ArticleAmerican journal of human genetics2003
Selection of genetic markers for association analyses, using linkage disequilibrium and haplotypes.
Article in American journal of human genetics, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
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- The polygenic implication of clopidogrel responsiveness: Insights from platelet reactivity analysis and next-generation sequencing.PloS one · 2024Article
- Genetic diversity and population structure analysis of a diverse panel of pea (Frontiers in genetics · 2024Article
- Gene transfer and nucleotide sequence evolution by Gossypium cytoplasmic genomes indicates novel evolutionary characteristics.Plant cell reports · 2020Article
- An evaluation of machine-learning for predicting phenotype: studies in yeast, rice, and wheat.Machine learning · 2020Article
- Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs.PloS one · 2020Article
- A novel linkage-disequilibrium corrected genomic relationship matrix for SNP-heritability estimation and genomic prediction.Heredity · 2018Article
- Heavy metals, organic solvents, and multiple sclerosis: An exploratory look at gene-environment interactions.Archives of environmental & occupational health · 2016Article
- Evaluating information content of SNPs for sample-tagging in re-sequencing projects.Scientific reports · 2015Article
- Genetic analysis and mapping of genes for resistance to multiple strains of Soybean mosaic virus in a single resistant soybean accession PI 96983.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2013Article
- Efficient techniques for genotype-phenotype correlational analysis.BMC medical informatics and decision making · 2013Article
- Article
- Matrix metalloproteinase-9 genetic polymorphisms and the risk for advanced pelvic organ prolapse.Obstetrics and gynecology · 2012Article
- Comprehensive analysis of LAMC1 genetic variants in advanced pelvic organ prolapse.American journal of obstetrics and gynecology · 2012Article
- Variable set enrichment analysis in genome-wide association studies.European journal of human genetics : EJHG · 2011Article
- Sequential Support Vector Regression with Embedded Entropy for SNP Selection and Disease Classification.Statistical analysis and data mining · 2011Article
- Association of genetic variation in mitotic kinases with breast cancer risk.Breast cancer research and treatment · 2010Article
- Gene discovery through imaging genetics: identification of two novel genes associated with schizophrenia.Molecular psychiatry · 2009Article
- Absence of association of asporin polymorphisms and osteoarthritis susceptibility in US Caucasians.Osteoarthritis and cartilage · 2008Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The genotyping of closely spaced single-nucleotide polymorphism (SNP) markers frequently yields highly correlated data, owing to extensive linkage disequilibrium (LD) between markers. The extent of LD varies widely across the genome and drives the number of frequent haplotypes observed in small regions. Several studies have illustrated the possibility that LD or haplotype data could be used to select a subset of SNPs that optimize the information retained in a genomic region while reducing the genotyping effort and simplifying the analysis. We propose a method based on the spectral decomposition of the matrices of pairwise LD between markers, and we select markers on the basis of their contributions to the total genetic variation. We also modify Clayton's "haplotype tagging SNP" selection method, which utilizes haplotype information. For both methods, we propose sliding window-based algorithms that allow the methods to be applied to large chromosomal regions. Our procedures require genotype information about a small number of individuals for an initial set of SNPs and selection of an optimum subset of SNPs that could be efficiently genotyped on larger numbers of samples while retaining most of the genetic variation in samples. We identify suitable parameter combinations for the procedures, and we show that a sample size of 50-100 individuals achieves consistent results in studies of simulated data sets in linkage equilibrium and LD. When applied to experimental data sets, both procedures were similarly effective at reducing the genotyping requirement while maintaining the genetic information content throughout the regions. We also show that haplotype-association results that Hosking et al. obtained near CYP2D6 were almost identical before and after marker selection.
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