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St. Jude, Sanger Institute to Share Genomic Databases

Jinghui Zhang

Jinghui Zhang (St. Jude Children’s Research Hospital)

Updated: 19 September 2016. A spokesperson quotes Jinghui Zhang, St. Jude hospital’s computational biology chair in an e-mail to Science & Enterprise, “The agreement will allow for an online comparison of pediatric cancer data and adult cancer data on a genomic data portal.”

16 September 2016. Two research institutes  — St. Jude Children’s Research Hospital and Wellcome Trust Sanger Institute — will share their databases on cancer genomics with the other institution’s scientists. Both of the databases are made available to researchers worldwide over the Web.

St. Jude hospital, in Memphis, maintains its ProteinPaint database, a repository of more than 1,900 pediatric cancer mutations from 1,856 patients. ProteinPaint charts mutations of individual genes that alter their instructions for encoding proteins. Results are displayed with graphical tools that are not often available in current visualization programs. Details provided include mutation type, frequency in cancer sub-type and location in the protein domain.

As reported in Science & Enterprise in December 2015, ProteinPaint is based on data from Pediatric Cancer Genome Project, a joint effort with Washington University in St. Louis, and National Cancer Institute’s TARGET database, short for Therapeutically Applicable Research to Generate Effective Treatments. Pediatric Cancer Genome Project collects genomic data on cancerous and healthy cells from more than 800 children. TARGET collects genomic data on childhood cancers from a network of participating researchers. ProteinPaint also stores data from other published studies.

The Sanger Institute in Hinxton, U.K. offers its Catalogue of Somatic Mutations In Cancer, or Cosmic, a database with more than 4.1 million mutations in human cells not inherited from germ line, or sperm and egg interactions. The database includes data derived from scientific literature, collected and curated by expert reviewers. Cosmic also captures data from systematic molecular screening studies that offer disease profiles across the entire genome.

Under the agreement, the two institutions will maintain their separate databases, but provide each partner organization with regular updates and data exchanges to ensure researchers have the latest data for all areas of cancer. Jinghui Zhang, who chairs St. Jude’s computational biology department, says in a joint statement. “We want this to be the definitive resource for genomic information for the pediatric cancer community.”

Simon Forbes, who heads the Cosmic program at the Sanger Institute adds that the collaboration should provide researchers with more insights into pediatric cancers. “Many of our users are supporting diagnostic and pharmaceutical discovery,” Forbes notes, “and in this way we hope to support future improvements for these young patients.”

The following video tells more about ProteinPaint.

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