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Series GSE8054 Query DataSets for GSE8054
Status Public on Jan 05, 2008
Title Allele-Specific Expression 1
Organism Homo sapiens
Experiment type Expression profiling by SNP array
Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Physiologic allele-specific expression (ASE) in germline tissues occurs during random X-chromosome inactivation and in genomic imprinting, wherein the two alleles of a gene in a heterozygous individual are not expressed equally. Recent studies have confirmed the existence of ASE in apparently non-imprinted autosomal genes; however, the extent of ASE in the human genome is unknown. We explored ASE in lymphoblastoid cell lines of 145 individuals using an oligonucleotide array based assay. ASE of autosomal genes was found to be a very common phenomenon in ~20% of heterozygotes at 78% of SNPs at 84% of the genes examined. Comparison of 100 affected individuals from familial pancreatic cancer kindreds and 45 controls revealed three types of changes in the germline: (a) loss of ASE, (b) gain of ASE, and, (c) rare instances of "extreme" (near monoallelic) ASE. The latter changes identified heterozygous deleterious mutations in a subset of these genes. Consequently, an ASE assay efficiently identifies candidate disease genes with altered germline expression properties as compared to controls, and provides insights into mechanisms that confer disease risk as for pancreatic cancer.
Keywords: allele-specific expression
 
Overall design The goal of this study is to identify genes showing allele-specific expression (ASE) in familial pancreatic cancer vs normal germline.

Please see readme.pdf for more details.
 
Contributor(s) Tan AC
Citation(s) 18059179
Submission date Jun 07, 2007
Last update date Mar 21, 2012
Contact name Aik Choon Tan
E-mail actan@jhu.edu
Phone 410-502-8743
Fax 410-614-9006
Organization name Johns Hopkins University
Department The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins
Street address 1650 Orleans Street, RM 1M86
City Baltimore
State/province MD
ZIP/Postal code 21231
Country USA
 
Platforms (1)
GPL5358 Homo sapiens 0.9 K allele specific expression 1
Samples (492)
GSM199481 Pancreatic cancer sample, Sample_ID = 1, DNA
GSM199482 Pancreatic cancer sample, Sample_ID = 100, DNA
GSM199483 Pancreatic cancer sample, Sample_ID = 101, DNA
This SubSeries is part of SuperSeries:
GSE9596 Allele-specific expression in familial pancreatic cancer
Relations
BioProject PRJNA123767

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE8054_readme.pdf 215.1 Kb (ftp)(http) PDF
Raw data not provided for this record
Processed data included within Sample table
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