title: Methodological considerations for gene expression profiling of human brain.
abstract: Gene expression profiles of postmortem brain tissue represent important resources for understanding neuropsychiatric illnesses. The impact(s) of quality covariables on the analysis and results of gene expression studies are important questions. This paper addressed critical variables which might affect gene expression in two brain regions. Four broad groups of quality indicators in gene expression profiling studies (clinical, tissue, RNA, and microarray quality) were identified. These quality control indicators were significantly correlated, however one quality variable did not account for the total variance in microarray gene expression. The data showed that agonal factors and low pH correlated with decreased integrity of extracted RNA in two brain regions. These three parameters also modulated the significance of alterations in mitochondrial-related genes. The average F-ratio summaries across all transcripts showed that RNA degradation from the AffyRNAdeg program accounted for higher variation than all other quality factors. Taken together, these findings confirmed prior studies, which indicated that quality parameters including RNA integrity, agonal factors, and pH are related to differences in gene expression profiles in postmortem brain. Individual candidate genes can be evaluated with these quality parameters in post hoc analysis to help strengthen the relevance to psychiatric disorders. We find that clinical, tissue, RNA, and microarray quality are all useful variables for collection and consideration in study design, analysis, and interpretation of gene expression results in human postmortem studies.
authors.affiliation: Department of Psychiatry and Human Behavior, College of Medicine, University of California, Irvine, CA, USA.
authors.forename: Mary
authors.initials: M
authors.lastname: Atz
authors.forename: David
authors.initials: D
authors.lastname: Walsh
authors.forename: Preston
authors.initials: P
authors.lastname: Cartagena
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.forename: Simon
authors.initials: S
authors.lastname: Evans
authors.forename: Prabhakara
authors.initials: P
authors.lastname: Choudary
authors.forename: Kevin
authors.initials: K
authors.lastname: Overman
authors.forename: Richard
authors.initials: R
authors.lastname: Stein
authors.forename: Hiro
authors.initials: H
authors.lastname: Tomita
authors.forename: Steven
authors.initials: S
authors.lastname: Potkin
authors.forename: Rick
authors.initials: R
authors.lastname: Myers
authors.forename: Stanley J
authors.initials: SJ
authors.lastname: Watson
authors.forename: E G
authors.initials: EG
authors.lastname: Jones
authors.forename: Huda
authors.initials: H
authors.lastname: Akil
authors.forename: William E
authors.initials: WE
authors.lastname: Bunney
authors.forename: Marquis P
authors.initials: MP
authors.lastname: Vawter
mesh_terms: D001921:Brain / Q000378:metabolism*; D001923:Brain Chemistry / Q000235:genetics*; D002531:Cerebellum / Q000737:chemistry / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000235:genetics; D006179:Gyrus Cinguli / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D020925:Hypoxia-Ischemia, Brain / Q000235:genetics / Q000378:metabolism; D001523:Mental Disorders / Q000175:diagnosis / Q000235:genetics / Q000378:metabolism; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011180:Postmortem Changes; D020871:RNA Stability / Q000235:genetics; D012333:RNA, Messenger / Q000032:analysis* / Q000235:genetics*
chemical_list: D012333:RNA, Messenger