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Title: NHGRI Tumor Sequencing Project (Lung Adenocarcinoma)      
citations:
18948947
17982442
description:
The Tumor Sequencing Project (TSP) Consortium is a collaboration among participants at the Baylor College of Medicine Human Genome Sequencing Center, the Broad Institute Genome Sequencing Platform, the Dana Farber Cancer Institute, the Memorial Sloan-Kettering Cancer Center, the Genome Sequencing Center and Siteman Cancer Center at Washington University, the M.D. Anderson Cancer Center and the University of Michigan Medical Center. The TSP Part A will pilot approaches to large-scale identification of genomic changes in tumors by sequencing the exonic regions of 623 genes in 188 specimens of adenocarcinoma of the lung, as well as using high density SNP genotyping arrays for high resolution identification of changes in chromosomal copy number. The TSP Part B will pilot approaches to tumor characterization of lung adenocarcinoma samples using next-generation sequencing technologies and benchmark those results against Part A data generated with ABI3730 instruments.
Identifier:
phs000144.v1.p1
accesstypes:
download
enclave
landingpage: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000144.v1.p1
authentication: simpleLogin
none
authorization:
none
duaIndividual
name:
Carcinoma, Non-Small-Cell Lung
Lung Neoplasms
Adenocarcinoma
affiliations:
Multiple
name:
TSP Consortium
roles:
Co-Investigators
affiliations:
National Institutes of Health, Bethesda, MD, USA
name:
U54HG003067
roles:
Funding Source
affiliations:
National Institutes of Health, Bethesda, MD, USA
name:
U54HG003079
roles:
Funding Source
affiliations:
National Institutes of Health, Bethesda, MD, USA
name:
U54HG003273
roles:
Funding Source
performedBy:
TitleNameInstitute Co-InvestigatorsTSP ConsortiumMultiple Funding SourceU54HG003067National Institutes of Health, Bethesda, MD, USA Funding SourceU54HG003079National Institutes of Health, Bethesda, MD, USA Funding SourceU54HG003273National Institutes of Health, Bethesda, MD, USA
downloadURL: https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=DUC&view_pdf&stacc=phs000144.v1.p1
Identifier:
phs000144.v1.p1_policy
name:
Data Use Certificate
Identifier:
1
name:
General Research Use
schedulesActivity:
TSP Timeline August 2005 - TSP Part A study begins. December 2007 - publication of copy number variation results from 371 lung adenocarcinoma samples. July 2008 - end of TSP Part A to examine copy number variation and mutations in 623 genes in 188 lung adenocarcinoma genomes. February 2008 - TSP Part B study begins.
alternateIdentifiers:
yes
selectionCriteria:

Purified DNA from several hundred biopsy samples were provided by pathology laboratories at Dana Farber Cancer Institute, Memorial Sloan-Kettering Cancer Center, and Washington University's Siteman Cancer Center. The three sequencing centers then evaluated the sample DNAs and subsequently developed a "gold set" of 188 tumor DNAs for sequencing. DNA from matched normal tissues samples was also prepared.

Three different types of samples were then obtained from each original sample that was to be included in the "gold set": native DNA from the tumor sample, whole genome amplified (WGA) DNA from the tumor samples and native DNA from the normal tissue. Each sample was then analyzed by high-density genotyping using Affymetrix 500K SNP arrays.

To confirm tumor purity, data from the SNP arrays were used in two ways: to look for LOH over a minimum of one chromosomal arm and to look at overall copy number changes by performing histogram analysis. The second analysis was a straightforward test that confirmed that genotypes are identical between each sample derivative, and that sample mix up or gross error in whole genome amplification did not occur. Samples included in the "gold set" needed to have near perfect concordance of genotypes between the amplified and unamplified DNA and perfect concordance of genotypes (in the majority of the genome that did not undergo loss in the tumors) between the tumor and normal sample. In total, of the 528 samples that were genotyping using the SNP arrays, 188 of them were included in the "gold set" for sequencing among the three centers. Each of the 188 primary lung adenocarcinomas contained a minimum of 70% tumor cells as determined by pathologists.

All patients were properly consented using consent forms approved by each Institutional Review Board at Dana Farber Cancer Institute, Memorial Sloan-Kettering Cancer Center, and Washington University's Siteman Cancer Center.

types:
Tumor vs. Matched-Normal
dateReleased:
08-18-2008
version:
phs000144.v1.p1
dateModified:
06-11-2010
abbreviation:
NHGRI
name:
National Human Genome Research Institute
ID:
0
name:
dbGaP