Quality control for microarray analysis of human brain samples: The impact of postmortem factors, RNA characteristics, and histopathology.

Author(s): Weis S, Llenos I C, Dulay J R, Elashoff M, Martinez-Murillo F, Miller C L

Publication: J Neurosci Methods, 2007, Vol. 165, Page 198

PubMed ID: 17628689 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this paper was to identify predictive factors, such as preanalytical variables (age, gender, diagnosis, postmortem interval, time at room temperature, brain pH) and RNA electropherogram characteristics, of cDNA microarray performance using RNA extracted from postmortem brain specimens. The authors evaluated gray matter and white matter from each pole of the brain (occipital and frontal).

   Summary of Findings:

   The quality of microarray results, as measured by percent positive call rate, were independent of all premortem variables. However, postmortem interval and time at room temperature had a significant and negative influence on microarray quality, although results were brain region specific. While 18S/baseline ratio and RIN were the most accurate means of identifying RNA of unacceptable and acceptable quality, respectively, no single measurement was an appropriate predictor of postmortem factor influence on microarray quality.

   Biospecimens

   • Tissue - Brain

   Preservative Types

   • None (Fresh)

   Diagnoses:

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

   Platform:

   Analyte	Technology Platform
   RNA	DNA microarray
   RNA	Automated electrophoresis/Bioanalyzer

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Preaquisition	Patient age	19 - 67
   Preaquisition	Patient gender	Female Male
   Biospecimen Acquisition	Organ measurements	1170g - 1698g
   Preaquisition	Postmortem interval	3 - 200 h
   Biospecimen Aliquots and Components	pH	Brain pH 5.68 - 7.03
   Storage	Time at room temperature	2 - 19 h
   Preaquisition	Diagnosis/ patient condition	Cause of death Alcohol abuse Street drug abuse Prescription drugs Psychosis Problems in utero Problems during birth Problems in childhood development

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2. Study Purpose

   The purpose of this study was to determine if brain pH is correlated to disease state, necrosis, or postmortem interval.

   Summary of Findings:

   Brain pH was significantly lower in cases with noted necrosis, and in patients diagnosed with schizophrenia and bipolar disorder. Brain pH was also negatively correlated to postmortem interval although the correlation coefficient was notably low.

   Biospecimens

   • Tissue - Brain

   Preservative Types

   • None (Fresh)

   Diagnoses:

   • Normal
   • Depression
   • Bipolar Disorder
   • Schizophrenia

   Platform:

   Analyte	Technology Platform
   RNA	DNA microarray
   RNA	Automated electrophoresis/Bioanalyzer

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Aliquots and Components	pH	5.68-7.03
   Preaquisition	Diagnosis/ patient condition	Schizophrenia Bipolar disorder Depression No history of mental illness

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