TY - JOUR
T1 - Methodological considerations for gene expression profiling of human brain
AU - Atz, Mary
AU - Walsh, David
AU - Cartagena, Preston
AU - Li, Jun
AU - Evans, Simon
AU - Choudary, Prabhakara
AU - Overman, Kevin
AU - Stein, Richard
AU - Tomita, Hiro
AU - Potkin, Steven
AU - Myers, Rick
AU - Watson, Stanley J.
AU - Jones, E. G.
AU - Akil, Huda
AU - Bunney, William E.
AU - Vawter, Marquis P.
N1 - Funding Information:
We acknowledge Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kathleen Burke, Sharon Burke, Xiaohong Fan, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Family Philanthropic Fund, William Lion Penzner Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). “The authors are members of a research consortium supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. An agreement exists between the fund and the University of Michigan, Stanford University, the Weill Medical College of Cornell University, the Universities of California at Davis, and at Irvine, to encourage the development of appropriate findings for research and clinical applications”.
Copyright:
Copyright 2008 Elsevier B.V., All rights reserved.
PY - 2007/7/30
Y1 - 2007/7/30
N2 - 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.
AB - 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.
KW - Agonal factors
KW - Gene expression
KW - Microarray
KW - Postmortem brain tissue
KW - RNA quality
KW - pH
UR - http://www.scopus.com/inward/record.url?scp=34249889834&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=34249889834&partnerID=8YFLogxK
U2 - 10.1016/j.jneumeth.2007.03.022
DO - 10.1016/j.jneumeth.2007.03.022
M3 - Article
C2 - 17512057
AN - SCOPUS:34249889834
VL - 163
SP - 295
EP - 309
JO - Journal of Neuroscience Methods
JF - Journal of Neuroscience Methods
SN - 0165-0270
IS - 2
ER -