ArticleProceedings of the National Academy of Sciences of the United States of America2003
Multipoint linkage-disequilibrium mapping narrows location interval and identifies mutation heterogeneity.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- A regression-based association test for case-control studies that uses inferred ancestral haplotype similarity.Annals of human genetics · 2009Article
- Genetic association mapping via evolution-based clustering of haplotypes.PLoS genetics · 2007Article
- Fine-scale linkage disequilibrium mapping of age-related macular degeneration in the complement factor H gene region.The British journal of ophthalmology · 2007Article
- Incorporating single-locus tests into haplotype cladistic analysis in case-control studies.PLoS genetics · 2007Article
- Association mapping of complex trait loci with context-dependent effects and unknown context variable.Genetics · 2006Article
- A flexible Bayesian framework for modeling haplotype association with disease, allowing for dominance effects of the underlying causative variants.American journal of human genetics · 2006Article
- Bayesian graphical models for genomewide association studies.American journal of human genetics · 2006Article
- Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes.PLoS genetics · 2005Article
- Linkage disequilibrium maps and association mapping.The Journal of clinical investigation · 2005Review
- Linkage disequilibrium and association studies in higher plants: present status and future prospects.Plant molecular biology · 2005Review
- Article
- Article
- Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps.Proceedings of the National Academy of Sciences of the United States of America · 2004Article
- Haplotype structure and phenotypic associations in the chromosomal regions surrounding two Arabidopsis thaliana flowering time loci.Genetics · 2004Article
- Little loss of information due to unknown phase for fine-scale linkage-disequilibrium mapping with single-nucleotide-polymorphism genotype data.American journal of human genetics · 2004Article
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5 authors.
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Abstract
Single-nucleotide polymorphism (SNP) genotypes were recently examined in an 890-kb region flanking the human gene CYP2D6. Single-marker and haplotype-based analyses identified, with genomewide significance (P < 10-7), a 403-kb interval displaying strong linkage disequilibrium (LD) with predicted poor-metabolizer phenotype. However, the width of this interval makes the location of causal variants difficult: for example, the interval contains seven known or predicted genes in addition to CYP2D6. We have developed the Bayesian fine-mapping software coldmap, which, applied to these genotype data, yields a 95% location interval covering only 185 kb and establishes genomewide significance for a causal locus within the region. Strikingly, our interval correctly excludes four SNPs, which individually display association with genomewide significance, including the SNP showing strongest LD (P < 10-34). In addition, coldmap distinguishes homozygous cases for the major CYP2D6 mutation from those bearing minor mutations. We further investigate a selection of SNP subsets and find that previously reported methods lead to a 38% savings in SNPs at the cost of an increase of <20% in the width of the location interval.
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