06 November 2014

US hospital to build store of cancer genetic data

An American university wants to build a store of genetic data about various metastatic cancer cases, theoretically sharpening treatment or even coming up with new therapies.


A major California university hospital is exploring ways to gather and use genetic information gathered from cancer patients, hoping to break new ground in a fledgling field of genomic medicine.

Read: What's your exercise DNA?

The University of California San Francisco said in an interview it is working on a new project with Silicon Valley start-up Syapse.

Data about cancer cases

Using Syapse's technology, it wants to build a store of genetic data about various metastatic cancer cases with patients' consent, theoretically sharpening treatment or even coming up with new therapies.

It plans to announce its initiative on Thursday.

The application of genomics to cancer care is a rapidly developing field. Companies such as Foundation Medicine Inc are taking specimens from tumour cells to find changes or vulnerabilities that can inform care.

But UCSF hopes its use of data analytics can set it apart: Few hospitals are setting aside resources for a database of genetic and medical information that a panel of experts can analyse as part of routine care.

Blood samples to assess cancer risk

What is unique about UCSF's methods is that its medical school is sequencing DNA from tumours and taking blood samples to assess overall cancer risk, said Robert Nussbaum, the medical geneticist leading the project. Nussbaum said he hopes to use the data to identify patients for targeted therapy as opposed to the usual chemotherapy.

With one such sample, UCSF's researchers say they will use Illumina Inc's technology to sequence more than 500 genes implicated in cancer.

Oncologists will recommend these genetic tests to patients with a recurrent cancer or those who are not responding well to treatment.

Read: Genes may determine how much coffee you drink

, one of the better-funded health providers in the region, would not say how much money has been set aside. Programme manager Kristen McCaleb said she expects it to last three years.

Six-year-old Syapse's technology stores genomics data in hospital IT systems. It integrates factors into its database such as whether the patient smokes, family history and the latest medical research.

McCaleb said while genetic tests are not new, the hospital had lacked the ability to integrate new data types into everyday care.

Aims to collect data from 2000 patients

The hospital aims to accumulate test results from about 2 000 patients per year. McCaleb selected Palo Alto-based Syapse after reviewing vendors including Oracle.

UCSF isn't the only hospital to apply genomics to cancer. MD Anderson Cancer Centre at the University of Texas and other facilities are launching similar initiatives to treat cancer patients.

Read: Scientists unravel the genetics of human height

But according to Luke Lee, an associate at venture firm Asset Management Ventures, only a small number of hospitals are actually investing in tools for cancer genomics. Gene-sequencing tests are expensive and many physicians are reluctant to order them for patients.

"We're in a Catch 22 bind: If we don't gather the data to indicate whether it's useful, we won't know if it's useful," said Nussbaum. "But if we don't know it's useful, no one pays for it. Someone has to break the cycle."

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