Peptide microarrays and novel biomarkers for celiac disease

A method of identifying novel epitopes for binding to an antibody associated with an autoimmune disorder, said method comprising:

• synthesizing a plurality of polypeptides on a first array, said plurality of polypeptides comprising overlapping polypeptide sequences from a protein suspected of comprising epitopes that bind to an antibody associated with an immune disorder;
• contacting said first array with a first sample from a subject with said immune disorder;
• determining which of said overlapping polypeptide sequences are bound to an antibody from said first sample to generate binding data;
• analyzing said binding data to identify a plurality of continuous epitopes in said protein;
• further analyzing each of said plurality of continuous epitopes to identify a plurality of discontinuous epitope pairs with the highest sensitivity of binding to said antibody from said sample, thereby identifying novel epitopes for binding to said antibody associated with said autoimmune disorder;
• synthesizing a plurality of synthetic polypeptides on a second array, each synthetic polypeptide comprising at least two of said plurality of discontinuous epitopes, each synthetic polypeptide further comprising a random polypeptide sequence;
• contacting said second array with a second sample from a subject with said immune disorder;
• determining the sensitivity and specificity of binding of antibodies from said second sample to each of said plurality of synthetic polypeptides;
• and
• identifying the synthetic polypeptides with a sensitivity of at least 30% and a specificity of 98-100% for binding to an antibody associated with said immune disorder, thereby identifying refined novel epitopes for binding to said antibody associated with said immune disorder.