The types of tumours 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", stated NCI Director John E. Niederhuber, M.D. "Our greatest challenge will be in applying the volumes of information TCGA will provide about tumours 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", stated 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 cells.
- City of Hope/Beckman Research Institute, Duarte, California; Gerd Pfeifer, Ph.D.; $465.000; DNA Methylation in Cancer Genomes. These researchers will work on approaches for analysing the methylation of DNA at high resolution across the genome using 1000 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. Allele is a term used by researchers to refer to the variant forms of a gene.
- Nimblegen Systems Inc., Madison, Wisconsin; 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 analysis.
- Stanford University, Stanford, California; 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.