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

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 URLs. Birdsuite, http://www.broad.mit.edu/mpg/birdsuite/; PLINK CNV analysis tools, http://pngu.mgh.harvard.edu/purcell/plink/cnv; 1000 Genomes, http://www.1000genomes.org. COMPETING INTERESTS STATEMENTThe authors declare competing financial interests: details accompany the full-text HTML version of the paper at http://www.nature.com/naturegenetics/. 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. NIH Public AccessStudies of SNPs and CNVs in human disease have to date been built on different analytical approaches, and somewhat based on conflicting assumptions. Specifically, SNP genotyping methods 1,2 assume that every individual has two copies of each locus, whereas studies of copy number variation assume that individuals vary in their copy number across the genome. Because SNPs and CNVs coexist throughout the genome, they influence one another's measurement, and may act both separately and in concert to influence human phenotypes. Ignoring CNVs during SNP genotyping results in failure to capture the true underlying sequence at many sites (genotypes like AAB and A), and can create the appearance of violations of mendelian inheritance or Hardy-Weinberg equilibrium where none in fact exists 3,4 . Ignoring SNPs in copy number analysis fails to incorporate allele-specific gains and losses, as well as the potential to exploit linkage disequilibrium between CNVs and nearby SNPs.In addition, methods for copy number analysis have not previously separated the ideas of genotyping known copy number polymorphisms (CNPs) from discovery of rare (and thus previously unobserved) copy number variants (CNVs) 5 . In the former case, as in SNP genotyping, existing information about known polymorphisms can be used to design arrays, train clustering algorithms and assign a prior probability of aberrant copy number to guide interpretation of measurements. Discovery of rare variants, as in sequence analysis for rare mutations, is a much more difficult problem-both because it is more difficult to detect a single event tha...

A panel of ancestry informative markers to estimate and correct potential effects of population stratification in Han Chinese

“…(Affymetrix, Inc.) Quality control was performed with 'apt-geno-qc' and genotype calling was performed with 'apt-probeset-genotype' in birdseed algorithm. 13 Only samples with call rate 40.86 were included in the downstream analyses.…”

Copy number variation in patients with cervical artery dissection

“…12,13 Quality filtering of the data sets. In a first exploration we analyzed the data sets from all patients and from 501 control subjects (Supplementary material 1), and identified for each patient all markers with copy number (CN) state a2 but with CN-state ¼ 2 in all the analyzed controls.…”

A genome-wide CNV association study on panic disorder in a Japanese population

“…The results of the SNP genome-wide association study are described elsewhere. 17 CNVs were determined with Birdsuite software 18 version 1.5.5 over the thresholds of logarithm of odds X10, 18,19 the number of probes in CNV X10 18,20,21 and individual CNVs o300. A total of 906 600 SNP probes and 946 000 CNV non-polymorphic probes on the chip were genotyped at the University of Tokyo, Graduate School of Medicine, according to the manufacturer's protocol.…”

“…PennCNV software 22 version 1 May 2010 was also used as an alternative algorithm to Birdsuite, to establish stringent CNV data; common CNVs were evaluated if they showed concordance rates of 40.90 between the algorithms. 18,23 Quality control A total of 157 subjects were excluded from further analysis, because they did not pass the quality control criteria for contrast quality control X0.4, 24 samplewise call rate X0.95, 25 ambiguous gender, unexpected duplicates, cryptic relatives or population stratifications. Ambiguous gender was assessed by sex check function in PLINK software 26 version 1.07.…”