comprises determining whether said sample includes an anti-neutrophil cytoplasmic antibody (ANCA).
  • 42. The method of claim 30, further comprising determining whether said subject has a CARD15 allele associated with Crohn's disease.
  • 43. The method of claim 42, wherein said method comprises determining whether said subject has the R702W, G908R, or 1007fs CARD15 allele.
  • 44. The method of claim 30, further comprising determining whether said subject with inflammatory bowel disease has strictures or fistulas.
  • 45. The method of claim 30, further comprising treating said subject with said antibodies for symptoms associated with severe Crohn's disease.
  • 46. The method of claim 45, wherein said treatment is surgery.
  • 47. The method of claim 30, wherein said anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, said anti-α-GalNAc antibody (AGCA), said anti-β-GalNAc, and said anti-laminarin antibody is an IgG antibody and said anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA) or said anti-β-GalNAc antibody is an IgA antibody.
  • 48. The method of claim 36, wherein said (gASCA) antibody, an anti-Man(α1,3)Man(α) antibody (AMCA) antibody, anti-Man(α1,6)Man(α) antibody (AMBA), anti-Man(α1,2)Man(α) antibody (AMNA), or anti-α-Man antibody (AMA) is an IgG antibody.
  • 49. The method of claim 35, wherein said anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, said anti-α-GalNAc antibody (AGCA), said anti-β-GalNAc antibody, and said anti-laminarin antibody are IgG antibodies and said anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA) and said anti-β-GalNAc antibodies are IgA antibodies.
  • 50. The method of claim 30, wherein said test sample is serum.
  • 51. The method of claim 30, wherein the presence of antibodies in said sample are determined using an enzyme-linked immunosorbent assay (ELISA).
  • 52. The method of claim 30, wherein said subject is determined to have severe Crohn's disease if when said ALCA level is above W, said AGCA is above X, said anti-laminarin antibody is above Y, and said ACCA level is above Z, wherein W, X, Y, and Z are independently selected to achieve an optimized clinical parameter selected from the group consisting of: sensitivity, specificity, negative predictive value, positive predictive value and overall agreement.
  • 53. The method of claim 30, wherein said subject is determined to have severe Crohn's disease, if when said gASCA level is above U, and said AMCA is above V, wherein U and V are independently selected to achieve an optimized clinical parameter selected from the group consisting of: sensitivity, specificity, negative predictive value, positive predictive value and overall agreement.
  • 54. The method of claim 30, wherein said method comprises determining the aggregate amount of ALCA, AGCA, anti-laminarin antibodies and ACCA, wherein the subject is determined to have severe Crohn's disease if the aggregate amount of said antibodies is greater than T.
RELATED APPLICATIONS

This application is a continuation of U.S. Ser. No. 11/351,185, filed Feb. 8, 2006, which is a continuation-in-part of U.S. Ser. No. 10/843,033, filed May 11, 2004, which is a continuation-in-part of U.S. Ser. No. 10/728,227, filed Dec. 3, 2003. The contents of these applications are incorporated by reference in their entireties.

Continuations (1)
Number Date Country
Parent 11351185 Feb 2006 US
Child 12605563 US
Continuation in Parts (2)
Number Date Country
Parent 10843033 May 2004 US
Child 11351185 US
Parent 10728227 Dec 2003 US
Child 10843033 US