Effect of agonal and postmortem factors on gene expression profile

Quality control in microarray analyses of postmortem human brain

Hiroaki Tomita, Marquis P. Vawter, David M. Walsh, Simon J. Evans, Prabhakara V Choudary, Jun Li, Kevin M. Overman, Mary E. Atz, Richard M. Myers, Edward G. Jones, Stanley J. Watson, Huda Akil, William E. Bunney

Research output: Contribution to journalArticle

234 Citations (Scopus)

Abstract

There are major concerns that specific agonal conditions, including coma and hypoxia, might affect ribonucleic acid (RNA) integrity in postmortem brain studies. We report that agonal factors significantly affect RNA integrity and have a major impact on gene expression profiles in microarrays. In contrast to agonal factors, gender, age, and postmortem factors have less effect on gene expression profiles. The Average Correlation Index is proposed as a method for evaluating RNA integrity on the basis of similarity of microarray profiles. Reducing the variance due to agonal factors is critical in investigating small but validated gene expression differences in messenger RNA levels between psychiatric patients and control subjects.

Original languageEnglish (US)
Pages (from-to)346-352
Number of pages7
JournalBiological Psychiatry
Volume55
Issue number4
DOIs
StatePublished - Feb 15 2004

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Microarray Analysis
Transcriptome
Quality Control
RNA
Brain
Age Factors
Coma
Psychiatry
Gene Expression

Keywords

  • Adenine-Uracil-rich elements
  • Bipolar disorder
  • Freezer interval
  • Iron-responsive element
  • Major depressive disorder
  • Postmortem interval

ASJC Scopus subject areas

  • Biological Psychiatry

Cite this

Effect of agonal and postmortem factors on gene expression profile : Quality control in microarray analyses of postmortem human brain. / Tomita, Hiroaki; Vawter, Marquis P.; Walsh, David M.; Evans, Simon J.; Choudary, Prabhakara V; Li, Jun; Overman, Kevin M.; Atz, Mary E.; Myers, Richard M.; Jones, Edward G.; Watson, Stanley J.; Akil, Huda; Bunney, William E.

In: Biological Psychiatry, Vol. 55, No. 4, 15.02.2004, p. 346-352.

Research output: Contribution to journalArticle

Tomita, H, Vawter, MP, Walsh, DM, Evans, SJ, Choudary, PV, Li, J, Overman, KM, Atz, ME, Myers, RM, Jones, EG, Watson, SJ, Akil, H & Bunney, WE 2004, 'Effect of agonal and postmortem factors on gene expression profile: Quality control in microarray analyses of postmortem human brain', Biological Psychiatry, vol. 55, no. 4, pp. 346-352. https://doi.org/10.1016/j.biopsych.2003.10.013
Tomita, Hiroaki ; Vawter, Marquis P. ; Walsh, David M. ; Evans, Simon J. ; Choudary, Prabhakara V ; Li, Jun ; Overman, Kevin M. ; Atz, Mary E. ; Myers, Richard M. ; Jones, Edward G. ; Watson, Stanley J. ; Akil, Huda ; Bunney, William E. / Effect of agonal and postmortem factors on gene expression profile : Quality control in microarray analyses of postmortem human brain. In: Biological Psychiatry. 2004 ; Vol. 55, No. 4. pp. 346-352.
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