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November 2009 Using GWAS Data to Identify Copy Number Variants Contributing to Common Complex Diseases
Sebastian Zöllner, Tanya M. Teslovich
Statist. Sci. 24(4): 530-546 (November 2009). DOI: 10.1214/09-STS304


Copy number variants (CNVs) account for more polymorphic base pairs in the human genome than do single nucleotide polymorphisms (SNPs). CNVs encompass genes as well as noncoding DNA, making these polymorphisms good candidates for functional variation. Consequently, most modern genome-wide association studies test CNVs along with SNPs, after inferring copy number status from the data generated by high-throughput genotyping platforms.

Here we give an overview of CNV genomics in humans, highlighting patterns that inform methods for identifying CNVs. We describe how genotyping signals are used to identify CNVs and provide an overview of existing statistical models and methods used to infer location and carrier status from such data, especially the most commonly used methods exploring hybridization intensity. We compare the power of such methods with the alternative method of using tag SNPs to identify CNV carriers. As such methods are only powerful when applied to common CNVs, we describe two alternative approaches that can be informative for identifying rare CNVs contributing to disease risk. We focus particularly on methods identifying de novo CNVs and show that such methods can be more powerful than case-control designs. Finally we present some recommendations for identifying CNVs contributing to common complex disorders.


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Sebastian Zöllner. Tanya M. Teslovich. "Using GWAS Data to Identify Copy Number Variants Contributing to Common Complex Diseases." Statist. Sci. 24 (4) 530 - 546, November 2009.


Published: November 2009
First available in Project Euclid: 20 April 2010

zbMATH: 1329.62441
MathSciNet: MR2779342
Digital Object Identifier: 10.1214/09-STS304

Rights: Copyright © 2009 Institute of Mathematical Statistics


Vol.24 • No. 4 • November 2009
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