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New data tool mines whole exome sequencing to match cancer with best drug


​A University of Colorado Cancer study published today in the Journal of the American Medical Informatics Association (JAMIA) describes a new tool that interprets the raw data of whole exome tumor sequencing and then matches the cancer’s unique genetics to FDA-approved targeted treatments.
 
“Whole exome sequencing is becoming more available to patients and this tool will help them distill the sequencing data to candidate genes and link them with therapies,” says Aik Choon Tan, PhD, investigator at the CU Cancer Center, associate professor of Bioinformatics at the CU School of Medicine, and the paper’s senior author.
 
The tool, called Integrating Molecular Profiles with Actionable Therapeutics, or IMPACT, starts with the data generated by whole-exome sequencing – a string of A, T, C and G hundreds of millions of letters long. IMPACT then maps this string onto the human genome to partition the raw data into segments that correspond to the body’s approximately 20,000 genes. The tool then compares the code of these genes to “normal” gene patterns to discover which genes differ in ways that could guide the development of cancer. (In a second step, IMPACT also counts the number of gene repeats, which when adjusted higher or lower can also drive the growth of cancer.)
 
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