Premium
An integrated approach for measuring copy number variation at the FCGR3 (CD16) locus
Author(s) -
Hollox Edward J.,
Detering JanChristoph,
Dehnugara Tushna
Publication year - 2009
Publication title -
human mutation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 162
eISSN - 1098-1004
pISSN - 1059-7794
DOI - 10.1002/humu.20911
Subject(s) - copy number variation , biology , genotyping , genetics , snp genotyping , genotype , computational biology , gene , genome
Copy number variation (CNV) is an important source of genomic diversity in humans, and influences disease susceptibility. The immunoglobulin‐receptor genes FCGR3A and FCGR3B on chromosome 1q23.3 show CNV, and CNV of the FCGR3B gene is associated with glomerulonephritis in systemic lupus erythematosus and organ‐specific autoimmunity. Large‐scale case‐control association studies of CNV require technologies that are amenable to high‐throughput analysis with low error rates. Here we propose an integrated suite of five assays, four of them duplexed to reduce DNA usage, that assays for CNV at FCGR3A and FCGR3B , and genotype the polymorphic neutrophil antigen HNA1. We show how a maximum‐likelihood (ML) approach to combining the results from these five assays allows estimation of statistical confidence for each individual copy number, and therefore an appropriate significance threshold to be set, controlling the error rate. This approach results in a high‐throughput copy number genotyping system, with demonstrable precision and accuracy, that can be applied to large case‐control cohort studies. We demonstrate Mendelian inheritance of this CNV, variation in frequency between Europeans and East Asians, and a lack of strong association between the CNV and flanking SNP genotypes, with important consequences for genome‐wide association studies. Hum Mutat 0, 1–8, 2008. © 2008 Wiley‐Liss, Inc.