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

doi:10.1016/j.biopsych.2003.10.013

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

MED - Medical Sciences

Research output: Contribution to journal › Review article › peer-review

268 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 language	English
Pages (from-to)	346-352
Number of pages	7
Journal	Biological Psychiatry
Volume	55
Issue number	4
DOIs	https://doi.org/10.1016/j.biopsych.2003.10.013
Publication status	Published - 2004 Feb 15

Keywords

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

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10.1016/j.biopsych.2003.10.013

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Tomita, H., Vawter, M. P., Walsh, D. M., Evans, S. J., Choudary, P. V., Li, J., Overman, K. M., Atz, M. E., Myers, R. M., Jones, E. G., Watson, S. J., Akil, H., & Bunney, W. E. (2004). Effect of agonal and postmortem factors on gene expression profile: Quality control in microarray analyses of postmortem human brain. Biological Psychiatry, 55(4), 346-352. https://doi.org/10.1016/j.biopsych.2003.10.013

@article{2966a8d482a4495596796dc0c5b88335,

title = "Effect of agonal and postmortem factors on gene expression profile: Quality control in microarray analyses of postmortem human brain",

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.",

keywords = "Adenine-Uracil-rich elements, Bipolar disorder, Freezer interval, Iron-responsive element, Major depressive disorder, Postmortem interval",

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

note = "Funding Information: This project was supported by National Institute of Mental Health (NIMH) Conte Center Grant P50 MH60398, the Pritzker Neuropsychiatric Disorders Research Consortium, the William Lion Penzner Foundation (UCI), the Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), the W.M. Keck Foundation (EGJ), and NIMH Program Project MH42251 (SJW and HA). ",

year = "2004",

month = feb,

day = "15",

doi = "10.1016/j.biopsych.2003.10.013",

language = "English",

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pages = "346--352",

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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

TY - JOUR

T1 - Effect of agonal and postmortem factors on gene expression profile

T2 - Quality control in microarray analyses of postmortem human brain

AU - Tomita, Hiroaki

AU - Vawter, Marquis P.

AU - Walsh, David M.

AU - Evans, Simon J.

AU - Choudary, Prabhakara V.

AU - Li, Jun

AU - Overman, Kevin M.

AU - Atz, Mary E.

AU - Myers, Richard M.

AU - Jones, Edward G.

AU - Watson, Stanley J.

AU - Akil, Huda

AU - Bunney, William E.

N1 - Funding Information: This project was supported by National Institute of Mental Health (NIMH) Conte Center Grant P50 MH60398, the Pritzker Neuropsychiatric Disorders Research Consortium, the William Lion Penzner Foundation (UCI), the Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), the W.M. Keck Foundation (EGJ), and NIMH Program Project MH42251 (SJW and HA).

PY - 2004/2/15

Y1 - 2004/2/15

N2 - 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.

AB - 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.

KW - Adenine-Uracil-rich elements

KW - Bipolar disorder

KW - Freezer interval

KW - Iron-responsive element

KW - Major depressive disorder

KW - Postmortem interval

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U2 - 10.1016/j.biopsych.2003.10.013

DO - 10.1016/j.biopsych.2003.10.013

M3 - Review article

C2 - 14960286

AN - SCOPUS:10744228401

SN - 0006-3223

VL - 55

SP - 346

EP - 352

JO - Biological Psychiatry

JF - Biological Psychiatry

IS - 4

ER -

Effect of agonal and postmortem factors on gene expression profile: Quality control in microarray analyses of postmortem human brain

Abstract

Keywords

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