The NHGRI-supported, large-scale sequencing centers have begun to tackle the unique challenges associated with using high-throughput DNA sequencing to characterize tumor genomes as described below. In addition to providing important data on genomic aberrations in select tumor types, this research serves to inform methods and systems development as The Cancer Genome Atlas [cancergenome.nih.gov] pilot project, jointly sponsored by NCI and NHGRI, gets underway.
Tumor Sequencing Project
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 will pilot approaches to large-scale identification of genomic changes in tumors and aims to sequence the exonic regions of 1,000 genes in almost 200 specimens of adenocarcinoma of the lung, as well as use high density SNP genotyping arrays for high resolution identification of changes in chromosomal copy number. A detailed description of this project is provided in the TSP Consortium white paper:
A Proposal for a Technical Demonstration Project.
Assessment of Sequencing Technologies for Analyzing Tumor DNA
A collaboration among investigators at the J. Craig Venter Institute (JCVI) and The Johns Hopkins University has been established to assess different technologies for sequencing tumor DNA. This project will analyze the DNA sequence of 37 genes in a collection of 20 glioblastoma tumors. Two sequencing technology platforms will be assessed for their ability to generate useful sequence data from heterogeneous tumor samples: the Sanger sequencing method as implemented on an ABI capillary electrophoresis instrument and the pyrosequencing method as implemented on the sequencing instrument from 454 Life SciencesTM. A detailed description of this project is provided in the JCVI white paper: Proposal for a Human Cancer Genome Project Demonstration Study.
Data generated by the two projects will be managed by the investigators and the NHGRI in collaboration with the NCI Center for Bioinformatics (NCICB) [ncicb.nci.nih.gov], using the NCI cancer Biomedical Informatics Grid (caBIG) [cabig.nci.nih.gov] infrastructure. caIntegrator [gforge.nci.nih.gov] provides a framework for integrating and aggregating biomedical research data and provides access to a variety of data types (e.g. microarray-based gene expression, Immunohistochemistry, SNPs, clinical trials data etc.) in a cohesive fashion.
Data release policies will be consistent with NHGRI's goals of rapid, complete data release except to the extent that doing so could potentially pose issues of conflict with the privacy of research participants. (See: Large-scale Sequencing Data Release Policy.) Investigators will rapidly release as much enabling data as possible without restrictions or controls, while at the same time adhering to the regulations and practices governing human subjects research and respecting the privacy of the research participants. The specimens being used in both projects have been anonymized, with no link being maintained between the sequence data and the participant identities. To provide further safeguards to protect the privacy of research participants, the data management plan will have two levels of access for the project data: open and controlled access.
Open access data that cannot be used to identify a participant will be released to the appropriate public databases.
The NHGRI Medical Sequencing Program has created procedures and policies that govern the access of controlled data. Follow the links below for more information or to initiate a request.
Data Access Policies
A brief description of NHGRI policies and procedures for initiating a request for access to controlled data.
Data Use Certification (DUC)
The terms and conditions for access and use of controlled data. All requesters seeking access to controlled data and their institutions must agree to the terms and conditions for data use as described in the DUC.
Top of page
Copyright
Print Version
