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Pediatric cancer sequencing project

Wednesday 10 February 2010

News

- February 10, 2010: Washington University in St. Louis and the St. Jude Children’s Research Hospital in Memphis announced that they are embarking on a large-scale sequencing project aimed at identifying genetic and epigenetic patterns in childhood cancers.

Researchers plan to sequence matched tumor-normal genomes from more than 600 pediatric cancer patients during the three-year. The budget of the project is $65 million project. The effort’s lead sponsor, Kay Jewelers, has committed $20 million to the sequencing study.

"This is going to be the most significant set of data that we could imagine in terms of understanding childhood cancers," National Institutes of Health Director Francis Collins said at the press briefing. Collins noted that the new sequencing study will complement existing projects, such as The Cancer Genome Atlas, which are aimed at understanding adult cancers.

Although the team has not determined the exact types and number of each cancer to be sequenced, Elaine Mardis, co-director of Washington University’s Genome Sequencing Center told GenomeWeb Daily News that it initially intends to focus on childhood leukemia as well as childhood brain and soft tissue tumors.

Those involved hope to find clues about genetic and epigenetic changes in childhood cancers that can inform mouse model, cell culture, and targeted studies of these conditions.

Because cancer is usually considered a disease of the genome, Mardis explained, researchers are keen to understand how childhood cancers differ from those in adults, whose cells have undergone far more cell divisions.

Although cure rates for childhood cancers have improved, Evans said, cancer is still the leading cause of death by disease in American children. Along with providing new insights into the mutations and regulatory changes underlying these cancers, those involved in the effort say the sequencing effort should uncover new therapeutic targets as well as information for guiding the use of existing treatments to make them more effective.

The pediatric project builds on cancer genome sequencing methods pioneered at Washington University. A Washington University-led team published the first cancer genome sequencing paper in 2008.

Samples are being provided by St. Jude, which has an extensive tissue bank of matched tumor-normal tissues and accompanying clinical data going back several decades.

Washington University’s Genome Sequencing Center plans to sequence the samples using Illumina’s new HiSeq 2000 platform in order to find SNPs, small indels, and structural variants that are involved in the cancers.

Meanwhile, collaborators at St. Jude intend to do additional analyses such as RNA-sequencing and methylation studies. Those involved in the new pediatric sequencing effort said they plan to make data from the project available to other researchers once the results have been validated.

References

- WashU, St. Jude Team Launches Pediatric Cancer Sequencing Project, GenomeWeb, January 25, 2010