NHGRI Tumor Sequencing Project (Lung Adenocarcinoma)

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.]]>
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.]]>
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.

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