| Quantitative trait prediction based on genetic marker-array data, a simulation study. | |
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MedLine Citation:
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PMID: 21285022 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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MOTIVATION: Using simulation studies for quantitative trait loci (QTL), we evaluate the prediction quality of regression models that include as covariates single-nucleotide polymorphism (SNP) genetic markers which did not achieve genome-wide significance in the original genome-wide association study, but were among the SNPs with the smallest P-value for the selected association test. We compare the results of such regression models to the standard approach which is to include only SNPs that achieve genome-wide significance. Using mean square prediction error as the model metric, our simulation results suggest that by using the coefficient of determination (R(2)) value as a guideline to increase or reduce the number of SNPs included in the regression model, we can achieve better prediction quality than the standard approach. However, important parameters such as trait heritability, the approximate number of QTLs, etc. have to be determined from previous studies or have to be estimated accurately. |
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Authors:
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Wai-Ki Yip; Christoph Lange |
Publication Detail:
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Type: Journal Article; Research Support, N.I.H., Extramural Date: 2011-01-31 |
Journal Detail:
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Title: Bioinformatics (Oxford, England) Volume: 27 ISSN: 1367-4811 ISO Abbreviation: Bioinformatics Publication Date: 2011 Mar |
Date Detail:
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Created Date: 2011-03-10 Completed Date: 2011-05-31 Revised Date: 2012-10-09 |
Medline Journal Info:
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Nlm Unique ID: 9808944 Medline TA: Bioinformatics Country: England |
Other Details:
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Languages: eng Pagination: 745-8 Citation Subset: IM |
Affiliation:
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Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA. wkyip@hsph.harvard.edu |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Chromosome Mapping
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methods Computer Simulation Genetic Markers Genome-Wide Association Study Genotype Humans Inheritance Patterns Models, Genetic* Phenotype Polymorphism, Single Nucleotide* Quantitative Trait Loci* Regression Analysis |
| Grant Support | |
ID/Acronym/Agency:
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R01 MH087590/MH/NIMH NIH HHS; R01 MH087590-03/MH/NIMH NIH HHS; R01MH081862/MH/NIMH NIH HHS; R01MH087590/MH/NIMH NIH HHS |
| Chemical | |
Reg. No./Substance:
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0/Genetic Markers |
| Comments/Corrections | |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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