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PubMed · 16690034

SNPs on chips: the hidden genetic code in expression arrays.

Elzbieta Sliwerska·Fan Meng·Terence P Speed·Edward G Jones·William E Bunney·Huda Akil·Stanley J Watson·Margit Burmeister
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Abstract

Gene expression microarray analysis in postmortem brains is one of the fastest growing fields of psychiatric research. Here we show that common polymorphisms (SNPs) present on probe sets can masquerade as significant "gene expression" differences. After first observing this artifact in the Catechol-O-methyl transferase (COMT) gene, we replicate the finding in two additional genes predicted to show this artifact. Many Affymetrix chips contain thousands of SNPs that are both common and in the central probe region affecting hybridization, and thus have the potential to confound expression analysis.

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Analysis of VarianceCatechol O-MethyltransferaseGene ExpressionGenetic CodeGenotypeHumansOligonucleotide Array Sequence AnalysisPolymorphism, GeneticJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov't

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Elzbieta Sliwerska, Fan Meng, Terence P Speed, Edward G Jones, William E Bunney, Huda Akil, Stanley J Watson, Margit Burmeister. 2006-05-11. SNPs on chips: the hidden genetic code in expression arrays.. https://doi.org/10.1016/j.biopsych.2006.01.023

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