Tagged: next gen sequencing

Observations from The Clinical Genome Conference

I am interested in the progress of “personalized medicine,” so I participated in TCGC — The Clinical Genome Conference in San Francisco this week.     It is a small conference, mostly academics and scientists.  The biology and statistics were over my head,  nonetheless, I’m glad I went.

The core question is — is NGS (next generation sequencing or whole genome sequencing) ready to be used (and how) in clinical medicine?     We all hear about the $1000 genome is around the corner (that is your whole genome sequenced for ~$1000) — but having this test done, will it enable a physician to a) better diagnose what is wrong with the patient and b) will it enable the physician to better treat the patient?

My quick observations are:

  • I was surprised by the number of teams working on various elements of the problem around the world.    Prior to the conference I was familiar with several efforts, but there must be literally hundreds of teams working on tools, pipelines, proprietary data sets etc.    Clearly many see the science and market opportunities and they are pursuing them.
  • Many of the presenters talked about the same problems — lack of clear interfaces across the pipeline, lack of a complete or gold reference standard, need different tools for different parts of the genome/exome, still lots of manual curation required etc.   Then there were some new problems raised like patient consent, patient/physician reporting and education, clarity around things like sensitivity and specificity of the results and recommendation.    Many of these issues were raised in the CLARITY challenge I posted about earlier.
  • Lots of teams/companies are going after building an end-to-end pipeline of tools, dbs and knowledge.    Most of the existing tools are open source, as are many of the knowledge sources.    Given the immaturity of the industry — perhaps a vertically integrated solution is the right business approach.   There seems to be a some  “build it and they will come” thinking around business models.
  • Few talked about what I think a central problem re: faster adoption of NGS in clinical medicine is — namely the lack of new, targeted, identified or approved treatment options.    The “test” potentially improves the physician’s ability to diagnose the problem or understand the root cause of the disease — but for many conditions there are no treatment options.    The science is learning faster around the diagnosis side of the equation, which is good — but the lag time around finding, building and approving treatments may be the rate limiter for growth of the sector.
  • There are some interesting ideas around sharing knowledge and “crowdsourcing” solutions to the tough problems that should accelerate growth and adoption.     I found this one intriguing www.bioplanet.com/gcat — trying to build truth sets.

The sector is super exciting for its potential and filled with really smart, interesting and passionate people.     I will continue to monitor and stay involved.