CNVrd, a read-depth algorithm for assigning copy-number at the FCGR locus: population-specific tagging of copy number variation at FCGR3B.

ABSTRACT: The extent of contribution from common gene copy number (CN) variants in human disease is currently unresolved. Part of the reason for this is the technical difficulty in directly measuring CN variation (CNV) using molecular methods, and the lack of single nucleotide polymorphisms (SNPs) that can tag complex CNV that has arisen multiple times on different SNP haplotypes. One CNV locus implicated in human disease is FCGR. Here we aimed to use next-generation sequencing (NGS) data from the 1000 Genomes Project to assign CN at FCGR3A and FCGR3B and to comprehensively assess the ability of SNPs to tag specific CN variants. A read-depth algorithm was developed (CNVrd) and validated on a subset of HapMap samples using CN assignments that had previously been determined using molecular and microar

SUBMITTER: tan Nguyen H 

PROVIDER: S-EPMC3640002 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature