ArticleGenetics2005
Linkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs.
Article in Genetics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Validating a Genomic Convergence and Network Analysis Approach Using Association Analysis of Identified Candidate Genes in Alzheimer's Disease.Frontiers in genetics · 2021Article
- Transposable elements have contributed human regulatory regions that are activated upon bacterial infection.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- Polymorphic markers for identification of parasite population in Plasmodium malariae.Malaria journal · 2020Article
- Regulatory variants: from detection to predicting impact.Briefings in bioinformatics · 2019Review
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- Pharmacogenomic Profiling of ADME Gene Variants: Current Challenges and Validation Perspectives.High-throughput · 2018Review
- Hypothesis-driven candidate gene association studies: practical design and analytical considerations.American journal of epidemiology · 2009Review
- Search for type 2 diabetes susceptibility genes on chromosomes 1q, 3q and 12q.Journal of human genetics · 2008Article
- HapMap coverage for SNPs in the Japanese population.Journal of human genetics · 2008Article
- HLA-E, HLA-F, and HLA-G polymorphism: genomic sequence defines haplotype structure and variation spanning the nonclassical class I genes.Immunogenetics · 2006Article
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- No evidence for association of the ENPP1 (PC-1) K121Q variant with risk of type 2 diabetes in a Japanese population.Journal of human genetics · 2006Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single nucleotide polymorphisms (SNPs) have been proposed to be grouped into haplotype blocks harboring a limited number of haplotypes. Within each block, the portion of haplotypes is expected to be tagged by a selected subset of SNPs; however, none of the proposed selection algorithms have been definitive. To address this issue, we developed a tag SNP selection algorithm based on grouping of SNPs by the linkage disequilibrium (LD) coefficient r(2) and examined five genes in three ethnic populations--the Japanese, African Americans, and Caucasians. Additionally, we investigated ethnic diversity by characterizing 979 SNPs distributed throughout the genome. Our algorithm could spare 60% of SNPs required for genotyping and limit the imprecision in allele-frequency estimation of nontag SNPs to 2% on average. We discovered the presence of a mosaic pattern of LD plots within a conventionally inferred haplotype block. This emerged because multiple groups of SNPs with strong intragroup LD were mingled in their physical positions. The pattern of LD plots showed some similarity, but the details of tag SNPs were not entirely concordant among three populations. Consequently, our algorithm utilizing LD grouping allows selection of a more faithful set of tag SNPs than do previous algorithms utilizing haplotype blocks.
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