Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs
Open accessAbstract
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.
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- Authors
- Korn, J. M., Kuruvilla, F. G., McCarroll, S. A., Wysoker, A., Nemesh, J., Cawley, S., Hubbell, E., Veitch, J., Collins, P. J., Darvishi, K., Lee, C., Nizzari, M. M., Gabriel, S. B., Purcell, S., Daly, M. J., & Altshuler, D.
- Affiliations
- Broad Institute (US)
- Affymetrix (United States) (US)
- Harvard University (US)
- Corresponding author
- Korn, Joshua M
- Altshuler, David
- ORCID
- Venue
- Nature Genetics
- Published
- 2008-09-07
- Volume
- 40
- Issue
- 10
- Pages
- 1253-1260
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC2756534
- OpenAlex
- W2140968934
- Cited by
- 783
- References
- 25
- Citations by year
- 2026: 4 · 2025: 7 · 2024: 9 · 2023: 15 · 2022: 21 · 2021: 17 · 2020: 23 · 2019: 29 · 2018: 35 · 2017: 44 · 2016: 42 · 2015: 54 · 2014: 65 · 2013: 73 · 2012: 95
- FWCI
- 47.30
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Human Genome Research Institute (T32HG002295)
- National Institute of General Medical Sciences (T32GM008313)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- genotype calling, copy number variation, single nucleotide polymorphisms, hidden Markov models, association analysis, rare CNVs, PLINK
- MeSH terms
- Algorithms, Chromosomes, Human, Chromosomes, Human, Pair 4, DNA, Female, Genotype, Haplotypes, Humans, Male, Markov Chains, Software, Models, Statistical, Genome, Human, Polymerase Chain Reaction, Gene Dosage, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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