HMS-CGCC
** News **
Nov-2006: 7 CGCCs Described: Broad, HMS, LBNL, MSKCC, JHU, Stanford, UNC)Oct-2006:UNC, DFCI-HMS-BWH & MSKCC using Agilent technologies for CGCCs
“The Cancer Genome Characterization Center at Harvard Medical School is composed of Raju Kucherlapati (PI), Isaac Kohane, Peter Park and Samuel Aronson (Harvard Partners Center for Genetics and Genomics), Lynda Chin (Dana Farber Cancer Institute) and George Church and Jonathan Seidman (Harvard Medical School). The goal of this Center is to identify novel genes important in initiation and progression of cancer by quantitating DNA and RNA dosage using array-CGH (Comparative Genomic Hybridization) and a novel, highly sensitive method called polony sequencing.”
U24 CA126554, Specific Aims (revised
21-Sep-2006).
1. Use the Agilent microarray technology to assess copy
number alterations in tumor DNA’s that will be provided to the Center. Achieve the rate of
examining 1,000 samples/year by the end of six months and complete 3,000
samples in three years. Identify
candidate genes from this effort for possible resequencing.
2. Assess the feasibility of using a novel SAGE
technology and polony sequencing technology for generating polony massive
analysis of gene expression (PMAGE) libraries during the first year and
sequence the tags generated from them.
Assess the quality control and quality assurance features of this procedure
and how it can be scaled to high throughput production level.
3. Initiate an effort to integrate the aCGH and PMAGE results to accurately identify candidate
genes for initiation and progression of cancer.
4. The IT system will provide support for laboratory LIMS
as well as storing and transmitting data in a CaBIG compliant
fashion.
Relevant
Publications:
Tonon G, Brennan C, Protopopov A, Maulik G, Feng B, Zhang Y, Khatry DB, You MJ, Aguirre AJ, Martin ES, Yang Z, Ji H, Chin L, Wong KK, Depinho RA (2005) Common and contrasting genomic profiles among the major human lung cancer subtypes. Cold Spring Harb Symp Quant Biol.70:11-24.
Lai WR, Johnson MD, Kucherlapati R, Park PJ. Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics. 2005 Oct 1;21(19):3763-70.
Shendure, J, Porreca, GJ, Reppas, NB, Lin, X, McCutcheon, JP, Rosenbaum, AM, Wang, MD , Zhang, K, Mitra, RD, Church, GM (2005) Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome Science 309:1728-32.
Turner DJ, Shendure J, Porreca G, Church G, Green P, Tyler-Smith C, Hurles ME (2006) Assaying chromosomal inversions by single-molecule haplotyping. Nat Methods. 3:439-45.
Carter SL, Eklund AC, Kohane IS,
The National Cancer Institute
(NCI) and the National Human Genome Research Institute (NHGRI), both part of
the National Institutes of Health (NIH), announced the first three cancers that
will be studied in the pilot phase of The Cancer Genome Atlas (TCGA) Project.
The source of the lung cancer biospecimens will be the Lung Cancer Tissue Bank of the
Cancer and Leukemia Group B (CALGB)
clinical trials group, which is housed at the Brigham and Women’s Hospital in