|The Cancer Genome Atlas Awards Funds for Technology
As part of The Cancer Genome Atlas (TCGA) pilot project, the National
Institutes of Health (NIH) today awarded eight two-year grants
totaling $3.4 million to support the development of innovative
technologies for exploring the genomic underpinnings of cancer.
The National Cancer Institute (NCI) and the National Human Genome
Research Institute (NHGRI), both part of NIH, announced the TCGA
pilot in December 2005 to test the feasibility of a large-scale,
systematic approach to identifying the changes that occur in the
genomes of cancer cells. The goal is to generate genomic information
that the research community can use to develop new and improved
strategies for detecting, treating and, ultimately, preventing
The types of tumors being studied in the pilot include brain cancer
(glioblastoma), ovarian cancer and lung cancer (squamous cell),
which together account for more than 200,000 cases of cancer in
the United States each year.
“In addition to the detailed genomic data it will generate, there
is great hope that TCGA will both advance technological development
and drive down its cost,” said NCI Director John E. Niederhuber,
M.D. “Our greatest challenge will be in applying the volumes of
information TCGA will provide about tumors to the genomic data
NCI is gathering from large cohorts of patients, in order to better
predict, and even prevent, the earliest development of cancer.”
“Cancer poses a very complex challenge. Each of the dozens of
types of cancer likely will have a different genomic profile or
set of profiles. We urgently need tools equal to this task,” said
NHGRI Director Francis S. Collins, M.D., Ph.D., whose institute
led the NIH component of the Human Genome Project. “One of the
major lessons we learned from the Human Genome Project is that
technology development is essential for success.”
The institutions and principal investigators chosen to receive
the two-year grants are:
Baylor College of Medicine, Houston; Aleksandar Milosavljevic,
Ph.D.; $413,000; Comprehensive High-Throughput Mapping
of Cancer Genomes. This project will develop
methods to utilize new highly parallel DNA sequencing platforms
to investigate structural variations in the genomes of cancer
City of Hope/Beckman Research Institute, Duarte, Calif.;
Gerd Pfeifer, Ph.D.; $465,000; DNA Methylation in Cancer
Genomes. These researchers will work on approaches
for analyzing the methylation of DNA at high resolution across
the genome using 1,000 cancer cells. Methylation, which involves
the addition of methyl groups to the backbone of the DNA
molecule, can change the way in which genes interact with
the transcriptional machinery that turns genes on or off.
Columbia University, New York; Benjamin Tycko, M.D.,
Ph.D.; $443,000; Genomic and Epigenomic Profiling by
MSNP. This team will focus on using high-density
oligonucleotide arrays to characterize genomic aberrations
and DNA methylation. Oligonucleotides are short sequences
of single-stranded DNA or RNA that are often used as probes
for detecting complementary DNA or RNA because they bind
readily to their complements.
Columbia University, New York; Timothy Bestor, Ph.D.;
$362,000; High-Throughput Profiling of Genomic Methylation
Patterns. These researchers will develop methods
for high-throughput, high-resolution profiling of DNA methylation.
Johns Hopkins University, Baltimore; Andrew Feinberg,
M.D., M.P.H.; $464,000; Functional Allelotyping.
This group will generate new approaches for investigating
allele-specific gene expression patterns. Researchers use
the term alleles to refer to the variant forms of a gene.
Nimblegen Systems, Inc., Madison, Wisc.; Thomas Albert,
Ph.D.; $415,000. Large-Scale Selection of Genomic Loci.
This team will use high-density oligonucleotide arrays in
an innovative fashion to select genomic regions for DNA sequence
Stanford University, Stanford, Calif; Ronald Davis,
Ph.D.; $429,000. Development of Selectors for Cancer
Mutation Analysis. This project will develop
methods for high-throughput isolation of genomic regions
for DNA sequence analysis.
University of California-Davis; Peggy Farnham, Ph.D.;
$418,000. Scaling the ChIP-chip Assay to Improve Analysis
of Clinical Biospecimens. These researchers
will work on methods that can be used to conduct high-throughput
investigations of cancer-associated changes in genomic regions
that are important in gene regulation, using small fragments
of cancer tissue.
The technology development efforts will influence other key components
of the TCGA pilot project: three Genome Sequencing Centers, seven
Cancer Genome Characterization Centers, a Data Coordination Center
and a Biospecimen Core Resource.
The pilot project will establish a publicly available integrated
database that individual researchers can use to study the genomic
changes of specific cancers to develop new targets for a new generation
of drugs and diagnostics. TCGA data will be made available through
public databases supported by NCI’s cancer Biomedical Informatics
Grid (caBIG:) and the National Library of Medicine’s
National Center for Biotechnology Information (NCBI). TCGA data
will be provided in a manner that meets the highest standards for
protection and respect of the research participants.
NCI and NHGRI are two of the 27 institutes and centers at NIH,
an agency of the U.S. Department of Health and Human Services.
For more details about The Cancer Genome Atlas, please go to http://cancergenome.nih.gov.
For more information about cancer and the National Cancer Institute,
please visit the NCI Web site at http://www.cancer.gov,
or call NCI’s Cancer Information Service at 1-800-4-CANCER (1-800-422-6237).
For more information about the National Human Genome Research
Institute, please visit the NHGRI Web site at http://www.genome.gov.
The National Institutes of Health (NIH) — The Nation's
Medical Research Agency — includes 27 Institutes and
Centers and is a component of the U.S. Department of Health and
Human Services. It is the primary federal agency for conducting
and supporting basic, clinical and translational medical research,
and it investigates the causes, treatments, and cures for both
common and rare diseases. For more information about NIH and
its programs, visit www.nih.gov.