Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs.

Nat Genet
Authors
Keywords
Abstract

Accurate and complete measurement of single nucleotide (SNP) and copy number (CNV) variants, both common and rare, will be required to understand the role of genetic variation in disease. We present Birdsuite, a four-stage analytical framework instantiated in software for deriving integrated and mutually consistent copy number and SNP genotypes. The method sequentially assigns copy number across regions of common copy number polymorphisms (CNPs), calls genotypes of SNPs, identifies rare CNVs via a hidden Markov model (HMM), and generates an integrated sequence and copy number genotype at every locus (for example, including genotypes such as A-null, AAB and BBB in addition to AA, AB and BB calls). Such genotypes more accurately depict the underlying sequence of each individual, reducing the rate of apparent mendelian inconsistencies. The Birdsuite software is applied here to data from the Affymetrix SNP 6.0 array. Additionally, we describe a method, implemented in PLINK, to utilize these combined SNP and CNV genotypes for association testing with a phenotype.

Year of Publication
2008
Journal
Nat Genet
Volume
40
Issue
10
Pages
1253-60
Date Published
2008 Oct
ISSN
1546-1718
URL
DOI
10.1038/ng.237
PubMed ID
18776909
PubMed Central ID
PMC2756534
Links
Grant list
T32 HG002295-03 / HG / NHGRI NIH HHS / United States
T32 HG002295 / HG / NHGRI NIH HHS / United States
T32 GM008313-18 / GM / NIGMS NIH HHS / United States
T32 GM008313-17 / GM / NIGMS NIH HHS / United States
T32 GM008313 / GM / NIGMS NIH HHS / United States
T32 HG002295-04 / HG / NHGRI NIH HHS / United States