Negligible impact on missing heritability of autoimmune-locus rare coding-region variants

Study ID Alternative Stable ID Type
EGAS00001000476 Resequencing

Study Description

Genome wide association studies (GWAS) have identified common variants of modest effect size at hundreds of loci for common autoimmune diseases - however a substantial fraction of heritability remains unexplained, and to which rare variants may contribute. To discover rare variants and test them for association with a phenotype, the majority of studies re-sequence a small initial sample size and then genotype the discovered variants in a larger sample set. This approach will fail to analyse a large fraction of the rare variants present in the entire sample set. Here we perform simultaneous amplicon sequencing-based variant discovery and genotyping for coding exons of 25 GWAS risk genes in 41,911 white-European origin UK subjects comprising 24,892 subjects with six autoimmune disease phenotypes and 17,019 controls, and show that rare coding-region variants at known loci play a negligible role in common autoimmune disease susceptibility. These results do not support the rare variant - synthetic genome-wide association hypothesis. Many known autoimmune disease risk loci contain ... (Show More)

Study Datasets 1 dataset.

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Dataset ID Description Technology Samples
This VCF contains the full sequence data post QC. This consists of 41,911 individuals. All polymorphic sites are present in this VCF.

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