SNPs on chips: the hidden genetic code in expression arrays.
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.
Sliwerska
Elzbieta
E
Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan 48109-2220, USA.
Meng
Fan
F
Speed
Terence P
TP
Jones
Edward G
EG
Bunney
William E
WE
Akil
Huda
H
Watson
Stanley J
SJ
Burmeister
Margit
M
D000704:Analysis of Variance; D002394:Catechol O-Methyltransferase / Q000235:genetics; D015870:Gene Expression / Q000502:physiology*; D005815:Genetic Code; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D011110:Polymorphism, Genetic
D002394:Catechol O-Methyltransferase