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Coverage and Characteristics of the Affymetrix GeneChip Human Mapping 100K SNP Set

Improvements in technology have made it possible to conduct genome-wide association mapping at costs within reach of academic investigators, and experiments are currently being conducted with a variety of high-throughput platforms. To provide an appropriate context for interpreting results of such s...

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Detalles Bibliográficos
Autores principales: Nicolae, Dan L, Wen, Xiaoquan, Voight, Benjamin F, Cox, Nancy J
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1456318/
https://www.ncbi.nlm.nih.gov/pubmed/16680197
http://dx.doi.org/10.1371/journal.pgen.0020067
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author Nicolae, Dan L
Wen, Xiaoquan
Voight, Benjamin F
Cox, Nancy J
author_facet Nicolae, Dan L
Wen, Xiaoquan
Voight, Benjamin F
Cox, Nancy J
author_sort Nicolae, Dan L
collection PubMed
description Improvements in technology have made it possible to conduct genome-wide association mapping at costs within reach of academic investigators, and experiments are currently being conducted with a variety of high-throughput platforms. To provide an appropriate context for interpreting results of such studies, we summarize here results of an investigation of one of the first of these technologies to be publicly available, the Affymetrix GeneChip Human Mapping 100K set of single nucleotide polymorphisms (SNPs). In a systematic analysis of the pattern and distribution of SNPs in the Mapping 100K set, we find that SNPs in this set are undersampled from coding regions (both nonsynonymous and synonymous) and oversampled from regions outside genes, relative to SNPs in the overall HapMap database. In addition, we utilize a novel multilocus linkage disequilibrium (LD) coefficient based on information content (analogous to the information content scores commonly used for linkage mapping) that is equivalent to the familiar measure r (2) in the special case of two loci. Using this approach, we are able to summarize for any subset of markers, such as the Affymetrix Mapping 100K set, the information available for association mapping in that subset, relative to the information available in the full set of markers included in the HapMap, and highlight circumstances in which this multilocus measure of LD provides substantial additional insight about the haplotype structure in a region over pairwise measures of LD.
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spelling pubmed-14563182006-05-26 Coverage and Characteristics of the Affymetrix GeneChip Human Mapping 100K SNP Set Nicolae, Dan L Wen, Xiaoquan Voight, Benjamin F Cox, Nancy J PLoS Genet Research Article Improvements in technology have made it possible to conduct genome-wide association mapping at costs within reach of academic investigators, and experiments are currently being conducted with a variety of high-throughput platforms. To provide an appropriate context for interpreting results of such studies, we summarize here results of an investigation of one of the first of these technologies to be publicly available, the Affymetrix GeneChip Human Mapping 100K set of single nucleotide polymorphisms (SNPs). In a systematic analysis of the pattern and distribution of SNPs in the Mapping 100K set, we find that SNPs in this set are undersampled from coding regions (both nonsynonymous and synonymous) and oversampled from regions outside genes, relative to SNPs in the overall HapMap database. In addition, we utilize a novel multilocus linkage disequilibrium (LD) coefficient based on information content (analogous to the information content scores commonly used for linkage mapping) that is equivalent to the familiar measure r (2) in the special case of two loci. Using this approach, we are able to summarize for any subset of markers, such as the Affymetrix Mapping 100K set, the information available for association mapping in that subset, relative to the information available in the full set of markers included in the HapMap, and highlight circumstances in which this multilocus measure of LD provides substantial additional insight about the haplotype structure in a region over pairwise measures of LD. Public Library of Science 2006-05 2006-05-05 /pmc/articles/PMC1456318/ /pubmed/16680197 http://dx.doi.org/10.1371/journal.pgen.0020067 Text en © 2006 Nicolae et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Nicolae, Dan L
Wen, Xiaoquan
Voight, Benjamin F
Cox, Nancy J
Coverage and Characteristics of the Affymetrix GeneChip Human Mapping 100K SNP Set
title Coverage and Characteristics of the Affymetrix GeneChip Human Mapping 100K SNP Set
title_full Coverage and Characteristics of the Affymetrix GeneChip Human Mapping 100K SNP Set
title_fullStr Coverage and Characteristics of the Affymetrix GeneChip Human Mapping 100K SNP Set
title_full_unstemmed Coverage and Characteristics of the Affymetrix GeneChip Human Mapping 100K SNP Set
title_short Coverage and Characteristics of the Affymetrix GeneChip Human Mapping 100K SNP Set
title_sort coverage and characteristics of the affymetrix genechip human mapping 100k snp set
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1456318/
https://www.ncbi.nlm.nih.gov/pubmed/16680197
http://dx.doi.org/10.1371/journal.pgen.0020067
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