Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs
By Joshua M. Korn, F. Kuruvilla, Steven A. McCarroll, Alec Wysoker, J. Nemesh, S. Cawley, Earl Hubbell, Jim Veitch, P. Collins, K. Darvishi and 6 more. Nature Genetics, 2008
833 citations recorded by the source corpus.
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.
Subfields: Genetics
View Paper: https://www.semanticscholar.org/paper/afa8fe1a6d2dea2769486b87ac571d528fa1e73a
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In Genetics
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Citations in the corpus
- Characterising and Predicting Haploinsufficiency in the Human Genome (2010, methodology): “0 platform, 210 unrelated HapMap individuals [28], 2,421 control individuals used in GWAS studies of bipolar and schizophrenia [17] and 6,000 individuals participating WTCCC2 as common controls, using Birdsuite [29].”
- Integrated detection and population-genetic analysis of SNPs and copy number variation (2008, methodology): “Initial performance evaluation Using a novel SNP genotyping algorith”
- Germline BAP1 mutations predispose to malignant mesothelioma (2011, methodology): “Allele calls were performed by plate using the BIRDSEED version 2 algorithm, resulting in 906,600 SNPs for quality-control analyse”
- Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer (2018, methodology): “Somatic Copy-Number Alterations— Somatic copy-number data were generated on Affymetrix SNP 6.0 arrays using standard protocols from the Genome Analysis Platform of the Broad Institute (McCarroll et al., 2008).”