Genetically indistinguishable SNPs and their influence on inferring the location of disease-associated variants

Lawrence, Robert, Evans, David M., Morris, Andrew P., Ke, Xiayi, Hunt, Sarah, Paolucci, Marta, Ragoussis, Jiannis, Deloukas, Panos, Bentley, David and Cardon, Lon R. (2005) Genetically indistinguishable SNPs and their influence on inferring the location of disease-associated variants. Genome Research, 15 11: 1503-1510. doi:10.1101/gr.4217605

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Author Lawrence, Robert
Evans, David M.
Morris, Andrew P.
Ke, Xiayi
Hunt, Sarah
Paolucci, Marta
Ragoussis, Jiannis
Deloukas, Panos
Bentley, David
Cardon, Lon R.
Title Genetically indistinguishable SNPs and their influence on inferring the location of disease-associated variants
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
Publication date 2005-01-01
Sub-type Article (original research)
DOI 10.1101/gr.4217605
Open Access Status File (Publisher version)
Volume 15
Issue 11
Start page 1503
End page 1510
Total pages 8
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Laboratory Press
Language eng
Abstract As part of a recent high-density linkage disequilibrium (LD) study of chromosome 20, we obtained genotypes for ∼30,000 SNPs at a density of 1 SNP/2 kb on four different population samples (47 CEPH founders; 91 UK unrelateds [unrelated white individuals of western European ancestry]; 97 African Americans; 42 East Asians). We observed that ∼50% of SNPs had at least one genetically indistinguishable partner; i.e., for every individual considered, their genotype at the first locus was identical to their genotype at the second locus, or in LD terms, the SNPs were in "perfect" LD (r2 = 1.0). These "genetically indistinguishable SNPs" (giSNPs) formed into clusters of varying size. The larger the cluster, the greater the tendency to be located within genes and to overlap with giSNP clusters in other population samples. As might be expected for this map density, many giSNPs were located close to one another, thus reflecting local regions of undetected recombination or haplotype blocks. However, ∼1/3 of giSNP clusters had intermingled, non-indistinguishable SNPs with incomplete LD (D′ and r2 <1), sometimes spanning hundreds of kilobases, comprising up to 70 indistinguishable markers and overlapping multiple haplotype blocks. These long-range, nonconsecutive giSNPs have implications for disease gene localization by allelic association as evidence for association at one locus will be indistinguishable from that at another locus, even though both loci may be situated far apart. We describe the distribution of giSNPs on this map of chromosome 20 and illustrate the potential impact they can have on association mapping.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: UQ Diamantina Institute - Open Access Collection
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