Dataset Information

Population Genetics Analysis Program: Immunity to Vaccines/Infections (NIAID/NIH)

ABSTRACT:

The study examines the role of candidate human immune response gene polymorphisms (and their receptors, expression and function) and variations in immune response, among 1,000 active duty members of the military who were recently vaccinated with ACAM2000 or Dryvax Smallpox vaccine.

In addition to the phenotype and genotype data available through dbGaP, extensive clinical data are available through NIAID's ImmPort data portal; information to map the the data available in dbGaP to the data available in ImmPort is provided in the dataset pht005302.v1.p1 of the current study, dbGaP phs001057.v1.p1.

PROVIDER: phs001057 | dbGaP |

SECONDARY ACCESSION(S): PRJNA308043PRJNA308044

REPOSITORIES: dbGaP

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	GapExchange_phs001057.v1.p1.xml	Xml
	dbGaPEx2.1.5.xsd	Other
	Study_Report.phs001057.PopulationGeneticsAnalysis.v1.p1.MULTI.pdf	Pdf
	manifest_phs001057.PopulationGeneticsAnalysis.v1.p1.c1.GRU-IRB.pdf	Pdf
	datadict_v2.xsl	Other

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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 DNA methylation, mRNA expression and microRNA (miRNA) expression in four distinct human brain regions. We show that brain tissues may be readily distinguished based on methylation status or expression profile. We find an abundance of genetic cis regulation mRNA expression and show for the first time abundant quantitative trait loci for DNA CpG methylation. 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.v1.p1 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, frontal cortex, pons and temporal cortex from 150 subjects (total 600 tissue samples). We undertook four separate assays across this series; first, genome-wide SNP genotyping; second, assay of >27,000 CpG methylation sites in each of the four brain regions; third, mRNA expression profiling of >22,000 transcripts in all four brain regions; and, fourth, miRNA expression profiling of 735 miRNA transcripts. Here we discuss the results of these experiments, particularly in the context of integrated datasets to define expression and CpG methylation quantitative trait loci (eQTL and methQTL) and detailing differences and similarities across brain regions.

Dataset Information

Population Genetics Analysis Program: Immunity to Vaccines/Infections (NIAID/NIH)

Dataset's files

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