By Julia Karow
This article, originally published Sept. 30, has been updated with comments from an NHGRI official.
The Cancer Genome Atlas has received $275 million in new funding from the National Institutes of Health — including about $125 million allocated for sequencing — to study more than 20 types of cancer over the next two years. Within the next five years, the project plans to generate comprehensive genomic maps for these cancers.
About $175 million of the funding comes from the 2009 American Recovery and Reinvestment Act, including $25 million in NIH Signature Project support. In addition, the National Cancer Institute and the National Human Genome Research Institute, which jointly administer TCGA, are each committing another $50 million in non-Recovery Act money to the project.
The institutes plan to use the funding over the next two years to collect more than 20,000 tissue samples from more than 20 cancer types, to generate comprehensive maps of genomic changes in 10 of these cancer types, analyzing up to 500 samples of both tumor and matched normal tissues for each type, and to sequence and characterize at least 100 tumors from up to 15 additional cancer types.
About $125 million of the overall funding, or 45 percent, will go towards DNA sequencing, according to Brad Ozenberger, a program director at NHGRI and a member of the TCGA project management team.
The three large-scale centers in charge of sequencing for TCGA — Baylor College of Medicine, the Broad Institute, and Washington University School of Medicine — are receiving $25 million in ARRA funding, he told In Sequence via e-mail this week. Another $50 million from the NCI's allocation of Recovery Act funding "are reserved for the genomic sequencing effort, but how they will be distributed has not been determined yet," he added.
On top of that, NHGRI's non-Recovery Act $50 million contribution will fund sequencing capacity at the three centers.
Over the next two years, Ozenberger said, TCGA is expected to produce 100 terabases of sequence data, ten times more than the approximately 10 terabases it generated over the last year.
"Roughly, the sequencing capacity for TCGA will be increased five-fold with the ARRA investment," he said.
As part of TCGA, the Broad Institute initially plans to sequence the exomes of the samples it receives, using an in-solution method it developed in-house, and to perform whole-genome sequencing for a subset of samples, Stacey Gabriel, the institute's co-director of genome sequencing and analysis, told In Sequence last week. "As the costs [of exome sequencing and whole-genome sequencing] converge, when it makes sense to transition, we will do whole-genome sequencing," she added.
Stimulus funding will also "fuel the development of new bioinformatics tools and computational models for analysis of integrated genomics data" and TCGA will use it "to build a more robust pipeline for acquiring large numbers of tumor and matched normal tissues samples."
Funding for the next phase of the project, expected to take another three years, "will be finalized shortly," according to a statement from the NCI. During that phase, the TCGA research network, which consists of more than 150 researchers at more than two dozen institutes across the US, will "broaden its mapping efforts" and analyze the cancers more in depth.
NCI and NHGRI are currently deciding which types of cancer to focus on, based on their frequency and severity, whether effective treatments exist, and whether high-quality tissue samples are available. The institutes will also take into account "mapping efforts being planned by other nations," presumably those participating in the International Cancer Genome Consortium.
Among cancer types "likely to be considered" a high priority for TCGA are clear cell renal cell carcinoma and invasive ductal carcinoma of the breast.
The additional funding for TCGA follows a three-year pilot project to develop the initiative's policies, production pipeline, collaborative research network, databases, and analytical tools. The pilot focused on glioblastoma, squamous lung carcinoma, and serous cystadenocarcinoma, a type of ovarian cancer. The TCGA research network published the first results from the glioblastoma samples last fall (see In Sequence 9/9/2008).