Methodological considerations for gene expression profiling of human brain.

Author(s): Atz M, Walsh D, Cartagena P, Li J, Evans S, Choudary P, Overman K, Stein R, Tomita H, Potkin S, Myers R, Watson SJ, Jones EG, Akil H, Bunney WE Jr, Vawter MP

Publication: J Neurosci Methods, 2007, Vol. 163, Page 295

PubMed ID: 17512057 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to identify potential sources of variability in microarray gene expression results due to variations in clinical parameters (agonal duration), tissue quality (brain pH, postmortem interval (PMI) and RNA quality.

   Summary of Findings:

   The authors report a significant correlation between rapidity of death and brain pH and between brain pH, RNA quality, and the quality of microarray performance. Postmortem interval and biospecimen storage duration showed no relationship to RNA quality. Microarray data show that mitochondrial gene overrepresentation was correlated with rapidity of death and brain pH.

   Biospecimens

   • Tissue - Brain

   Preservative Types

   • Frozen

   Diagnoses:

   • Bipolar Disorder
   • Schizophrenia
   • Autopsy
   • Not specified
   • Depression

   Platform:

   Analyte	Technology Platform
   RNA	Automated electrophoresis/Bioanalyzer
   RNA	DNA microarray
   RNA	Electrophoresis

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Preaquisition	Rapidity of death	Terminal phase of 10 min or fewer > 10 min terminal phase
   Storage	Storage duration	2.9 +/- 3.3 years
   Preaquisition	Postmortem interval	24.1 +/- 8.6 h
   Biospecimen Aliquots and Components	pH	Brain pH 6.3 - 7.26

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2. Study Purpose

   The purpose of this study was to evaluate the influence of freeze-thaw cycling on RNA quality of postmortem brain specimens.

   Summary of Findings:

   Significant RNA degradation was observed after 2 freeze thaw cycles, detectable by RIN but not 28S/18S ratio. Poorer quality total RNA was associated with lower brain pH and shorter cRNA transcripts.

   Biospecimens

   • Tissue - Brain

   Preservative Types

   • Frozen

   Diagnoses:

   • Bipolar Disorder
   • Schizophrenia
   • Autopsy
   • Not specified
   • Depression

   Platform:

   Analyte	Technology Platform
   RNA	Automated electrophoresis/Bioanalyzer
   RNA	DNA microarray
   RNA	Electrophoresis

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Aliquots and Components	pH	Brain pH < 6.6 Brain pH > 6.6
   Storage	Freeze/thaw cycling	No freeze/thaw events 1 Freeze/thaw cycle 2 Freeze/thaw cycles

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