I Technology Development

Advancing Cancer Genome Characterization and Sequencing Technologies

• Improve the quality, throughput, and cost of gene expression and other molecular characterization methods;
• Decrease the costs of DNA sequencing while maintaining quality;
• Improve the detection and throughput of technologies for detecting epigenomic changes, while also decreasing cost; and
• Develop new and more effective methods of correlating disease state with genomic changes.

Though some high-throughput, cost-effective technologies for cancer genome analyses already exist, further improvements are needed and new innovative approaches are required to address issues of small tumor size, cellular heterogeneity, and normal cell contamination. The TCGA project team is enabling technology development efforts to address these issues.

In 2007, the National Institutes of Health announced the award of eight two-year grants totaling $3.4 million to support the development of innovative technologies for exploring the genomic underpinnings of cancer as part of TCGA.

The technology development areas and institutions receiving awards include:

• Comprehensive High-Throughput Mapping of Cancer Genomes.
  Baylor College of Medicine, Houston; Aleksandar Milosavljevic, Ph.D.; $413,000. The Baylor research team is developing methods to utilize new, highly parallel DNA sequencing platforms to investigate structural variations in the genomes of cancer cells.



• DNA Methylation in Cancer Genomes.
  City of Hope/Beckman Research Institute, Duarte, Calif.; Gerd Pfeifer, Ph.D.; $465,000. As part of this effort, researchers are working 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.



• Genomic and Epigenomic Profiling by MSNP.
  Columbia University, New York; Benjamin Tycko, M.D., Ph.D.; $443,000. This team is focusing 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.



• High-Throughput Profiling of Genomic Methylation Patterns.
  Columbia University, New York; Timothy Bestor, Ph.D.; $362,000. The Columbia research team is developing methods for high-throughput, high-resolution profiling of DNA methylation.



• Functional Allelotyping.
  Johns Hopkins University (JHU), Baltimore; Andrew Feinberg, M.D., M.P.H.; $464,000. As part of this effort, JHU is supporting TCGA by generating 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.



• Large-Scale Selection of Genomic Loci.
  Nimblegen Systems, Inc., Madison, Wisc.; Thomas Albert, Ph.D.; $415,000. This team is using high-density oligonucleotide arrays in an innovative fashion to select genomic regions for DNA sequence analysis.



• Development of Selectors for Cancer Mutation Analysis.
  Stanford University, Stanford, Calif; Ronald Davis, Ph.D.; $429,000. This project is supporting the technology goals of TCGA by developing methods for high-throughput isolation of genomic regions for DNA sequence analysis.



• Scaling the ChIP-chip Assay to Improve Analysis of Clinical Biospecimens.
  University of California-Davis; Peggy Farnham, Ph.D.; $418,000. These researchers are working 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.

These technology development grants are also working to advance the techonologies used by the other key components of the Pilot Project, including TCGA Genome Sequencing Centers, Cancer Genome Characterization Centers, Data Coordinating Center, and the Biospecimen Core Resource.