Methodological considerations for gene expression profiling of human brain

Mary Atz, David Walsh, Preston Cartagena, Jun Li, Simon Evans, Prabhakara V Choudary, Kevin Overman, Richard Stein, Hiro Tomita, Steven Potkin, Rick Myers, Stanley J. Watson, E. G. Jones, Huda Akil, William E. Bunney, Marquis P. Vawter

Research output: Contribution to journalArticle

90 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)295-309
Number of pages15
JournalJournal of Neuroscience Methods
Volume163
Issue number2
DOIs
StatePublished - Jul 30 2007

Fingerprint

Gene Expression Profiling
RNA
Gene Expression
Brain
Transcriptome
Mitochondrial Genes
RNA Stability
Quality Control
Psychiatry
Genes

Keywords

  • Agonal factors
  • Gene expression
  • Microarray
  • pH
  • Postmortem brain tissue
  • RNA quality

ASJC Scopus subject areas

  • Neuroscience(all)

Cite this

Atz, M., Walsh, D., Cartagena, P., Li, J., Evans, S., Choudary, P. V., ... Vawter, M. P. (2007). Methodological considerations for gene expression profiling of human brain. Journal of Neuroscience Methods, 163(2), 295-309. https://doi.org/10.1016/j.jneumeth.2007.03.022

Methodological considerations for gene expression profiling of human brain. / Atz, Mary; Walsh, David; Cartagena, Preston; Li, Jun; Evans, Simon; Choudary, Prabhakara V; Overman, Kevin; Stein, Richard; Tomita, Hiro; Potkin, Steven; Myers, Rick; Watson, Stanley J.; Jones, E. G.; Akil, Huda; Bunney, William E.; Vawter, Marquis P.

In: Journal of Neuroscience Methods, Vol. 163, No. 2, 30.07.2007, p. 295-309.

Research output: Contribution to journalArticle

Atz, M, Walsh, D, Cartagena, P, Li, J, Evans, S, Choudary, PV, Overman, K, Stein, R, Tomita, H, Potkin, S, Myers, R, Watson, SJ, Jones, EG, Akil, H, Bunney, WE & Vawter, MP 2007, 'Methodological considerations for gene expression profiling of human brain', Journal of Neuroscience Methods, vol. 163, no. 2, pp. 295-309. https://doi.org/10.1016/j.jneumeth.2007.03.022
Atz, Mary ; Walsh, David ; Cartagena, Preston ; Li, Jun ; Evans, Simon ; Choudary, Prabhakara V ; Overman, Kevin ; Stein, Richard ; Tomita, Hiro ; Potkin, Steven ; Myers, Rick ; Watson, Stanley J. ; Jones, E. G. ; Akil, Huda ; Bunney, William E. ; Vawter, Marquis P. / Methodological considerations for gene expression profiling of human brain. In: Journal of Neuroscience Methods. 2007 ; Vol. 163, No. 2. pp. 295-309.
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