UCSF Partners with UCLA in New Exome Sequencing Initiative

UCLA has agreed to make available the entire exome sequencing data set to UCSF reearchers by secure download. This information could have potential research and clinical implications.

Clinical Laboratories at UCSF Medical Center have entered into a partnership with UCLA to have their laboratories perform exome sequencing for inherited disorders on UC San Francisco patients, effective April 14.

The human genome – or the total genetic content of a human being – is stored on 23 chromosome pairs. Broken down further, the human genome occupies more than 3 billion DNA base pairs. Just a small fraction – 1.5 percent – is translated into proteins, the functional players in the body.

This exome sequencing project moves UCSF one step closer toward the goal of precision medicine.

The exome consists of all the genome’s exons, which are the coding portions of the genes. Exome sequencing selectively sequences the coding regions of the genome as an inexpensive but still effective alternative to whole genome sequencing.

This partnership with UCLA simplifies the processing and handling of the exome samples for both providers and laboratory staff. All five UC-based medical centers have been working as a consortium for the past 15 years.

“UCLA is the only other UC that is doing exome sequencing. It keep things within the UC system,” said Timothy Hamill, MD, director of clinical laboratories at UCSF Medical Center’s China Basin and Parnassus campuses. “And they're going to provide us some significant value add that we don't get from the reference labs, such as the ability of our faculty to be able to sit in via a secure web conference to the actual sign out of the cases where they can discuss the clinical finding for the individual, their phenotype or the problem they're trying to diagnose.”

Timothy Hamill, MD

From there, the clinician can go over with the geneticist what the exome sequencing found and which of the abnormalities or findings might apply to the disorder they're looking for.

UCLA has also agreed to make available the entire exome sequencing data set to UCSF researchers by secure download. This information could have potential research and clinical implications.

Working directly with UCLA also gives UCSF researchers a trusted partner to help validate tests, which is a requirement per federal regulations, according to Hamill.

“So not only can our clinicians reexamine it whenever they want, they would also be able to run it through various bioinfomatics pipelines to see if they get different results for research purposes,” Hamill said. “So there's a lot of interplay that will go along in working with UCLA.”

This exome sequencing project moves UCSF one step closer toward the goal of personalized medicine.

“What you know about a person's genomic makeup will go a long way to customizing care for them in terms of risk factors for inherited disorders,” Hamill said. “There's a whole other level of exome sequencing for cancer. If you’re able to understand the exome for a tumor, you may be able to significantly impact therapy. If you know what the tumor abnormalities are, then you can start targeted therapy.”

Timothy Hamill, MD, left, and Farid Chehab, PhD, examine one of the machines that are instrumental in the exome sequencing project.

Exome sequencing also can be cost-effective compared to sequential targeted gene sequencing. The former costs roughly $2,800 for an individual while the latter can run easily cost $10,000 to $15,000.

“The cost of exome sequencing has come down so rapidly that it's going to be the cheaper way to go and give you more information than trying to do all these one-offs,” Hamill said. “Looking at each particular gene can become an odyssey of trying to figure out which is the mutation whereas an exome will do it in one fell swoop.”

Hamill’s work runs in parallel with Robert Nussbaum, MD’s Genomic Medicine Initiative, which focuses on the research side. Hamill is focusing on the clinical side, providing the clinical testing arm that complements Dr. Nussbaum’s work.

Photos by Leland Kim

Blog Type:  Research Publications