Abstract

Schizophrenia and bipolar disorder are serious mental illnesses that affect more than 2% of adults. While large-scale genetics studies have identified genomic regions associated with disease risk, less is known about the molecular mechanisms by which risk alleles with small effects lead to schizophrenia and bipolar disorder. In order to fill this gap between genetics and disease phenotype, we have undertaken a multi-cohort genomics study of postmortem brains from controls, individuals with schizophrenia and bipolar disorder. Here we present a public resource of functional genomic data from the dorsolateral prefrontal cortex (DLPFC; Brodmann areas 9 and 46) of 986 individuals from 4 separate brain banks, including 353 diagnosed with schizophrenia and 120 with bipolar disorder. The genomic data include RNA-seq and SNP genotypes on 980 individuals, and ATAC-seq on 269 individuals, of which 264 are a subset of individuals with RNA-seq. We have performed extensive preprocessing and quality control on these data so that the research community can take advantage of this public resource available on the Synapse platform at http://CommonMind.org.

Alternate abstract:

Measurement(s)genotype • assay for transposase-accessible chromatin using sequencing • transcription profiling assay • bipolar disorder • schizophreniaTechnology Type(s)RNA sequencing • genotyping • ATAC-seqFactor Type(s)postmortem interval • age • biological sex • experimental groupSample Characteristic - OrganismHomo sapiens

Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.9747479

Details

Title
CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder
Author
Hoffman, Gabriel E 1   VIAFID ORCID Logo  ; Bendl, Jaroslav 2 ; Voloudakis, Georgios 2   VIAFID ORCID Logo  ; Montgomery, Kelsey S 3   VIAFID ORCID Logo  ; Sloofman, Laura 2 ; Wang, Ying-Chih 4 ; Shah, Hardik R 4 ; Hauberg, Mads E 2 ; Johnson, Jessica S 5 ; Girdhar, Kiran 2 ; Song, Lingyun 6 ; Fullard, John F 5 ; Kramer, Robin 7 ; Hahn, Chang-Gyu 8 ; Gur, Raquel 9 ; Marenco, Stefano 7   VIAFID ORCID Logo  ; Lipska, Barbara K 7 ; Lewis, David A 10 ; Haroutunian, Vahram 11 ; Hemby, Scott 12 ; Sullivan, Patrick 13 ; Akbarian, Schahram 14   VIAFID ORCID Logo  ; Chess, Andrew 4 ; Buxbaum, Joseph D 15 ; Crawford, Greg E 6 ; Domenici, Enrico 16   VIAFID ORCID Logo  ; Devlin, Bernie 10 ; Sieberts, Solveig K 3   VIAFID ORCID Logo  ; Peters, Mette A 3 ; Roussos, Panos 17   VIAFID ORCID Logo 

 Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Icahn Institute for Data Science and Genomic Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA 
 Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Icahn Institute for Data Science and Genomic Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA 
 Sage Bionetworks, Seattle, Washington, USA 
 Icahn Institute for Data Science and Genomic Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA 
 Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA 
 Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA 
 Human Brain Collection Core, National Institutes of Health, NIMH, Bethesda, Maryland, USA 
 Neuropsychiatric Signaling Program, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA 
 Neuropsychiatry Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA 
10  Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA 
11  Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Psychiatry, JJ Peters VA Medical Center, Bronx, New York, USA 
12  Department of Basic Pharmaceutical Sciences, Fred Wilson School of Pharmacy at High Point University, North Carolina, USA 
13  Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA 
14  Division of Psychiatric Epigenomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA 
15  Seaver Autism for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA 
16  Laboratory of Neurogenomic Biomarkers, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy 
17  Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Icahn Institute for Data Science and Genomic Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Psychiatry, JJ Peters VA Medical Center, Bronx, New York, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA 
Pages
1-14
Publication year
2019
Publication date
Dec 2019
Publisher
Nature Publishing Group
e-ISSN
20524463
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2296636202
Copyright
© 2019. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.