ArticleAmerican journal of human genetics2004
Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium.
Article in American journal of human genetics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 767 papers, 2 of them syntheses that pooled it.
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Who cites it
767 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Biological annotation of genetic loci associated with intelligence in a meta-analysis of 87,740 individuals.Molecular psychiatry · 2019Pooled it
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- Association of the CHRNA4 neuronal nicotinic receptor subunit gene with frequency of binge drinking in young adults.Alcoholism, clinical and experimental research · 2014Trial
- Germline variation in NCF4, an innate immunity gene, is associated with an increased risk of colorectal cancer.International journal of cancer · 2014Trial
- Innate immunity gene polymorphisms and the risk of colorectal neoplasia.Carcinogenesis · 2013Trial
- Impact of genetic polymorphisms on adenoma recurrence and toxicity in a COX2 inhibitor (celecoxib) trial: results from a pilot study.Pharmacogenetics and genomics · 2013Trial
- Common single nucleotide polymorphisms in genes related to immune function and risk of papillary thyroid cancer.PloS one · 2013Trial
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- Identification of Growth-Related Single-Nucleotide Polymorphisms in the cAMP-Dependent Protein Kinase Type I Regulatory Subunit-like Gene of the Oriental River Prawn,International journal of molecular sciences · 2026Article
- Toward minimal SNP sets for record-matching with CODIS STR profiles.European journal of human genetics : EJHG · 2026Article
- A breeding strategy for high-oleic acid content and high-yield peanut using Tag SNPs and genomic selection.BMC plant biology · 2026Article
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- Biocultural vulnerability of traditional crops in the Indian Trans-Himalaya.Science advances · 2025Article
- EBMGP: a deep learning model for genomic prediction based on Elastic Net feature selection and bidirectional encoder representations from transformer's embedding and multi-head attention pooling.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Integrated genomic analysis and CRISPRi implicatesNPJ dementia · 2025Article
- Polygenic Indices (a.k.a. Polygenic Scores) in Social Science: A Guide for Interpretation and Evaluation.Sociological methodology · 2024Article
- Unraveling the genomic landscape ofEcology and evolution · 2024Article
707 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
Common genetic polymorphisms may explain a portion of the heritable risk for common diseases. Within candidate genes, the number of common polymorphisms is finite, but direct assay of all existing common polymorphism is inefficient, because genotypes at many of these sites are strongly correlated. Thus, it is not necessary to assay all common variants if the patterns of allelic association between common variants can be described. We have developed an algorithm to select the maximally informative set of common single-nucleotide polymorphisms (tagSNPs) to assay in candidate-gene association studies, such that all known common polymorphisms either are directly assayed or exceed a threshold level of association with a tagSNP. The algorithm is based on the r(2) linkage disequilibrium (LD) statistic, because r(2) is directly related to statistical power to detect disease associations with unassayed sites. We show that, at a relatively stringent r(2) threshold (r2>0.8), the LD-selected tagSNPs resolve >80% of all haplotypes across a set of 100 candidate genes, regardless of recombination, and tag specific haplotypes and clades of related haplotypes in nonrecombinant regions. Thus, if the patterns of common variation are described for a candidate gene, analysis of the tagSNP set can comprehensively interrogate for main effects from common functional variation. We demonstrate that, although common variation tends to be shared between populations, tagSNPs should be selected separately for populations with different ancestries.
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