Whole Exome Sequencing in Alopecia Areata Identifies Rare Mutations in KRT82

Alopecia areata (AA) is an autoimmune disorder, in which the body's own immune cells attack hair follicels resulting in hair loss. It is a complex genetic disease with 14 associated loci previously identified in our genome-wide association study (GWAS). In the study, we performed the whole-exome sequencing (WES) on 849 AA patients with the aim to identify the novel rare variants in genes contributing to AA susceptibility. We performed gene-collapsing analyses and identified keratin 82 (KRT82 Gene ID: 3888) as the highest associated AA gene in the three rare damaging collapsing models with p<6.7E-07 in one of the models. The KRT82 gene is a hair-specific type II keratin expressed in the hair shaft cuticle during the anagen phase of the hair cycle. We reported the lower expression of KRT82 in AA hair follicles, compared to controls, and the KRT82 expression is absent from the bulb region, the site of AA immune attack. This study emphasizes the significance of using WES and gene collapsing analyses to identify rare variation in a functionally relevant risk gene using a moderate sample size.  ]]>
Samples reporting greater than eight percent contamination according to VerifyBamID were excluded. KING was used to ensure only unrelated (up to third-degree) individuals contributed to the analysis. Furthermore, to be eligible for analysis, we required samples to have >87% of the consensus coding sequence (CCDS) covered at 10X. Once we controlled for low quality and related samples, we applied an additional analysis to control for population stratification by using EIGENSTRAT to remove samples that were considered as genetic outliers. This ensured that the main cluster of samples was of similar genetic origins and would not be biased by sub-population that are genotypic outliers.]]>