Genome-Wide Association Study of HIV Whole Genome Sequences Validated using Drug Resistance.

ABSTRACT:

Background

Genome-wide association studies (GWAS) have considerably advanced our understanding of human traits and diseases. With the increasing availability of whole genome sequences (WGS) for pathogens, it is important to establish whether GWAS of viral genomes could reveal important biological insights. Here we perform the first proof of concept viral GWAS examining drug resistance (DR), a phenotype with well understood genetics.

Method

We performed a GWAS of DR in a sample of 343 HIV subtype C patients failing 1st line antiretroviral treatment in rural KwaZulu-Natal, South Africa. The majority and minority variants within each sequence were called using PILON, and GWAS was performed within PLINK. HIV WGS from patients failing on different antiretroviral treatments were c

SUBMITTER: Power RA 

PROVIDER: S-EPMC5038937 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature