Hope for Cancer Patients in Genomic Data Sharing

By Sunny Lewis

BELFAST, Northern Ireland, May 23, 2016 (Maximpact.com News) – Oncologists share information about their cancer cases through medical journals and conferences, but now cancer experts want to assemble big data files on millions of cancer patients from around the world for high-performance computers to analyze.

Professor Mark Lawler of Queen’s University Belfast’s Centre for Cancer Research and Cell Biology believes analysis of patients’ genetic information will reveal relationships that could hold the keys to revolutionizing cancer prevention and care.

“Cancer is an incredibly complex disease, and it is constantly changing. Each person’s cancer is different,” Lawler said. “The key to staying ahead in the fight against cancer is to properly understand how the disease evolves. We need to look at the big picture and identify patterns between groups of patients, whose information currently resides in different databases and institutions.”

Professor Lawler is corresponding author of a paper on the subject published last week in the international journal “Nature Medicine.“

“The term ‘big data’ refers to huge amounts of information that can be analyzed by high-performance computers to reveal patterns, trends and associations,” said Lawler. “In medical terms, this includes clinical and genomic data that is derived from patients during, for example, diagnostic testing and treatment.”

“Imagine if we could create a searchable cancer database that allowed doctors to match patients from different parts of the world with suitable clinical trials,” Lawler said. “This genetic matchmaking approach would allow us to develop personalized treatments for each individual’s cancer, precisely targeting rogue cells and improving outcomes for patients.”

 Professor Lillian Siu from Princess Margaret Cancer Centre and the University of Toronto is joint lead author on this study. “With the development of new technologies that have enabled the rapid and affordable profiling of cancer tumors, there has been an explosion of clinical and genomic data,” she explained.

 “Hospitals, laboratories and research facilities around the world hold huge amounts of this data from cancer patients. But this information is currently held in isolated ‘silos’ that don’t talk to each other,” said Siu. “It is this lack of information sharing that threatens the advancement of tailored patient care.”

The paper by Lawler and Siu highlights the potential of ‘big data’ to unlock the secrets inside cancer cells and enable the development of more effective personalized treatments.

“To do this,” said Lawler, “we must break down the ‘data silos’ that Professor Siu refers to and ensure that genetic and clinical information is shared.”

For example, an experimental drug that stimulates the immune system, used in combination with chemotherapy, shrank tumors in patients with pancreatic cancer, according to a preliminary U.S. clinical trial of 47 patients published in April in “The Lancet Oncology.”

Pancreatic cancer is often diagnosed too late for patients to have surgery, as their disease has started to spread. At this point, doctors can use chemotherapy and combinations of other therapies to control the disease, but survival remains low for these patients.

 The immunotherapy drug, known as PF-04136309, attacks certain immune cells found in pancreatic tumors. These cells prevent other parts of the immune system from attacking the cancer. Research has shown that the drug can alter this response, and help turn the immune system on again.

Professor Andrew Biankin, a Cancer Research UK expert in pancreatic cancer based in Glasgow, said, “There is a desperate need for new ways to treat pancreatic cancer. And this promising early stage study suggests that treatments that harness the power of the immune system may be of benefit to people with pancreatic cancer when combined with chemotherapy.”

If shared, the genomic data from the 47 test patients in this initial study could be of great help to others with similar pancreatic cancers.

Lawler also co-chairs the Cancer Task Team of the Global Alliance for Genomics and Health (GA4GH), established in 2013 to create a common framework for the responsible, voluntary and secure sharing of patients’ clinical and genomic data.

GA4GH’s founder, David Haussler of the Genomics Institute at the University of California Santa Cruz, is a co-author of the genomics data-sharing paper with Lawler and Siu.

Growing quickly, GA4GH is a partnership among scientists, clinicians, patients and the IT and Life Sciences industry involving more than 400 organizations in over 40 countries.

Members range from small hospitals and laboratories to major genomic centers like the Broad Institute in the United States, BGI in China, and the Wellcome Trust Sanger Institute in the United Kingdom, even Google and Amazon.

Writing in Bio-IT World, Aaron Krol points out, “These members have signed on to GA4GH out of recognition that, twelve years after the completion of the Human Genome Project, the growth of genomic data has outstripped the containers built to hold it. Most of the computational structures that scientists use to deal with DNA data were invented ad hoc, at a time when sequencing even the genome of a single bacterium was a huge accomplishment. Through its Data Working Group, GA4GH wants to replace many existing standards, conventions, and file formats with new ones that will scale to searching through genomes at the level of whole populations – and, crucially, make it easier for separate organizations to share data.”

It may be a good idea to share genomic data in an effort to conquer cancer, but there are many challenges, as Professor Lawler acknowledges.

“This data sharing presents logistical, technical and ethical challenges. Our paper highlights these challenges and proposes potential solutions to allow the sharing of data in a timely, responsible and effective manner,” Lawler said. “We hope this blueprint will be adopted by researchers around the world and enable a unified global approach to unlocking the value of data for enhanced patient care.”

Professor Lawler is funded by the Medical Research Council and Cancer Research UK. The paper, entitled ‘Facilitating a culture of responsible and effective sharing of cancer genome data’ is published in “Nature Medicine,” Volume 22, Number 5, pp 464-471 May 2016.

Video by David Haussler: The Quest to Conquer Cancer: Computer Geeks to the Rescue! (14 minutes)

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Featured Image : Scanning electron micrograph of a multi-cellular prostate tumor treated with nanomedicines carrying the anticancer drug doxorubicin. The purple regions show areas of cells dying through programmed cell death, or apoptosis, while the yellow-green regions are healthy cells. (Photo by Khuloud T. Al-Jamal & Izzat Suffian / Wellcome Images) Creative Commons license via Flickr