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.
Overall Design:
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.
Platforms:
Rosetta/Merck Human 44k 1.1 microarray
Data Source Acknowledgements:
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. 2008 May 6;6(5):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. 2010 Aug;20(8):1020-36.
Data Source:
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.]
