GigaScience was on hand to witness plenty of lively discussion last week at the annual American Society of Human Genetics jamboree: the International Conference of Human Genetics in Montreal. As always, the meeting had a strong medical genetics presence but the rapid growth and uptake of genomics technologies in the field produced much fascinating work on display this year. However, some amongst the heavy clinical contingent were obviously uncomfortable with the lack of clinical validation of much of this work and debate was heated in many of the plenary debate sessions. This can be followed if you are patient enough to trawl the >4700 tweets utilizing the hashtag #ichg2011 or, fortunately, a growing number of ICHG 2011 webcasts.
The scene was set in the opening “Whole Genome Sequencing: To Do It or Not to Do It?” panel (involving the always controversial James Watson memorably talking about “Genetic Losers”) and the technology v. medicine debate was particularly polarized in the “Current and Emerging Sequencing Technologies” panel the following day (nicely summarized by Luke Jostins in his blog). Whilst there was a consensus that sequencing will become a standard tool in the diagnosis of genetic diseases, the second panel was divided on whether this approach should be a purely targeted one, restricted to finding the pathogenic mutations causing a disease. Some of the more clinically focused members argued that medical genome sequencing was “hype”, held back by the lack of genetic councilors, lack of clear policies from healthcare providers and insurance companies, and a very poor level of genetic training of clinicians in general.
The concerns raised have much merit but the circular arguments and calls for further debate didn’t really acknowledge that technological advances and events on the ground are threatening to make them redundant. It was obvious that panelists such as Rade Drmanac from Complete Genomics were going to argue against genomics technology in the clinic, but some of the clinicians on the board provided evidence that many physicians are already using them on a large scale. Joris Veltman provided examples from his recent work using exome sequencing rather than single gene tests on 500 individuals, and our editorial board member Ming Qi also admitted to doing similar work in the clinic. With one lucky attendee at the conference winning the chance to have their exome sequenced from 23 & Me (market value of 999 USD from 23 & Me – or BGI), many on Twitter pointed out that the market will likely decide the debates’ outcome.
Also on display at the meeting were many examples of larger and larger projects utilizing exomic or even whole genome sequencing. Announcements were made at the meeting from Autism Speaks and our colleagues at the BGI about a new project to sequence 10,000 individuals with Autism spectrum disorders. Initial data was presented by Tim Spector of his EpiTwin project, a BGI collaboration to sequence the epigenome of 5,000 twins. Cisca Wijmenga also presented an overview of the “Genome of the Netherlands“, another BGI collaboration that has already sequenced 250 Dutch trios. With many similar scale projects presented at the meeting such as Nick Schork‘s work with Complete Genomics to produce 1000 human reference genomes of the “Wellderly“, it’s clear that the field is having to deal with bigger and bigger datasets. A nice visual representation of this was shown by Cisca Wijmenga when she presented a slide showing the number of discs needed to transfer 770 whole genomes worth of GoNL project data from BGI back to the Netherlands.
The particularly challenging issues of scale remain. Hints of future ways this is likely to be tackled included an announcement at the meeting from DNAnexus about their tie-in with Google to host a mirror of the (no longer defunct) Short Read Archive in the cloud. The prickly topic of patient data security also needs resolving, and there were promising posters on display trying to improve utility and security of this type of data with tools such as MedSavant by Marc Fiume and GWAS data encryption protocols from Itsik Pe’er. All of these issues surrounding data handling are very relevant to the scope of GigaScience, and we are currently commissioning papers covering the many issues surrounding the handling of medical data. If you have an interesting point of view you would like to put forward as a commentary or review in this area or if you have useful research or tools relating to this, please contact us at firstname.lastname@example.org about submitting to the journal. Whilst there is a huge amount still to resolve and do, these areas are of great interest and we are keen to follow and be part of the debate in the future.