Sequencing TRAF1 in patients with rheumatoid arthritis Bruce C. Jobse Medical and Population Genetics Broad Institute

The Purpose of the Experiment To identify, via sequencing, any novel casual DNA variants capable of explaining increased RA-risk in Humans

What is Rheumatoid Arthritis (RA)? Chronic autoimmune disorder Afflicts 1% of adults worldwide 60% heritable

The TRAF1-C5 Region: Associated to risk of RA rs – odds-ratio increase of 1.30 common allele – found in 30-40% of population two genes of immunological relevance – TRAF1-C5 1,522 CCP+ RA cases, 1,850 controls (NARAC-I, EIRA-I) 997 CCP+ RA cases, 1,777 controls (NARAC-II, EIRA-II)

Experimental Schema Generated sequence data: – Coding exons, 5’ UTR, 3’ UTR – 96 patients with RA using Sanger sequencing (Broad) – Automated SNP calling algorithms Validated sequence data: – Genotyped all novel SNPs in same RA samples Assessed LD structure – genotyped in CEU HapMap samples – Determined r2 with RA-associated SNP (rs )

Results 29 SNPs were identified (4.5 kb of sequence) – MAF >5%n=8all were in dbSNP – MAF <5%n=2114 were novel 19 out of 22 were genotyped by Sequenom in same 96 patients – SNPs that failed genotyping did not pass quality control tests – Currently assessing SNPs to validate whether real or artifact No significant LD with the RA risk variant in HapMap Assess putative functional SNPs – MAF >5%no missense or functional alleles – MAF <5%4 novel missense alleles

Conclusion No DNA variant found that would disrupt transcript- signals or conserved sequence motifs Further examination of 4 discovered missense SNPs – needs further retesting in the population

Acknowledgements SRPG Program: Bruce Birren Shawna Young Lucia Vielma Mentor: Robert Plenge Broad Institute: Eric Lander David Altshuler Metabolics Group: Candace Guiducci Gabe Crawford