A Cancer Data Pipeline in the Clouds

Over the decade since the completion of the Human Genome Project, next-generation sequencing has spurred the field of genomics to a faster and faster pace.

Laboratories studying the genetics of disease can gather detailed data from more patients at a cheaper price than ever before, bringing scientists closer to new treatments and realizing the vision of personalized medicine. But even as the speed of sequencing shifts into a higher gear, other research tasks lag behind, producing unnecessary drag that prevents the science from truly taking flight.

Kenan Onel, MD, PhD

Globus Genomics is a new cloud-based platform designed to eliminate these hindrances, combining data management tools, elastic computation and a graphical workflow environment. In one of the first Globus Genomics pilot projects, the platform helped the laboratory of Kenan Onel, MD, PhD, associate professor of pediatrics and director of the Familial Cancer Clinic at University of Chicago Medicine, tackle the growing data challenges involved in studying the genetics of cancer.

 

A LARGER HAYSTACK FOR CANCER GENETICS

The six researchers in the Onel lab search for genetic variants associated with predisposition to cancers, inflammatory bowel disease and other conditions. In a typical study, the laboratory gathers genetic information from multiple members of a family to look for variants that appear in those with the target disease, but do not appear in their healthy relatives. In one 2011 study, published in Nature Medicine, the laboratory discovered two genetic variants that predict a higher risk for therapy-induced secondary cancers in Hodgkin’s Lymphoma patients.

Recently, the Onel lab moved from genome-wide association studies (GWAS) to more detailed whole-exome sequencing. In GWAS, researchers look for hundreds of thousands of pre-chosen gene variants in a subject’s DNA, sampling only a small fraction of the genome. But whole-exome sequencing reads every piece of the genome that encodes proteins, allowing researchers to more easily discover unknown and rare variants.

Read more here about Globus Genomics and the Onel lab.

About Rob Mitchum (526 Articles)
Rob Mitchum is communications manager at the Computation Institute, a joint initiative between The University of Chicago and Argonne National Laboratory.
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