NDLI: Multipoint linkage-disequilibrium mapping narrows location interval and identifies mutation heterogeneity.

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Multipoint linkage-disequilibrium mapping narrows location interval and identifies mutation heterogeneity.

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Multipoint linkage-disequilibrium mapping narrows location interval and identifies mutation heterogeneity.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Whittaker, John C. Xu, Chun-fang Hosking, Louise K. Balding, David J. Morris, Andrew P.
Description	Author Affiliation: Morris AP ( Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom.);
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.
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	23
Volume Number	100
Language	English
Publisher	National Academy of Sciences
Publisher Date	2003-11-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Chromosome Mapping Linkage Disequilibrium Mutation Bayes Theorem Cytochrome P-450 CYP2D6 Genetics Genotype Models, Genetic Phenotype Phylogeny Polymorphism, Single Nucleotide Research Support, Non-U.S. Gov't Multidisciplinary
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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