publication date: Jul. 17, 2020

Clinical Roundup

St. Jude researchers create analytic tool to identify what drives tumor growth

St. Jude Children’s Research Hospital scientists have developed a computational tool to identify alterations that drive tumor formation in 98% of the genome. Gene coding regions constitute 2% of the human genome.

The method will aid discovery of oncogenes and advances in precision medicine for children and adults with cancer.

The approach, detailed in Nature Genetics, is called cis-expression or cis-X. Researchers developed the innovative analytic method to identify novel pathogenic variants and oncogenes activated by such variants in regulatory noncoding DNA of patient tumors. Cis-X works by identifying abnormal expression of tumor RNA. Investigators analyzed leukemia and solid tumors and demonstrated the power of the approach.

Noncoding DNA, which does not encode genes, makes up 98% of the human genome. However, growing evidence suggests that more than 80% of the noncoding genome is functional and may regulate gene expression. Population studies have identified variants in noncoding DNA that are associated with an elevated cancer risk. But only a small number of noncoding variants in tumor genomes that contribute to tumor initiation have been discovered. Finding these variants required whole genome sequencing analysis of a large number of tumor samples.  

“Cis-X is a fundamental change from existing approaches that require thousands of tumor samples and only identify noncoding variants that happen recurrently,” Jinghui Zhang, St. Jude chair of the Department of Computational Biology, said in a statement. She and Yu Liu, previously of St. Jude and now of Shanghai Children’s Medical Center, are the corresponding authors. Liu is also a first author.

“By using aberrant gene transcription to reveal the function of noncoding variants, we … Continue reading St. Jude researchers create analytic tool to identify what drives tumor growth

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