title: Quality control parameters on a large dataset of regionally dissected human control brains for whole genome expression studies.
abstract: We are building an open-access database of regional human brain expression designed to allow the genome-wide assessment of genetic variability on expression. Array and RNA sequencing technologies make assessment of genome-wide expression possible. Human brain tissue is a challenging source for this work because it can only be obtained several and variable hours post-mortem and after varying agonal states. These variables alter RNA integrity in a complex manner. In this report, we assess the effect of post-mortem delay, agonal state and age on gene expression, and the utility of pH and RNA integrity number as predictors of gene expression as measured on 1266 Affymetrix Exon Arrays. We assessed the accuracy of the array data using QuantiGene, as an independent non-PCR-based method. These quality control parameters will allow database users to assess data accuracy. We report that within the parameters of this study post-mortem delay, agonal state and age have little impact on array quality, array data are robust to variable RNA integrity, and brain pH has only a small effect on array performance. QuantiGene gave very similar expression profiles as array data. This study is the first step in our initiative to make human, regional brain expression freely available.
authors.affiliation: Reta Lilla Weston Laboratories and Departments of Molecular Neuroscience, UCL Institute of Neurology, London, UK.
authors.forename: Daniah
authors.initials: D
authors.lastname: Trabzuni
authors.forename: Mina
authors.initials: M
authors.lastname: Ryten
authors.forename: Robert
authors.initials: R
authors.lastname: Walker
authors.forename: Colin
authors.initials: C
authors.lastname: Smith
authors.forename: Sabaena
authors.initials: S
authors.lastname: Imran
authors.forename: Adaikalavan
authors.initials: A
authors.lastname: Ramasamy
authors.forename: Michael E
authors.initials: ME
authors.lastname: Weale
authors.forename: John
authors.initials: J
authors.lastname: Hardy
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000375:Aging / Q000502:physiology; D001923:Brain Chemistry / Q000235:genetics*; D002423:Cause of Death; D018076:DNA, Complementary / Q000235:genetics; D030541:Databases, Genetic / Q000592:standards*; D005091:Exons / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods / Q000592:standards*; D006801:Humans; D006863:Hydrogen-Ion Concentration; D008297:Male; D046228:Microarray Analysis; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D011786:Quality Control; D012313:RNA / Q000032:analysis / Q000235:genetics / Q000302:isolation & purification; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012727:Sex Characteristics; D014015:Tissue Banks; D006113:United Kingdom; D014481:United States; D055815:Young Adult
chemical_list: D018076:DNA, Complementary; D012313:RNA