Integrated detection and population-genetic analysis of SNPs and copy number variation
Abstract
Dissecting the genetic basis of disease risk requires measuring all forms of genetic variation, including SNPs and copy number variants (CNVs), and is enabled by accurate maps of their locations, frequencies and population-genetic properties. We designed a hybrid genotyping array (Affymetrix SNP 6.0) to simultaneously measure 906,600 SNPs and copy number at 1.8 million genomic locations. By characterizing 270 HapMap samples, we developed a map of human CNV (at 2-kb breakpoint resolution) informed by integer genotypes for 1,320 copy number polymorphisms (CNPs) that segregate at an allele frequency >1%. More than 80% of the sequence in previously reported CNV regions fell outside our estimated CNV boundaries, indicating that large (>100 kb) CNVs affect much less of the genome than initially reported. Approximately 80% of observed copy number differences between pairs of individuals were due to common CNPs with an allele frequency >5%, and more than 99% derived from inheritance rather than new mutation. Most common, diallelic CNPs were in strong linkage disequilibrium with SNPs, and most low-frequency CNVs segregated on specific SNP haplotypes.
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Most variants present in an individual human genome are common alleles.
“In truth, structural variants come in many shapes, sizes and allele frequencies, and a majority of variants present in an individual genome are common alleles (Conrad et al., 2010; McCarroll et al., 2008; Mills et al., 2011; Sudmant et al., 2010).”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as McCarroll et al., 2008
Deletion discovery sensitivity was assessed against a gold standard assembled from four earlier surveys.
“We further assessed the sensitivity of deletion discovery methods by collating data from four earlier surveys1,13,22,28 into a gold standard”
From Mapping copy number variation by population-scale genome sequencing (2011) · cites this paper as [13]
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Study, D. (. D. I. S. A. C., Liu, J., Zhou, Y., Liu, S., Song, X., Yang, X.-Z., Fan, Y., Chen, W., Akdemir, Z. C., Yan, Z., et al. (2018) · Human Genetics · doi:10.1007/s00439-018-1910-3 · Cited by 77 · see citing works
Copy number variations and cancer susceptibility
Shlien, A., & Malkin, D. (2010) · Current Opinion in Oncology · doi:10.1097/cco.0b013e328333dca4 · Cited by 77 · see citing works
RetractedCarter, M., Nikkel, S., Fernandez, B., Marshall, C., Noor, A., Lionel, A., Prasad, A., Pinto, D., Joseph-George, A., Noakes, C., et al. (2011) · Clinical Genetics · doi:10.1111/j.1399-0004.2010.01578.x · Cited by 77 · see citing works
Genome-wide association studies and the genetic dissection of complex traits
Sebastiani, P., Timofeev, N., Dworkis, D. A., Perls, T. T., & Steinberg, M. H. (2009) · American Journal of Hematology · doi:10.1002/ajh.21440 · Cited by 67 · see citing works
The role of copy number variation in schizophrenia
Kirov, G. (2010) · Expert Review of Neurotherapeutics · doi:10.1586/ern.09.133 · Cited by 52 · see citing works
Evolving toward a human-cell based and multiscale approach to drug discovery for CNS disorders
Schadt, E. E., Buchanan, S., Brennand, K. J., & Merchant, K. M. (2014) · Frontiers in Pharmacology · doi:10.3389/fphar.2014.00252 · Cited by 39 · see citing works
- Authors
- McCarroll, S. A., Kuruvilla, F. G., Korn, J. M., Cawley, S., Nemesh, J., Wysoker, A., Shapero, M. H., de Bakker, P. I. W., Maller, J. B., Kirby, A., Elliott, A. L., Parkin, M., Hubbell, E., Webster, T., Mei, R., Veitch, J., Collins, P. J., Handsaker, R., Lincoln, S., Nizzari, M., Blume, J., Jones, K. W., Rava, R., Daly, M. J., Gabriel, S. B., & Altshuler, D.
- Affiliations
- Broad Institute (US)
- Affymetrix (United States) (US)
- Massachusetts General Hospital (US)
- Corresponding author
- McCarroll, Steven A
- Altshuler, David
- ORCID
- Venue
- Nature Genetics
- Published
- 2008-09-07
- Volume
- 40
- Issue
- 10
- Pages
- 1166-1174
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W2047361940
- Cited by
- 936
- References
- 34
- Citations by year
- 2026: 3 · 2025: 7 · 2024: 10 · 2023: 19 · 2022: 12 · 2021: 26 · 2020: 21 · 2019: 24 · 2018: 50 · 2017: 39 · 2016: 39 · 2015: 47 · 2014: 62 · 2013: 72 · 2012: 99
- FWCI
- 76.13
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- 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 › Genetics › Forensic and Genetic Research
- Keywords
- copy number variation, HapMap, population genetics, linkage disequilibrium, novel mutations
- MeSH terms
- Chromosomes, Human, DNA, Haplotypes, Humans, Genetic Variation, Genome, Human, Polymerase Chain Reaction, Gene Dosage, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Population Groups
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