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A better tool for mining the cancer genome

Drs. Zhang and Chen writing on board

Shortly after the St. Jude Children’s Research Hospital – Washington University Pediatric Cancer Genome Project began, scientists realized they had a problem. The existing computer tools often missed important genetic changes. These changes were buried in billions of pieces of information created by sequencing the human genome.

The changes involved copying, removing or rearranging pieces of the genome. Those changes offer clues about how tumors begin and spread. The details could lead to better methods of finding and treating cancer.

So Jinghui Zhang, PhD, of St. Jude Computational Biology, and her team developed a much better tool. St. Jude named the tool CONSERTING and made it available for free to scientists around the world. There is even a cloud version so researchers can access through Amazon Web Services and upload data for analysis.

The new tool has helped researchers find genetic changes driving both childhood and adult cancers. Those cancers include brain tumors, leukemia and the eye tumor retinoblastoma.

“CONSERTING has helped us to harness the power of whole genome sequencing to better understand how cancer begins and spreads,” Zhang said. “From that understanding will come the next generation of cancer treatment.”

CONSERTING is the focus of research published in Nature Methods.

May 4, 2015

Read the news release