Low-, high-coverage, and two-stage DNA sequencing in the design of the genetic association study.

ABSTRACT: Next-generation sequencing-based genetic association study (GAS) is a powerful tool to identify candidate disease variants and genomic regions. Although low-coverage sequencing offers low cost but inadequacy in calling rare variants, high coverage is able to detect essentially every variant but at a high cost. Two-stage sequencing may be an economical way to conduct GAS without losing power. In two-stage sequencing, an affordable number of samples are sequenced at high coverage as the reference panel, then to impute in a larger sample is sequenced at low coverage. As unit sequencing costs continue to decrease, investigators can now conduct GAS with more flexible sequencing depths. Here, we systematically evaluate the effect of the read depth and sample size on the variant discovery power a

SUBMITTER: Xu C 

PROVIDER: S-EPMC5363279 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature