CNVs Mainly Deletions and Disorders

Published by the University of Chicago Press
Title
Simultaneous Discovery and Testing of Deletions for Disease Association in SNP Genotyping Studies
Author(s)
Jared R. Kohler and David J. Cutler
Identifiers
The American Journal of Human Genetics, volume 81 (2007), page 000 DOI: 10.1086/520823
Availability
This site: PS HTML PDF (1.4M)
Copyright
© 2007, The American Society of Human Genetics.
Abstract
Copy-number variation (CNV), and deletions in particular, can play a crucial, causative role in rare disorders. The extent to which CNV contributes to common, complex disease etiology, however, is largely unknown. Current techniques to detect CNV are relatively expensive and time consuming, making it difficult to conduct the necessary large-scale genetic studies. SNP genotyping technologies, on the other hand, are relatively cheap, thereby facilitating large study designs. We have developed a computational tool capable of harnessing the information in SNP genotype data to detect deletions. Our approach not only detects deletions with high power but also returns accurate estimates of both the population frequency and the transmission frequency. This tool, therefore, lends itself to the discovery of deletions in large familial SNP genotype data sets and to simultaneous testing of the discovered deletion for association, with the use of both frequency-based and transmission/disequilibrium testbased designs. We demonstrate the effectiveness of our computer program (microdel), available for download at no cost, with both simulated and real data. Here, we report 693 deletions in the HapMap 16c collection, with each deletion assigned a population frequency.