Sequence Polymorphisms Cause Many False cis eQTLs
| Autor: | Jan-Peter Nap, Ritsert C. Jansen, Peter Terpstra, Rudi Alberts, Yang Li, Rainer Breitling |
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| Přispěvatelé: | Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Bioinformatics, Faculteit Medische Wetenschappen/UMCG |
| Jazyk: | angličtina |
| Rok vydání: | 2007 |
| Předmět: |
Microarray
Quantitative Trait Loci lcsh:Medicine Genome-wide association study Genomics Genetics and Genomics/Complex Traits Quantitative trait locus Biology Polymorphism Single Nucleotide Mice Gene mapping Animals Humans Lymphocytes RNA Messenger lcsh:Science Gene Oligonucleotide Array Sequence Analysis Genetics Analysis of Variance Polymorphism Genetic Multidisciplinary Base Sequence lcsh:R Chromosome Mapping Reproducibility of Results Genetics and Genomics/Gene Expression Phenotype Expression quantitative trait loci lcsh:Q DNA microarray Research Article Genome-Wide Association Study |
| Zdroj: | PLoS ONE, Vol 2, Iss 7, p e622 (2007) PLoS ONE, 2(7):622, 132-136. PUBLIC LIBRARY SCIENCE PLoS ONE |
| ISSN: | 1932-6203 |
| Popis: | Many investigations have reported the successful mapping of quantitative trait loci (QTLs) for gene expression phenotypes (eQTLs). Local eQTLs, where expression phenotypes map to the genes themselves, are of especially great interest, because they are direct candidates for previously mapped physiological QTLs. Here we show that many mapped local eQTLs in genetical genomics experiments do not reflect actual expression differences caused by sequence polymorphisms in cis-acting factors changing mRNA levels. Instead they indicate hybridization differences caused by sequence polymorphisms in the mRNA region that is targeted by the microarray probes. Many such polymorphisms can be detected by a sensitive and novel statistical approach that takes the individual probe signals into account. Applying this approach to recent mouse and human eQTL data, we demonstrate that indeed many local eQTLs are falsely reported as "cis-acting'' or "cis'' and can be successfully detected and eliminated with this approach. |
| Databáze: | OpenAIRE |
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