Data Set Group2: GSE9588 Human Liver Normal (Mar11)

Data Set: GSE9588 Human Liver Normal (Mar11) Females GN Accession: GN384 GEO Series: GSE9588 Title: Mapping the Genetic Architecture of Gene Expression in Human Liver Organism: Human (Homo sapiens, hg19) Group: HLC Tissue: Liver mRNA Dataset Status: Public Platforms: Custom SAGE Bionetworks Agilent Array Normalization: mlratio

Contact Information Eric E Schadt Merck Research Laboratories 401 Terry Ave N Seattle, WA 98109 USA Tel. 800-637-4624 eric_schadt@merck.com Website Download datasets and supplementary data files GN384_MeanDataAnnotated_rev081815.txt (N/A) GN384_StdError_rev081815.txt (N/A)

Specifics of this Data Set:

None

Summary:

The Human Liver Cohort (HLC) study aimed to characterize the genetic architecture of gene expression in human liver using genotyping, gene expression profiling, and enzyme activity measurements of Cytochrom P450. The HLC was assembled from a total of 780 liver samples screened. These liver samples were acquired from caucasian individuals from three independant tissue collection centers. DNA samples were genotyped on the Affymetrix 500K SNP and Illumina 650Y SNP genotyping arrays representing a total of 782,476 unique single nucleotide polymorphisms (SNPs). Only the genotype data from those samples which were collected postmortem are accessible in dbGap. These 228 samples represent a subset of the 427 samples included in the Human Liver Cohort Publication (Schadt, Molony et al. 2008). RNA samples were profiled on a custom Agilent 44,000 feature microarray composed of 39,280 oligonucleotide probes targeting transcripts representing 34,266 known and predicted genes, including high-confidence, noncoding RNA sequences. Each of the liver samples was processed into cytosol and microsomes using a standard differential centrifugation method. The activities of nine P450 enzymes (CYP1A2, 2A6, 2B6, 2C8, 2C9, 2C19, 2D6, 2E1, and 3A4) in isolated microsomes from 398 HLC liver samples were measured in the microsome preparations using probe substrate metabolism assays expressed as nmol/min/mg protein. Each was measured with a single substrate except for the CYP3A4 activity that was measured using two substrates, midazolam and testosterone. To uncover the genetic determinants affecting expression in a metabolically active tissue relevant to the study of obesity, diabetes, atherosclerosis, and other common human diseases, we profiled 427 human liver samples on a comprehensive gene expression microarray targeting greater than 40,000 transcripts and genotyped DNA from each of these samples at greater than 1,000,000 SNPs. The relatively large sample size of this study and the large number of SNPs genotyped provided the means to assess the relationship between genetic variants and gene expression and it provided this look for the first time in a non-blood derived, metabolically active tissue. A comprehensive analysis of the liver gene expression traits revealed that thousands of these traits are under the control of well defined genetic loci, with many of the genes having already been implicated in a number of human diseases. Clincal data was requested, but not provided by submitter. Keywords: eQTL

About the cases used to generate this set of data:

About the tissue used to generate this set of data:

About the array platform:

Rosetta/Merck Human 44k 1.1 microarray

About data values and data processing:

Notes:

Experiment Type:

Liver samples (1-2 g) were acquired from Caucasian individuals from three independent liver collections at tissue resource centers at Vanderbilt University, University of Pittsburg, and Merck Research Laboratories. All individuals were compared to a common pool created from equal portions of RNA from 191 (111 from Vanderbilt University and 80 from University of Pittsburg) samples.

Contributor:

Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum P, Kasarskis A, Zhang B, Wang S, Suver C, Zhu J, Millstein J, Sieberts S, Lamb J, Guhathakurta D, Derry J, Storey J, Mehrabian M, Drake TA, Lusis AJ, Smith R, Guengerich P, Strom SC, Schuetz E, Rushmore T, Ulrich R

Citation:

Schadt EE, Molony C, Chudin E, Hao K et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol 2008 May 6;6(5):e107. PMID: 18462017

Data source acknowledgment:

Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, Zhu J, Millstein J, Sieberts S, Lamb J, GuhaThakurta D, Derry J, Storey JD, Avila-Campillo I, Kruger MJ, Johnson JM, Rohl CA, van Nas A, Mehrabian M, Drake TA, Lusis AJ, Smith RC, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich R (2008) Mapping the genetic architecture of gene expression in human liver. PLoS Biol 6:e107. Full text Yang X, Zhang B, Molony C, Chudin E, Hao K, Zhu J, Gaedigk A, Suver C, Zhong H, Leeder JS, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich RG, Slatter JG, Schadt EE, Kasarskis A, Lum PY (2010) Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver. Genome Res. 20:1020-36. GEO Series GSE9588 Genotype data for 228 individuals who satisfy privacy policy have been submitted to the NCBI dbGaP (http://www.ncbi.nlm.nih.gov/gap/) under accession no. phs000253.v1.p1.]

Study Id:

107

• The UT Center for Integrative and Translational Genomics
• NIGMS Systems Genetics and Precision Medicine project (R01 GM123489, 2017-2021)
• NIDA NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022)
• NIA Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
• NIAAA Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
• NIDA, NIMH, and NIAAA (P20-DA 21131, 2001-2012)
• NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)