149 (Part VII) Controls (~5%) Both biological and technical controls were included in the antigen phage library. For biological controls, we included B-lymphocyte-derived antigens from proteins of infectious diseases and human auto-antigens extracted from the Immune Epitope Database (IEDB), a public repository covering a wide range of well-established antigens. Antigens from B-cell assays of infectious diseases (excluding parasites) were incorporated, amounting to 290 different proteins represented by 4,250 oligos. Antigens from B-cell assays of human autoimmune diseases were selected as negative controls, which accounted for 430 different proteins represented by 7,700 oligos. Additional negative control antigens that were added to the library (~300 oligos) included antigens of viral proteins (derived from a previous phage-display sequencing study7) and various peptides that were not expected to trigger antibody responses in our cohorts, including antigens from the Ebola virus, and human antigens such as serum albumin, histone proteins, glycolytic enzymes and ribosomal proteins. Further details and experiments using these controls have previously beendescribed.1 Aside frombiological positive andnegative controls, technical controls (~550 oligos) were included in the phage library for experimental validation and contained some random sequences that should not be recognized by antibodies. In addition, codon optimization replicate controls (~350 oligos) were incorporated to exclude potential bias from different DNA oligonucleotides that might represent the same antigen amino acid sequence. Finally, 50 oligos were included that consisted of very short amino acid sequences (<45 aa) to test for the effects of varying length of the random sequences at the 3’-terminus. The antibody epitope repertoire in IBD
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