Methodological considerations for gene expression profiling of human brain.
paper
Cited
Public
Unavailable
- Authors
- Atz, Mary; Walsh, David; Cartagena, Preston; Li, Jun; Evans, Simon; Choudary, Prabhakara; Overman, Kevin; Stein, Richard; Tomita, Hiro; Potkin, Steven; Myers, Rick; Watson, Stanley J; Jones, E G; Akil, Huda; Bunney, William E; Vawter, Marquis P; Members of National Institute of Mental Health Conte Center and Pritzker Neuropsychiatric Disorders Research Consortium
- Year
- 2007
- Journal
- Journal of neuroscience methods
- PMID
- 17512057
- DOI
- 10.1016/j.jneumeth.2007.03.022
- PMCID
- PMC3835340
Gene expression profiles of postmortem brain tissue represent important resources for understanding neuropsychiatric illnesses. The impact(s) of quality covariables on the analysis and results of gene expression studies are important questions. This paper addressed critical variables which might affect gene expression in two brain regions. Four broad groups of quality indicators in gene expression profiling studies (clinical, tissue, RNA, and microarray quality) were identified. These quality control indicators were significantly correlated, however one quality variable did not account for the total variance in microarray gene expression. The data showed that agonal factors and low pH correlated with decreased integrity of extracted RNA in two brain regions. These three parameters also modulated the significance of alterations in mitochondrial-related genes. The average F-ratio summaries across all transcripts showed that RNA degradation from the AffyRNAdeg program accounted for higher variation than all other quality factors. Taken together, these findings confirmed prior studies, which indicated that quality parameters including RNA integrity, agonal factors, and pH are related to differences in gene expression profiles in postmortem brain. Individual candidate genes can be evaluated with these quality parameters in post hoc analysis to help strengthen the relevance to psychiatric disorders. We find that clinical, tissue, RNA, and microarray quality are all useful variables for collection and consideration in study design, analysis, and interpretation of gene expression results in human postmortem studies.
No figures extracted from this document.
No chunks β full text not yet ingested.
No entities extracted from this document yet.
No uploaded files.
Not in any collection.
No citations found.
In this knowledge base
External
| Title | Authors | Journal | Year | Link |
|---|---|---|---|---|
| Effect of Different Staining Methods on Brain Cryosections. | Zhou Y et al. | β | 2024 | β |
| Neurotransmission-related gene expression in the frontal pole is altered in subjects with bipolar disorder and schizophrenia. | Medina AM et al. | β | 2023 | β |
| The influence of tissue pH and RNA integrity number on gene expression of human postmortem brain. | Miyahara K et al. | β | 2023 | β |
| Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection. | Almeida D et al. | β | 2022 | β |
| Agonal Factors Distort Gene-Expression Patterns in Human Postmortem Brains. | Dai J et al. | β | 2021 | β |
| A Sensitization-Free Dimethyl Fumarate Prodrug, Isosorbide Di-(Methyl Fumarate), Provides a Topical Treatment Candidate for Psoriasis. | Bojanowski K et al. | β | 2021 | β |
| Declining RNA integrity in control autopsy brain tissue is robustly and asymmetrically associated with selective neuronal mRNA signal loss | Johnson ES et al. | β | 2021 | β |
| Matching of the postmortem hypothalamus from patients and controls. | Swaab DF et al. | β | 2021 | β |
| Pathology and Biobanking. | Talu CK et al. | β | 2020 | β |
| Identification of potential diagnostic biomarkers for Parkinson's disease. | Jiang F et al. | β | 2019 | β |
| The Effects of Surgical Antiseptics and Time Delays on RNA Isolated From Human and Rodent Peripheral Nerves. | Wilcox M et al. | β | 2019 | β |
| Brain donation at autopsy: clinical characterization and toxicologic analyses. | Mighdoll MI et al. | β | 2018 | β |
| Inference of cell type content from human brain transcriptomic datasets illuminates the effects of age, manner of death, dissection, and psychiatric diagnosis. | Hagenauer MH et al. | β | 2018 | β |
| Mitochondrial Complex I Deficiency in Schizophrenia and Bipolar Disorder and Medication Influence. | Rollins BL et al. | β | 2018 | β |
| The art of matching brain tissue from patients and controls for postmortem research. | Bao AM et al. | β | 2018 | β |
| The Netherlands Brain Bank for Psychiatry. | Rademaker MC et al. | β | 2018 | β |
| Concordance analysis of microarray studies identifies representative gene expression changes in Parkinson's disease: a comparison of 33 human and animal studies. | Oerton E et al. | β | 2017 | β |
| Neuropathological and transcriptomic characteristics of the aged brain. | Miller JA et al. | β | 2017 | β |
| Blood gene expression studies in migraine: Potential and caveats. | Gerring Z et al. | β | 2016 | β |
| Characterization of gene expression profiling of mouse tissues obtained during the postmortem interval. | Sobue S et al. | β | 2016 | β |
| Characterization of RNA isolated from eighteen different human tissues: results from a rapid human autopsy program. | Walker DG et al. | β | 2016 | β |
| Improving Ribosomal RNA Integrity in Surgically Resected Human Brain Tumor Biopsies. | Castells Domingo X et al. | β | 2016 | β |
| Molecular Risk Factors for Schizophrenia. | Modai S et al. | β | 2016 | β |
| Translational Research in Pediatrics IV: Solid Tissue Collection and Processing. | Gillio-Meina C et al. | β | 2016 | β |
| Biobanking for Personalized Medicine. | Liu A et al. | β | 2015 | β |
| Elevated Hippocampal Cholinergic Neurostimulating Peptide precursor protein (HCNP-pp) mRNA in the amygdala in major depression. | Bassi S et al. | β | 2015 | β |
| NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases. | Bagewadi S et al. | β | 2015 | β |
| SNAP-25a/b Isoform Levels in Human Brain Dorsolateral Prefrontal Cortex and Anterior Cingulate Cortex. | Thompson PM et al. | β | 2015 | β |
| Comorbidities, confounders, and the white matter transcriptome in chronic alcoholism. | Sutherland GT et al. | β | 2014 | β |
| Integrative RNA-seq and microarray data analysis reveals GC content and gene length biases in the psoriasis transcriptome. | Swindell WR et al. | β | 2014 | β |
| The alternative splicing of the apolipoprotein E gene is unperturbed in the brains of Alzheimer's disease patients. | Mills JD et al. | β | 2014 | β |
| The procurement, storage, and quality assurance of frozen blood and tissue biospecimens in pathology, biorepository, and biobank settings. | Shabihkhani M et al. | β | 2014 | β |
| Analysis of miR-137 expression and rs1625579 in dorsolateral prefrontal cortex. | Guella I et al. | β | 2013 | β |
| Behavior genetics: past, present, future. | Jaffee SR et al. | β | 2013 | β |
| Enhanced striatal Ξ²1-adrenergic receptor expression following hormone loss in adulthood is programmed by both early sexual differentiation and puberty: a study of humans and rats. | Meitzen J et al. | β | 2013 | β |
| G protein-linked signaling pathways in bipolar and major depressive disorders. | Tomita H et al. | β | 2013 | β |
| Quality control of RNA preservation and extraction from paraffin-embedded tissue: implications for RT-PCR and microarray analysis. | Kashofer K et al. | β | 2013 | β |
| Review: activation patterns of microglia and their identification in the human brain. | Boche D et al. | β | 2013 | β |
| RNA-Seq and human complex diseases: recent accomplishments and future perspectives. | Costa V et al. | β | 2013 | β |
| Small RNA sequencing-microarray analyses in Parkinson leukocytes reveal deep brain stimulation-induced splicing changes that classify brain region transcriptomes. | Soreq L et al. | β | 2013 | β |
| Stress-response pathways are altered in the hippocampus of chronic alcoholics. | McClintick JN et al. | β | 2013 | β |
| Alternative splicing of mRNA in the molecular pathology of neurodegenerative diseases. | Mills JD et al. | β | 2012 | β |
| Blood-based gene expression profiles models for classification of subsyndromal symptomatic depression and major depressive disorder. | Yi Z et al. | β | 2012 | β |
| Brain expression genome-wide association study (eGWAS) identifies human disease-associated variants. | Zou F et al. | β | 2012 | β |
| Brazilian psychiatric brain bank: a new contribution tool to network studies. | de Oliveira KC et al. | β | 2012 | β |
| Concise review: Patient-derived olfactory stem cells: new models for brain diseases. | Mackay-Sim A | β | 2012 | β |
| Defective dentate nucleus GABA receptors in essential tremor. | Paris-Robidas S et al. | β | 2012 | β |
| Evidence for transcriptional factor dysregulation in the dorsal raphe nucleus of patients with major depressive disorder. | Kerman IA et al. | β | 2012 | β |
| Expression profiling in neuropsychiatric disorders: emphasis on glutamate receptors in bipolar disorder. | Ginsberg SD et al. | β | 2012 | β |
| Gene expression changes in the prefrontal cortex, anterior cingulate cortex and nucleus accumbens of mood disorders subjects that committed suicide. | Sequeira A et al. | β | 2012 | β |
| Influence of liver pathology on markers of postmortem brain tissue quality. | Sheedy D et al. | β | 2012 | β |
| Interleukin-33 upregulation in peripheral leukocytes and CNS of multiple sclerosis patients. | Christophi GP et al. | β | 2012 | β |
| MetaQC: objective quality control and inclusion/exclusion criteria for genomic meta-analysis. | Kang DD et al. | β | 2012 | β |
| Serotonin receptor, SERT mRNA and correlations with symptoms in males with alcohol dependence and suicide. | Thompson PM et al. | β | 2012 | β |
| Sex-specific differences in the dynamics of cocaine- and amphetamine-regulated transcript and nesfatin-1 expressions in the midbrain of depressed suicide victims vs. controls. | Bloem B et al. | β | 2012 | β |
| The first decade and beyond of transcriptional profiling in schizophrenia. | Sequeira PA et al. | β | 2012 | β |
| Altered expression of glutamate signaling, growth factor, and glia genes in the locus coeruleus of patients with major depression. | Bernard R et al. | β | 2011 | β |
| An integrative functional genomics approach for discovering biomarkers in schizophrenia. | Vawter MP et al. | β | 2011 | β |
| Evidence for disease and antipsychotic medication effects in post-mortem brain from schizophrenia patients. | Chan MK et al. | β | 2011 | β |
| Expression analysis of dopaminergic neurons in Parkinson's disease and aging links transcriptional dysregulation of energy metabolism to cell death. | Elstner M et al. | β | 2011 | β |
| Gene expression endophenotypes: a novel approach for gene discovery in Alzheimer's disease. | Ertekin-Taner N | β | 2011 | β |
| Molecular targets of alcohol action: Translational research for pharmacotherapy development and screening. | Gorini G et al. | β | 2011 | β |
| Novel approaches to the study of postmortem brain in psychiatric illness: old limitations and new challenges. | McCullumsmith RE et al. | β | 2011 | β |
| Region-specific in situ hybridization-guided laser-capture microdissection on postmortem human brain tissue coupled with gene expression quantification. | Bernard R et al. | β | 2011 | β |
| RNA integrity in post-mortem samples: influencing parameters and implications on RT-qPCR assays. | Koppelkamm A et al. | β | 2011 | β |
| RT-qPCR study on post-mortem brain samples from patients with major psychiatric disorders: reference genes and specimen characteristics. | Abasolo N et al. | β | 2011 | β |
| Survey of the effect of genetic variations on gene expression in human prefrontal cortex and its application to genetics of psychiatric disorders. | Iwamoto K et al. | β | 2011 | β |
| Understanding the pathogenesis of Alzheimer's disease: will RNA-Seq realize the promise of transcriptomics? | Sutherland GT et al. | β | 2011 | β |
| Whole transcriptome sequencing reveals gene expression and splicing differences in brain regions affected by Alzheimer's disease. | Twine NA et al. | β | 2011 | β |
| Analysis of whole genome biomarker expression in blood and brain. | Rollins B et al. | β | 2010 | β |
| Bioelectromagnetics, complex behaviour and psychotherapeutic potential. | Pooley DT | β | 2010 | β |
| Blood mononuclear cell gene expression signature of postpartum depression. | Segman RH et al. | β | 2010 | β |
| Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways. | Miller JA et al. | β | 2010 | β |
| mRNA profiling in forensic genetics I: Possibilities and limitations. | Vennemann M et al. | β | 2010 | β |
| Postmortem mRNA profiling II: Practical considerations. | Vennemann M et al. | β | 2010 | β |
| Selection of reference gene expression in a schizophrenia brain cohort. | Weickert CS et al. | β | 2010 | β |
| A cross-study transcriptional analysis of Parkinson's disease. | Sutherland GT et al. | β | 2009 | β |
| A functional haplotype implicated in vulnerability to develop cocaine dependence is associated with reduced PDYN expression in human brain. | Yuferov V et al. | β | 2009 | β |
| Gene expression profiling of neurochemically defined regions of the human brain by in situ hybridization-guided laser capture microdissection. | Bernard R et al. | β | 2009 | β |
| Improved RNA preservation for immunolabeling and laser microdissection. | Brown AL et al. | β | 2009 | β |
| Profiling brain expression of the spermidine/spermine N1-acetyltransferase 1 (SAT1) gene in suicide. | Klempan TA et al. | β | 2009 | β |
| Quality control in microarray assessment of gene expression in human airway epithelium. | Raman T et al. | β | 2009 | β |
| Suicide neurobiology. | Ernst C et al. | β | 2009 | β |
| Systematic comparison of RNA extraction techniques from frozen and fresh lung tissues: checkpoint towards gene expression studies. | Muyal JP et al. | β | 2009 | β |
| Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues. | Popova T et al. | β | 2008 | β |
| Genetic factors influencing alcohol dependence. | Mayfield RD et al. | β | 2008 | β |
| Increased lactate levels and reduced pH in postmortem brains of schizophrenics: medication confounds. | Halim ND et al. | β | 2008 | β |
| Influence of evolution in tumor biobanking on the interpretation of translational research. | Barnes RO et al. | β | 2008 | β |
| Microtransplantation of neurotransmitter receptors from postmortem autistic brains to Xenopus oocytes. | Limon A et al. | β | 2008 | β |
| Mitochondrial involvement in psychiatric disorders. | Shao L et al. | β | 2008 | β |
| Shared gene expression alterations in schizophrenia and bipolar disorder. | Shao L et al. | β | 2008 | β |
| The high-affinity niacin receptor HM74A is decreased in the anterior cingulate cortex of individuals with schizophrenia. | Miller CL et al. | β | 2008 | β |
| Sample matching by inferred agonal stress in gene expression analyses of the brain. | Li JZ et al. | β | 2007 | β |