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Genotyping DNA pools on microarrays: Tackling the QTL problem of large samples and large numbers of SNPs
BACKGROUND: Quantitative trait locus (QTL) theory predicts that genetic influence on complex traits involves multiple genes of small effect size. To detect QTL associations of small effect size, large samples and systematic screens of thousands of DNA markers are required. An efficient solution is t...
Autores principales: | , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2005
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1079828/ https://www.ncbi.nlm.nih.gov/pubmed/15811185 http://dx.doi.org/10.1186/1471-2164-6-52 |
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author | Meaburn, Emma Butcher, Lee M Liu, Lin Fernandes, Cathy Hansen, Valerie Al-Chalabi, Ammar Plomin, Robert Craig, Ian Schalkwyk, Leonard C |
author_facet | Meaburn, Emma Butcher, Lee M Liu, Lin Fernandes, Cathy Hansen, Valerie Al-Chalabi, Ammar Plomin, Robert Craig, Ian Schalkwyk, Leonard C |
author_sort | Meaburn, Emma |
collection | PubMed |
description | BACKGROUND: Quantitative trait locus (QTL) theory predicts that genetic influence on complex traits involves multiple genes of small effect size. To detect QTL associations of small effect size, large samples and systematic screens of thousands of DNA markers are required. An efficient solution is to genotype case and control DNA pools using SNP microarrays. We demonstrate that this is practical using DNA pools of 100 individuals. RESULTS: Using standard microarray protocols for the Affymetrix GeneChip(® )Mapping 10 K Array Xba 131, we show that relative allele signal (RAS) values provide a quantitative index of allele frequencies in pooled DNA that correlate 0.986 with allele frequencies for 104 SNPs that were genotyped individually for 100 individuals. The sensitivity of the assay was demonstrated empirically in a spiking experiment in which 15% and 20% of one individual's DNA was added to a DNA pool. CONCLUSION: We conclude that this approach, which we call SNP-MaP (SNP microarrays and pooling), is rapid, cost effective and promises to be a valuable initial screening method in the hunt for QTLs. |
format | Text |
id | pubmed-1079828 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2005 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-10798282005-04-15 Genotyping DNA pools on microarrays: Tackling the QTL problem of large samples and large numbers of SNPs Meaburn, Emma Butcher, Lee M Liu, Lin Fernandes, Cathy Hansen, Valerie Al-Chalabi, Ammar Plomin, Robert Craig, Ian Schalkwyk, Leonard C BMC Genomics Research Article BACKGROUND: Quantitative trait locus (QTL) theory predicts that genetic influence on complex traits involves multiple genes of small effect size. To detect QTL associations of small effect size, large samples and systematic screens of thousands of DNA markers are required. An efficient solution is to genotype case and control DNA pools using SNP microarrays. We demonstrate that this is practical using DNA pools of 100 individuals. RESULTS: Using standard microarray protocols for the Affymetrix GeneChip(® )Mapping 10 K Array Xba 131, we show that relative allele signal (RAS) values provide a quantitative index of allele frequencies in pooled DNA that correlate 0.986 with allele frequencies for 104 SNPs that were genotyped individually for 100 individuals. The sensitivity of the assay was demonstrated empirically in a spiking experiment in which 15% and 20% of one individual's DNA was added to a DNA pool. CONCLUSION: We conclude that this approach, which we call SNP-MaP (SNP microarrays and pooling), is rapid, cost effective and promises to be a valuable initial screening method in the hunt for QTLs. BioMed Central 2005-04-05 /pmc/articles/PMC1079828/ /pubmed/15811185 http://dx.doi.org/10.1186/1471-2164-6-52 Text en Copyright © 2005 Meaburn et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Meaburn, Emma Butcher, Lee M Liu, Lin Fernandes, Cathy Hansen, Valerie Al-Chalabi, Ammar Plomin, Robert Craig, Ian Schalkwyk, Leonard C Genotyping DNA pools on microarrays: Tackling the QTL problem of large samples and large numbers of SNPs |
title | Genotyping DNA pools on microarrays: Tackling the QTL problem of large samples and large numbers of SNPs |
title_full | Genotyping DNA pools on microarrays: Tackling the QTL problem of large samples and large numbers of SNPs |
title_fullStr | Genotyping DNA pools on microarrays: Tackling the QTL problem of large samples and large numbers of SNPs |
title_full_unstemmed | Genotyping DNA pools on microarrays: Tackling the QTL problem of large samples and large numbers of SNPs |
title_short | Genotyping DNA pools on microarrays: Tackling the QTL problem of large samples and large numbers of SNPs |
title_sort | genotyping dna pools on microarrays: tackling the qtl problem of large samples and large numbers of snps |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1079828/ https://www.ncbi.nlm.nih.gov/pubmed/15811185 http://dx.doi.org/10.1186/1471-2164-6-52 |
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