NABEC: North American Brain Expression Consortium
Ontology highlight
ABSTRACT: This study utilized neurologically normal control samples deposited in North American Brain Expression Consortium (NABEC). This top-level study, phs001300, makes available all phenotype data of the NABEC study participants.
In addition, molecular data of six sub-studies are available through dbGaP:
SECONDARY ACCESSION(S): PRJNA375877PRJNA375878
REPOSITORIES: dbGaP
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Project description:This SuperSeries is composed of the SubSeries listed below. The raw sequencing data is available through dbGaP (controlled access) due to patient privacy concerns. https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001961.v1.p1
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<p>This data includes that from subjects both banked in the <a href="http://ccr.coriell.org/Sections/Collections/NINDS/?SsId=10">
NINDS repository</a> with biologicals publicly available, and those whose samples are not banked/not available.
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<p>This study utilized the <a href="./study.cgi?id=phs000005">NINDS Repository Cerebrovascular/Stroke Study</a>,
and <a href="./study.cgi?id=phs000004">neurologically normal controls</a> from the sample population which are banked in the National
Institute of Neurological Disorders and Stroke (NINDS Repository) collection for a first stage whole genome analysis.</p>
| phs000102.v1.p1 | EGA
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Project description:We assayed CpG methylation in cerebral cortex of neurologically and psychiatrically normal human postmortem specimens, as well as mouse forebrain specimens. Cross-species human-mouse DNA methylation conservation analysis shows that DNA methylation is not correlated with sequence conservation. Instead, greater DNA methylation conservation is correlated with increasing CpG density. We identified key genomic features that can be targeted for identification of epigenetic loci that may be developmentally and evolutionarily conserved and wherein aberrations in DNA methylation patterns can confer risk for disease.
2011-10-05 | GSE32647 | GEO
Project description:A fundamental challenge in the post-genome era is to understand and annotate the consequences of genetic variation, particularly within the context of human tissues. We describe a set of integrated experiments designed to investigate the effects of common genetic variability on mRNA expression distinct human brain regions. We show that brain tissues may be readily distinguished based on expression profile. We find an abundance of genetic cis regulation mRNA expression. We observe that the largest magnitude effects occur across distinct brain regions. We believe these data, which we have made publicly available, will be useful in understanding the biological effects of genetic variation. Authorized Access data: Mapping of GEO sample accessions to dbGaP subject/sample IDs is available through dbGaP Authorized Access, see http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000249 Because of our interest in genomic regulation of expression and neurological disorders we embarked upon a series of experiments to provide a brain region-specific contextual framework for genetic and epigenetic regulation of gene expression. We obtained frozen brain tissue from the cerebellum and frontal cortex from 396 subjects (total 911 tissue samples).
2012-05-08 | E-GEOD-36192 | biostudies-arrayexpress
Project description:In order to gain a global molecular perspective on how the human genome gives rise to the brain, we explore the temporal dynamics and genetic control of transcription in human dorsolateral prefrontal cortex in an extensive series of brain tissue from fetal development through aging. We discover a wave of gene expression changes occurring during fetal development which are reversed in early postnatal life. One half century later in life, this phenomenon is mirrored in aging as well as neurodegeneration. While we identify thousands of robust associations of individual genetic polymorphisms with gene expression, we also demonstrate that there is no association between the total extent of genetic differences between subjects and the global similarity of their transcriptional profiles. Hence, the human genome produces a consistent molecular architecture in the prefrontal cortex, despite millions of genetic differences across individuals and races. To enable further discovery, this entire dataset is freely available (GEO). RNA from 269 human prefrontal cortex samples ranging from fetal development (negative ages) through aging (80 years) were analyzed on custom 2-color microarrays from the National Human Genome Research Institute (NHGRI) microarray core facility using a reference RNA comprised of a pool of all samples. SNP genotype data for these subjects can be found in dbGAP under Study ID *phs000417.v1.p1* http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000417.v1.p1 Both the gene expression and SNP data from this study can be interrogated gene-by-gene with a biologist-friendly stand-alone application available at http://www.libd.org/braincloud . The original publication of this data appeared in the Oct. 27th 2011 volume of Nature: http://www.nature.com/nature/journal/v478/n7370/full/nature10524.html .
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Project description:<p>The Columbia GENIE study contributes and shares phenotype and genotype data for individuals who were treated with our healthcare facilities and consented to share their data with dbGaP for scientific discovery. Some of these individuals have kidney or neurological problems and some are healthy volunteers from the Washington Height patient community. The purpose of this NOMAS study is to obtain information about physical features of the brain, carotid arteries, and heart. Some of our patients are pediatric patients with cardiac conditions.</p> <p>The study sample consists of four patient cohorts:</p> <ol> <li>Northern Manhattan Study (NOMAS), N=1072</li> <li>Pediatric Cardiac Genomic Consortium (<a href="study.cgi?study_id=phs000571">PCGC</a>), n=374</li> <li>Caribbean Hispanics with Familial and Sporadic Late Onset Alzheimer's disease (<a href="study.cgi?study_id=phs000496">Caribbean Hispanics/AD</a>), n=330</li> <li>Alzheimer's Disease Sequencing Project (<a href="study.cgi?study_id=phs000572">ADSP</a>, n=44)</li> <li>Genetics of Chronic Kidney Disease Study, n=1256</li> </ol>
| phs000961 | dbGaP