367physicians and scientists can compare patients’ tissues with digitally archived
cancerous tissues for which genomic and proteomic data is available. This will not
only lead to more personalized treatment, but will also enhance cell and radiological
cancer studies. The initiative was funded by grant from the NIH as an extension of
the 2006 “Help Defeat Cancer” campaign. For that project, researchers used IBM’s
World Community Grid − a virtual supercomputer based on unused computer time
donated by volunteers − to create an expression signature library for breast, colon,
head, and neck cancers and to develop reliable analytical tools for high-throughput
tissue microarrays. In the next phase, the project will expand into other types of
cancer and also create a Center for High-Throughput Data Analysis for Cancer
Research. The Center will rely on pattern recognition algorithms for developing
diagnostic tools based on archived cancer specimens and radiology images. That
information will be integrated with proteomic and genomic data to aid treatment
recommendations. Several other institutions, including Rutgers University, Arizona
State University, Ohio State University, and the University of Pennsylvania are
involved in the project. IBM has donated high-performance systems to the Center,
which use grid technology that allows collaborators from around the US access the
Center’s database and software.
Genomic Cancer Care Alliance
Genomic Cancer Care Alliance – which currently involves founding organizations
Fox Chase Cancer Center, Scripps Genomic Medicine, Omicia, El Camino Hospital,
and the Translational Genomics Research Institute – launched a pilot study in 2010
to investigate the ability of whole-genome sequencing to guide treatment for patients
who have responded poorly to initial therapy. The alliance is primarily funded by
Life Technologies at present and uses the company’s SOLiD 4 sequencing
platform.
Integrated Genome-Wide Analysis of Cancer
for Personalized Therapy
An integrated genome-wide analysis of CNV in breast and colorectal cancers using
approaches that can reliably detect homozygous deletions and amplifi cations such
as SNP analysis and digital karyotyping, has revealed that the number of genes
altered by major CNVs, deletion of all copies or amplifi cation to at least a dozen
copies per cell (Leary et al. 2008 ). This study has identifi ed genes and cellular path-
ways affected by both CNVs and point alterations. Pathways enriched for genetic
alterations included those controlling cell adhesion, intracellular signaling, DNA
topological change, and cell cycle control. A comprehensive picture of genetic
alterations in human cancer should therefore include the integration of sequence-
based alterations together with copy number gains and losses. Combining copy
Future of Cancer Therapy