From The Broad to the Clinic | Front Line Genomics
Cambridge, MA, Broad Institute (June 27, 2016) –
A room containing over 50 sequencers makes an odd noise. For one thing it’s very cold – all that machinery pumps out some serious heat – so there is a constant whoosh of air-conditioning. The machines themselves whirr softly, punctuated by a constant Morse code of beeps. That is the sound of data generation on a phenomenal scale. This was the final room on our tour of The Broad Institute, which so far had taken in everything from DNA extraction to seriously advanced automated sample preparation.
The Broad Institute, the largest sequencing laboratory in the world, has 28 Illumina HiSeqX sequencing machines (and 25 from previous iterations of the platform), each producing 1 terabyte of data every 2-3 days. This rate of production is so prodigious that the Institute has now moved its data storage out of a physical central server and into the cloud.
Aside from getting my first look at the legendary HiSeqX in action, the visit to The Broad also brought home just how much of a challenge the $1000 genome really is. For one thing, the electricity bill to run a sequencing room like this one runs into the millions. And outsourcing data into the cloud is not always a cheap option, although it does save on valuable floor space that could be taken up with MORE SEQUENCERS. In reality, even working at this kind of scale the costs of data storage and library generation alone put the cost of a whole genome at closer to $2000.
Meanwhile, back onsite, Carl and Eleanor were deep in the workshops, learning how this tidal wave of information can be put to good use!
Getting all that data to the clinic
While Liz was out at the Broad Institute, it was seminar heaven here at the Festival grounds. ‘Translating NGS Data Into The Clinic’ was one of the morning’s most popular sessions. Danielle Greenawalt (Bristol-Myers Squibb), Long Phi Le (Massachusetts General Hospital), and Carl Barrett (AstraZeneca), did a fantastic job presenting the reality behind getting NGS into the clinic.
While the technology is there, the centralised standards are not. It was also startling to hear just how difficult it is to get a diagnostic approved. We hear a lot about how inexpensive NGS is these days, but it is still prohibitively expensive for many hospitals. At the moment, it’s really only the big hospitals who can afford it (and the teams you need to make it all work!).
There is still a lot of figuring out to be done. Sequencing will continue to get cheaper. When that barrier to entry drops again, we need to have standards in place and a good idea of how NGS should work efficiently in the clinic. If that happens, it will make widespread adoption a much more realistic possibility.
Actionable information for patients and their physicians
Xuan Shirley Li, Chief Scientific Officer at Molecular Match, started off the workshop by saying that we still had a long way to go to achieve the cancer moonshoot laid out by Vice President Joe Biden. Although around 300 thousand genomes and exomes of Americans have been sequenced, that still only makes up less than 0.1% of the population.
James Walsh, MD Anderson Cancer Center, was up next. He started his career at Genentech, and now works at MD Anderson Cancer Center on lung cancer. Along with some amusing slides on God’s disapproval of the annoying hackers discovering the genome, he covered the great begin done around the EGFR gene mutation. There is still resistance, both against the treatment due to mutations, as well as in the clinic because of the high number of molecular profile subsets of the variant.
Jack Whelan, a research and patient advocate, took the stand and brought the audience back down to Earth as he described what it was like living a rare diagnosis. “It’s like the feeling you get on a roller coaster”, he said. He gave great positive vibes as he described the importance he placed on laughter as the best medicine, and how involving patients in clinical trials is just as importance as the research. ‘Patient-centric’ can be just a buzz word for some bio-pharma, the importance should be placed on compassion.
Finally, Corrie Painter, Associate Director of Operations and Scientific Outreach at the Broad Institute, explored the importance of support from fellow patients, such as finding a Facebook support group on Angiosarcoma, a rare blood vessel tumour with effects only 21 people in the world every year. The knowledge that people had in that group went far beyond anything else Corrie could find and highlighted the importance of the engaged patient. If they could crowd source photos of themselves for the Facebook group, why couldn’t they crowd source their tumours?
There were also some great questions raised, such as the need to improve IT as part of healthcare strategy, with Jack Whelan making the point that his car dealership had better patient, or customer, data than hospitals! All round a great sharing of ideas and for someone coming to patient data fairly new, it was eye-opening to see just how involved some patients are prepared to get.
Today also saw the inaugural Drug Development Leaders Meeting at the Festival. Senior representatives from Regeneron, Takeda, Merck, AstraZeneca, Pfizer, Teva, and Roche, met to discuss a range of topics: patient access and clinical trials, using real world data, companion diagnostics, collaborations, and the Precision Medicine Initiative.
After four hours of talks, we look forward to the white paper to follow!