Common deletions and SNPs are in linkage disequilibrium in the human genome
Abstract
Humans show great variation in phenotypic traits such as height, eye color and susceptibility to disease. Genomic DNA sequence differences among individuals are responsible for the inherited components of these complex traits. Reports suggest that intermediate and large-scale DNA copy number and structural variations are prevalent enough to be an important source of genetic variation between individuals. Because association studies to identify genomic loci associated with particular phenotypic traits have focused primarily on genotyping SNPs, it is important to determine whether common structural polymorphisms are in linkage disequilibrium with common SNPs, and thus can be assessed indirectly in SNP-based studies. Here we examine 100 deletion polymorphisms ranging from 70 bp to 7 kb. We show that common deletions and SNPs ascertained with similar criteria have essentially the same distribution of linkage disequilibrium with surrounding SNPs, indicating that these polymorphisms may share evolutionary history and that most deletion polymorphisms are effectively assayed by proxy in SNP-based association studies.
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TIGRA-targeted assembly identified breakpoints for an additional 4,188 deletions and 160 tandem duplications initially discovered by read-depth, read-pair, and paired-depth methods.
“Using the TIGRA-targeted assembly approach38 we further identified the breakpoints of an additional 4,188 deletions and 160 tandem duplications, initially discovered by RD, RP, and PD methods”
From Mapping copy number variation by population-scale genome sequencing (2011) · cites this paper as [38]
Many copy-number variations (CNVs) display tight LD with nearby SNPs and thus can be proxied by nearby SNPs in GWASs.
“Many CNVs display tight LD with nearby SNPs (56, 57) and thus can be proxied by nearby SNPs in GWASs.”
From Genetic Mapping in Human Disease (2008) · cites this paper as [56]
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- Authors
- Hinds, D. A., Kloek, A. P., Jen, M., Chen, X., & Frazer, K. A.
- Affiliations
- Perlegen (United States) (US)
- Corresponding author
- Frazer, Kelly A
- Venue
- Nature Genetics
- Published
- 2005-12-04
- Volume
- 38
- Issue
- 1
- Pages
- 82-85
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W2087198772
- Cited by
- 372
- References
- 32
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 3 · 2023: 4 · 2022: 5 · 2021: 9 · 2020: 6 · 2019: 5 · 2018: 7 · 2017: 6 · 2016: 6 · 2015: 10 · 2014: 9 · 2013: 9 · 2012: 20
- FWCI
- 31.64
- 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
- common deletion, single nucleotide polymorphisms, linkage disequilibrium, structural variants, copy number variation, genetic variation, human genome
- MeSH terms
- Gene Frequency, Humans, Polymorphism, Genetic, Genetic Variation, Linkage Disequilibrium, Genome, Human, Sequence Deletion, Polymorphism, Single Nucleotide, Racial Groups, Microarray Analysis
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