Communicated by Sergio Ottolenghi
An integrated approach for measuring copy number variation at the FCGR3 (CD16) locus
Article first published online: 13 JAN 2009
© 2008 Wiley-Liss, Inc.
Volume 30, Issue 3, pages 477–484, March 2009
How to Cite
Hollox, E. J., Detering, J.-C. and Dehnugara, T. (2009), An integrated approach for measuring copy number variation at the FCGR3 (CD16) locus. Hum. Mutat., 30: 477–484. doi: 10.1002/humu.20911
- Issue published online: 24 FEB 2009
- Article first published online: 13 JAN 2009
- Manuscript Accepted: 28 AUG 2008
- Manuscript Received: 1 JUL 2008
- Fc receptor;
- copy number variation;
- paralog ratio test;
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.