Microbial and autoantibody immunogenic repertoires in TIF1? autoantibody positive dermatomyositis

Spyridon Megremis; Thomas Walker; Xiaotong He; James O'Sullivan; William E.R. Ollier; Hector Chinoy; Neil Pendleton; Antony Payton; Lynne Hampson; Ian Hampson; Janine Lamb

Epitope annotation and rank scoring: M6 15,522 DM-associated and 4,817 HC-associated unique epitopes were retrieved for DM patients. Only 0.65% of the DM pool comprised peptide sequences common to HC. Of these epitopes common by sequence, the DM enrichment score ranged between 5-fold and 546-fold the healthy control score ( Figure 1 ) (Figure S1A-S1F). Epitopes were annotated by our modified BLASTp (Henikoff and Henikoff, 1992) approach at 100% minimum identity ( Figure S1G -S1I). This facilitates short AAsequence inputs and resolves protein annotation confidence scores per epitope with statistical control of epitope-protein annotation confidence, intra-protein dis-contiguous sequence matches, redundancy of protein isoforms and common sequence matches, single-epitope multi-protein parsing, and set analysis of resultant patient cohort organisms lists. These were tuned per each epitope's NGS read . CC-BY-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.25.007534 doi: bioRxiv preprint count. 6.745x106 (DM patients) and 2.250x106 (HC) total protein annotations were retrieved ( Figure 1 ).