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Thursday, April 9, 2009

BC Genome Forum 2009

I had a lot of stuff to blog about, but just haven't had the time to write any of it down. I haven't forgotten about any of it, but it's just not going to happen before this weekend. I'm currently bogged down in debugging something that I REALLY want to get working (and mostly is, but still has something slightly fishy going on...), and just too much going on outside of work to get it done otherwise.

Still, I figured I should mention a few things of interest before I forget to discuss them at all.

I attended some of the BC Genome forum lectures on Friday. I skipped the morning, since they seemed mainly irrelevant to anything I do - which was later confirmed - but caught the session on personal medicine. For the most part, it was focused the ethics of personal medicine. I was considering blogging those talks, but they just didn't have enough interest factor, individually.

For the most part, the speakers were caught in a pre-2006 time warp. Everything was about micro-arrays. One of the speakers even said something to the effect of "maybe one day we'll be able to sequence the whole human genome for patients, but we're no where near that yet." Needless to say my coleagues and I all exchanged startled glances.

Still, there were a few things of interest: There was a lot of discussion about what conditions you find in genomic screens that you should feel obligated to discuss with the DNA donor. They gave the example of one volunteer to tested positive for a condition that could be life threatening if they were to undergo surgery for any reason. It's easily treated, and can be easily managed - if you're aware of it. Since the donor was in the healthy control group, they were clearly unaware that they had the condition. In this condition, where the donor was clearly at risk, the penetrance of the gene is 100%, and the patient could clearly do something about the problem, it was "a no-brainer" that the donor should be notified.

However, for most of the information people are pulling from arrays, it's not always clear if the ethics tilt so heavily towards breaking confidentiality and reporting information to the patient. How this type of situation should be managed was touched upon by several of the speakers. The best solution we'd heard during the forum was one group who had set up an advisory board who sits down on a yearly/6-month basis to determine which - if any - conditions should be returned to the donors.

Unfortunately, no one described the criteria used to make that decision, but the concept is pretty solid.

The surprising thing for me was that after several years of using mechanisms like this, only 12-20 conditions were being returned. In the world of genomics, that's a VERY small number, but is probably more representative of the fact that they're using arrays to do genome screens.

And that is one of the reasons why it felt like 2006 all over again. All the mechanisms they've put in place are fine when you're talking about a couple of nnew conditions being screened each year. Within 2 years we'll be routinely doing whole genome sequencing with Pacific Biosciences SMRT (or the equivalent) systems, and whole genome association studies will become vastly more plentiful and powerful. Thus, when your independent board gets 1200 candidate diagnostic genes with actionable outcomes per year, that mechanism won't fly.

What's realy needed (in my humble opinion) is for a national board to be created in each country to determine what gene information should be disseminated as useful and actionable - possibly as part of the FDA in the states. That would also be very useful for reining in companies like 23andMe and the like... but that's another story altogether.

Moving along, there were a few other interesting things at the event. My personal favorite was from the Smit lab in the microbiology & immunology department at UBC, presented by Dr. John Nomelini, who I know from my days in the same department. They have a pretty cool system, based on the caulobacter bacterial system, where they can pull down antibodies (similarly to streptavadin beads) but using a much cheaper and easier system. While I don't know the legal issues around the university's licencing of the technology, Dr Nomelini is trying to find people interested in using the technology for ChIP experiments. I've proposed the idea to a few people here to test it out on ChIP-Seq, which would help bring the cost down by a few $100. We'll see if it gets off the ground.

So, if you've made it this far, hopefully you've gleaned something useful from this rambling post. I have some coding to do before my parents arrive for the easter weekend. Time to get back to debugging...

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