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PCGP Releases Genome Sequence Data for Hundreds of Tumor-Normal Pairs

NEW YORK (GenomeWeb News) – The St. Jude Children's Research Hospital-Washington University Pediatric Cancer Genome Project announced today that it is releasing genome sequence data for hundreds of matched tumor-normal samples assessed through the collaboration.

The announcement coincides with the online publication of a perspectives article in Nature Genetics that outlines the rationale behind the PCGP, the types of tumors selected for the project, and progress made by PCGP so far. The article also touches on some of the challenges associated with interpreting cancer genome data and details the team's data release policy.

"Although these projects are still deep in the phase of generating primary DNA sequence data, important results are emerging and valuable community resources are being generated that should catalyze future cancer research," St. Jude researchers James Downing and William Evans, co-corresponding authors on the perspectives article, and their colleagues wrote.

The three-year, $65 million PCGP effort, funded by St. Jude's and Kay Jewelers, was launched in 2010 as a strategy for better understanding childhood cancers. Researchers involved in the effort plan to sequence around 1,200 genomes by the end of this year.

Sequence data released today represents some 520 genomes sequenced to an average depth of 30 times and includes matched tumor and normal samples from 260 individuals with a range of pediatric blood, eye, and brain cancers.

The sequence data has already served as the basis for several published studies offering insights into cancers such as neuroblastoma, diffuse intrinsic pontine glioma, retinoblastoma, and early T-precursor acute lymphoblastic leukemia.

"This approach has been more valuable that anyone could have predicted," Richard Wilson, director of Washington University School of Medicine's Genome Institute, said in a statement. "We have identified unusual, 'cryptic' changes in many patients' cancer cells that we would not have found using other methods.

"We are pleased to be able to share this data with the research community in hopes that others can build upon our initial discoveries," Wilson said.

"We want to make this information available to the broader scientific community so that, collectively, we can explore new treatment options for these children," added Downing, scientific director at St. Jude. "By sharing the information even before we analyze it ourselves, we're hoping that other researchers can use this rich resource for insights into many other types of diseases in children and adults."

Sequence files for the first 260 individuals sequenced through PCGP is being made available through the European Bioinformatics Institute's European Genome-Phenome archive, authors of the Nature Genetics article noted. Other data from published PCGP studies are also available through the database of Genotypes and Phenotypes and the Sequence Read Archive.

"Despite the fact that the PCGP is privately funded, we have decided to institute an overall data release policy that is consistent with that of the other major publicly funded genome sequencing projects," they wrote. "However, we will require users to agree that the information will be used exclusively for biomedical research and to abide by a moratorium on submission or presentation of work that incorporates these data for a 9-month period following the data's release date."

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