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Saturday, November 22, 2008

Is medicine ready for 2nd Generation Genomics?

Yesterday was the second day of the 10th Annual B.C. Cancer Conference, which draws in researchers, practitioners and cancer survivors from around BC and the world. It also draws in a lot of drug companies, but that's somewhat besides the point.

One particular part of the conference caught my eye as a must see: the Cancer Genetics Laboratory Open House. This event was a set of posters and hands-on demonstrations for how genetics can be used to help cure cancer. Since that's essentially my thesis project, I figured I absolutely had to attend it.

Unfortunately, I was rather disappointed in the scope of the work they do, though not because they do poor work, but rather that my expectations were too high. For breast cancer, they only screen people who have a family history of breast cancer, and even then they only look for two markers in BRCA1 and BRCA2. That's not a bad thing, though - those two genes make up a significant portion of the hereditary breast cancer risk for women. What surprised me was how reactive the technology was - the lab only screens patients with a high likelihood of carrying the mutant genes, and only patients referred to them by physicians who suspect the familial disease association. Again, this is pretty standard, so there's no criticism meant.

However, what concerns me is whether these people will be ready for the onslaught of information that's about to hit them. Ina couple of years, genetics researchers will be handing off the testing of tens of thousands of simultaneous genes, gene splicing defects, and complete analyses of transcriptomes/genomes, which are currently being done in the lab, as we speak. This is a far cry from doing PCR on two genes to look for SNPs, with a massive technology gap in between.

The Cancer Genetics Lab appears to have 15 doctors and technologists, which is a small staff to support a whole city of several million people, let alone the whole province. I have to wonder if any of them have any experience with 2nd-generation sequencing, seriously high throughput genetic screens, or even the concept of how to do genetic councilling about risk factors in the "whole genome diagnostics" age. Of course, I didn't spend too long at the session, so I don't know if anyone there is an expert, however the few people I spoke to weren't really talking about the upcoming changes to their discipline, so I'm a little skeptical.

In any case, I do have to wonder how this pandoras box of information we're unleashing about the makeup of patient's cell and heredity will effect the downstream medical practitioners, and how well they are prepared to deal with it. Are the seminars to bring these people up to speed on what's coming at them? Are the agencies ready to shell out the money for the infrastructure they'll need? Are the people writing the textbooks that educate these people including chapters on the subject?

It's all nice that I talk about trying to understand how a cancer works in the lab through 2nd-generation sequencing, but I have to wonder what we should be doing in the meantime to prepare them from the firehose of information that we're going to point at them and let loose. The personal genomics revolution is poised to land on these people like a ton of bricks, and with about as much mercy.

Then again, lest we be smug about it, how many of us are writing aligners for SMRT sequencing that's already on the horizon in our own field. Preparing for the future is definitely hard when we're still coping with the present. I'm sure it's no different for the Hospital Genetics Labs, even if they're 15 years behind the cutting edge.

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Anonymous Michael said...

To see it from the positive side, I am sure there will be plenty of business opportunities at the interface between 2nd gen sequencing and healthcare.

November 22, 2008 8:20:00 PM PST  
Blogger Anthony said...

There is always opportunity in adversity. (=

November 22, 2008 9:59:00 PM PST  
Blogger Cath@VWXYNot? said...

Hello from a fellow blogger who also works at the BCCA! I attended that same session and I have to admit that your point didn't even occur to me - I was enjoying the presentations too much.

I prefer not to blog too much about the specifics of my job, but I have been involved in biomarker projects where the logistics of implementation were (peripherally) discussed. It is certainly going to be challenging!

November 28, 2008 4:10:00 PM PST  
Blogger Anthony said...

Hi Cath@VWXYNot?,

Thanks for your comment! I have to admit, I also enjoyed the presentations a lot - they were very good. (I hope it didn't leave any impressions to the contrary.)

Your point is well taken though - I know people at the BCCA are thinking about it, and I kinda get the impression that they're aware it's going to be a big shock, but I don't know who's really going to lead the charge in making it happen. (As a grad student, people don't tell me these things, so I can only guess at what's going on.)

Like all medical paradigms, nothing ever goes straight from the labs to the doctors who need it most, but I'm sure it will get there eventually. I just hope the transition won't be too hard on the people who are currently doing the work. (=

At any rate, thanks for mentioning your blog as well. I'll definitely be reading it in the future!


November 28, 2008 4:17:00 PM PST  
Blogger Cath@VWXYNot? said...

Jolly good, just please don't expect too much scientific content!

December 2, 2008 4:39:00 PM PST  

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