In a study carried out at St. Jude Children’s Research Hospital, researchers have developed a computational tool to detect alterations that become cause of tumor formation in 98% of genome. The tool will aid to detect oncogenes and advances in precision medicine for adults and children with cancer.
The approachcalled as cis-expression is published in the journal Nature Genetics. For the study part, researchers developed the innovative analytic technique to detect novel pathogenic variants. And, to detect oncogenes stimulated by such variants in DNA of patient tumors. The approach works by detecting abnormal expression of tumor RNA. To validate the approach, investigators examined solid tumors and leukemia and demonstrated the strength of the approach.
Meanwhile, noncoding DNA accounts for 98% of the human genome. Nonetheless, rise in number of evidence suggests more than 80% of noncoding genome is functional and may control gene expression. In studies carried out in populations, it is foundvariants in noncoding DNA are associated with higher cancer risk. However, only a small number of noncoding variants in tumor genes contributing to initiation of tumor have been discovered. To find the variants, it required a whole genome sequencing analysis of many tumor samples.
The Cis-X approach is a fundamental deviation from currently used approaches that require a very large number of tumor samples. The existing approach can only detect noncoding variants that occur recurrently.
Meanwhile, cis-X is developed by means of use of aberrant gene transcription to reveal the function of noncoding variants. This is to enable the discovery of noncoding variants that drives cancer in individual tumor genomes. The detection of variants that result in dysregulation of oncogenes can extend the scope of precision medicine to noncoding regions.