Whole genome sequencing of 4,787 individuals identifies gene-based rare variants in age-related macular degeneration
Alan Kwong, Matthew Zawistowski, Lars G. Fritsche, Xiaowei Zhan, Jennifer L. Bragg‐Gresham, Kari Branham, Jayshree Advani, Mohammad Othman, Rinki Ratnapriya, Tanya M. Teslovich, Dwight Stambolian, Emily Y. Chew, Gonçalo R. Abecasis, Anand Swaroop
Abstract
Genome-wide association studies have contributed extensively to the discovery of disease-associated common variants. However, the genetic contribution to complex traits is still largely difficult to interpret. We report a genome-wide association study of 2394 cases and 2393 controls for age-related macular degeneration (AMD) via whole-genome sequencing, with 46.9 million genetic variants. Our study reveals significant single-variant association signals at four loci and independent gene-based signals in CFH, C2, C3, and NRTN. Using data from the Exome Aggregation Consortium (ExAC) for a gene-based test, we demonstrate an enrichment of predicted rare loss-of-function variants in CFH, CFI, and an as-yet unreported gene in AMD, ORMDL2. Our method of using a large variant list without individual-level genotypes as an external reference provides a flexible and convenient approach to leverage the publicly available variant datasets to augment the search for rare variant associations, which can explain additional disease risk in AMD.