ID

45202

Description

Principal Investigator: Joel E. Kleinman, MD, PhD, National Institutes of Health, Bethesda, MD, USA MeSH: Growth and Development,Aging https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000417 This study explores the temporal dynamics and genetic control of transcription and DNA methylation in the human dorsolateral prefrontal cortex in postmortem tissue. This study examines 269 subjects for gene expression (version 1) and 108 subjects for DNA methylation (version 2). The subjects are normal controls without neuropathological and neuropsychiatric diagnosis and range in age from fetal weeks 14-20 through old age (80). We discover fast changes in gene expression occurring during early brain development. Later in life, the changes are considerably slower. Many genes reverse pattern of expression between fetal and early postnatal development. We identify thousands of strong associations of SNPs with gene expression. We examine DNA methylation in ~14,500 genes at ~27,000 CpG loci focused on 5' promoter regions. The fastest changes in DNA methylation also occur during the prenatal period, slow down markedly after birth and continue to slow further with aging. DNA methylation is strongly associated with genotypic variants and correlates with expression of a subset of genes. DNA for genotyping was obtained from the cerebella and applied to either Illumina 650K or 1 million BeadArrays - only genotypes common to both platforms are analyzed here. Genotypes were called using BeadExpress software. Doi: 10.1038/nature10524 Nature, 478:519-524, 2011; doi:10.1016/j.ajhg.2011.12.020, AJHG 90, 1-13, Feb 10, 2012. The methylation data can be downloaded at: BrainCloud.

Link

dbGaP study = phs000417

Keywords

Versions (2)
  1. 8/17/22 8/17/22 - Chiara Middel
  2. 10/12/22 10/12/22 - Adrian Schulz
Copyright Holder

Joel E. Kleinman, MD, PhD, National Institutes of Health, Bethesda, MD, USA

Uploaded on

October 12, 2022

DOI

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License

Creative Commons BY 4.0
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dbGaP phs000417 BrainCloud: Data from Human Postmortem Brain Across the Lifespan

English

Eligibility Criteria

6 forms  
Inclusion and exclusion criteria
Description

Inclusion and exclusion criteria

Postmortem human brains from the NIMH Brain Tissue Collection in the Clinical Brain Disorders Branch (NIMH, CBDB) were obtained at autopsy primarily from the Offices of the Chief Medical Examiner of the District of Columbia, and of the Commonwealth of Virginia, Northern District, all with informed consent from the legal next of kin (protocol #90-M-0142 approved by the NIMH/NIH Institutional Review Board). Additional postmortem fetal, infant, child, and adolescent brain tissue samples were provided by the National Institute of Child Health and Human Development Brain and Tissue Bank for Developmental Disorders (BTB: www.BTBank.org) under contracts NO1-HD-4-3368 and NO1-HD-4-3383. Toxicological analysis was performed on every case. Subjects with evidence of macro- or microscopic neuropathology, drug use, alcohol abuse, or psychiatric illness were excluded. SNPs were removed if the call rate was <98% (mean call rate for this study >99%), if not in HWE (p<0.001) in Cauc or AA, or not polymorphic (MAF<0.01). The total number of SNPs remaining in the analysis was 605,371.
Description

Elig.phs000417.v2.p1.1

Data type

boolean

Alias
UMLS CUI [1,1]
C0683946
UMLS CUI [1,2]
C0006104
UMLS CUI [1,3]
C0004398
UMLS CUI [2,1]
C0021430
UMLS CUI [2,2]
C1548348
UMLS CUI [3,1]
C0205472
UMLS CUI [3,2]
C0936012
UMLS CUI [4,1]
C0680251
UMLS CUI [4,2]
C0876934
UMLS CUI [4,3]
C2239127
UMLS CUI [4,4]
C0085762
UMLS CUI [4,5]
C0004936
UMLS CUI [5,1]
C0680251
UMLS CUI [5,2]
C0752046
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Similar models

Eligibility Criteria

6 forms
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
Inclusion and exclusion criteria
Elig.phs000417.v2.p1.1
Item
Postmortem human brains from the NIMH Brain Tissue Collection in the Clinical Brain Disorders Branch (NIMH, CBDB) were obtained at autopsy primarily from the Offices of the Chief Medical Examiner of the District of Columbia, and of the Commonwealth of Virginia, Northern District, all with informed consent from the legal next of kin (protocol #90-M-0142 approved by the NIMH/NIH Institutional Review Board). Additional postmortem fetal, infant, child, and adolescent brain tissue samples were provided by the National Institute of Child Health and Human Development Brain and Tissue Bank for Developmental Disorders (BTB: www.BTBank.org) under contracts NO1-HD-4-3368 and NO1-HD-4-3383. Toxicological analysis was performed on every case. Subjects with evidence of macro- or microscopic neuropathology, drug use, alcohol abuse, or psychiatric illness were excluded. SNPs were removed if the call rate was <98% (mean call rate for this study >99%), if not in HWE (p<0.001) in Cauc or AA, or not polymorphic (MAF<0.01). The total number of SNPs remaining in the analysis was 605,371.
boolean
C0683946 (UMLS CUI [1,1])
C0006104 (UMLS CUI [1,2])
C0004398 (UMLS CUI [1,3])
C0021430 (UMLS CUI [2,1])
C1548348 (UMLS CUI [2,2])
C0205472 (UMLS CUI [3,1])
C0936012 (UMLS CUI [3,2])
C0680251 (UMLS CUI [4,1])
C0876934 (UMLS CUI [4,2])
C2239127 (UMLS CUI [4,3])
C0085762 (UMLS CUI [4,4])
C0004936 (UMLS CUI [4,5])
C0680251 (UMLS CUI [5,1])
C0752046 (UMLS CUI [5,2])
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