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Biology of Genomes 2011 is keeping up the momentum, and the third day had some great talks, along with some sort-of-great burgers. The live coverage continues apace on the #BG2011 hashtag.

As a slightly different approach to the last two days, all the talks I am going to report on today are based on one concept. Suppose you have sequenced a new genome, and you want to get the best out of it. Maybe you want to find a Mendelian mutation or a large-effect risk factor, or just look at personal genome for overall assessment. Today’s Computational Genomics session was full of great ideas for what you can do to get the most out of your shiny new genome sequence. Continue reading →

The second day of Biology of Genomes has been and gone, and a brief wine-and-cheese interlude followed by talks to 11pm has ensured that everyone came away with a warm, if somewhat fuzzy, overview of the final session on Cancer and Functional Genomics.

Ewan Birney presented a deluge of information on ENCODE data with a host of interesting insights that I was entirely too jetlagged to take in at all, so will not attempt to discuss. However, there were a few interesting talks that I think I followed well enough to communicate.

As usual, you can follow live tweets from the conference at #bg2011. While poor WiFi performance has lead to somewhat patchy coverage of talks, most presentations have at least one person reporting on them.

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The first day of Biology of Genomes has now come and gone. The ambiguities about twitter and blog reporting have been resolved, and tweeting has started in earnest; you can follow live coverage of most of the talks on the #BG2011 hashtag.

The subject of the evening session was high- throughput genomics. There were a lot of cool talks, but two in particular got my excited, for reasons that I will explain at the end of the post. Both describe very elegant new sequencing-based techniques for studying gene regulation through transcription factor binding.

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As those of you who check this blog regularly (hi mum!) may know, I haven’t written anything since the American Society of Human Genetics conference at the end of last year. I tend to only really write posts here during conferences, when I try make daily blog posts about the talks I attend. In that vein, starting tomorrow is the Biology of Genomes meeting at Cold Spring Harbour; a major annual genomics meeting that marks the start of the conference cycle. I am here with fellow GNZer Daniel MacArthur, and hopefully both of us will get some content out, be it here, at Daniel’s Wired blog, at Genomes Unzipped, or on our respective twitter feeds.

The Biology of Genomes meeting can be somewhat difficult to navigate for a blogger and tweeter. There has been some controversy about the extent to which scientists can write about the conference via social media platforms, and I have no interest in pissing people off, so we will have to see what I can and cannot write about. I hope to put together posts about talks where the speakers specifically allow blogging coverage.

One thing I can write about is the laboritory itself. Me and Daniel are staying in a bizarrely picturesque little wood cabin in the woods on the Cold Spring Harbour Lab site:

CSHL is full of interesting wildlife, such like geese and swans, along with squirrels and a host of birds. As a European, one of the most exciting aspects is the presence of Eastern Chipmunks, which hang around in the woods around the cabins, looking cute but very slightly like they are planning something:

The contrast between my experiences this year and last is stark. This year, I have already had a good flight, a pretty wood cabin and an unexpected wine and cheese party and poster session with a group of honeybee scientists. Last year, I had an airway full of ash clouds, a dingy motel on a busy road, and a rickey old school bus with dodgy seatbelts and a tendency to violently launch you into the air at every bump. So all bodes well so far.

The cabi image is actually from Hugh Robertson’s website, and the chipmunk is from Wikipedia.

ASHG 2010 is now over, and I am back on Albion. Either me, or Daniel, or both (or, indeed, any of the other GNZers) will have personal genomics roundup over at Genomes Unzipped sometime this week.

For the last of these posts, however, I thought I would just report on the entirety of the Exome Sequencing session on the final day of the conference. I loved this session for the diversity, the number of different projects that are using exome sequencing to address old questions. It shows how much biology is tech-limited: the moment a powerful new technology becomes available at a low price it is used in every field by a flood of researchers who have been waiting for exactly this sort of data.

Other than that, there wasn’t an overall theme to the session (or to this blog post), other than Exome Sequencing Is Cool.

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Another interesting day at ASHG so far (and not over yet). As with last year, genotype imputation (using reference sets to infer the genotype of untyped variants in your samples) has been a pretty major subject of the meeting. In particular, the idea of using large sequencing refernce sets like the 1000 Genomes Project to infer lower frequency variation in existing Genome-Wide Association Study datasets has been raising people’s hopes for accessing new types of variation “for free” (i.e. without having to regenotype samples).

Getting at Low-Frequency Variation

The “Genome-Wide Association Studies and Imputation” session started off with Vasyl Pihur’s somewhat provocatively titled talk “Neither common nor rare variation can explain much of phenotypic variation”. The point he was making (and confirmed with some model fitting to existing datasets) was that it is hard for very rare variation to explain much heritability, because so few people carry any particular variant, and very common variation has still left much heritability unexplained, so our best bet for filling in “missing heritability” is varients of intermediate frequency, the neither-common-nor-rare “low frequency” band that lives between 0.5% and 5%.

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I’d like to introduce a new group blog, called Genomes Unzipped.

Genomes Unzipped is written by a number of major genetics bloggers, including Daniel MacArthur of Genetic Future, Dan Vorhaus of Genomics Law Report, Caroline Wright of the PHG Foundation, and Jan Aerts of Saaien Tist, as well as a number of other geneticists who are new to blogging. And me, of course.

The really exciting thing about this blog is the diversity of people who are working on it. We have people from a range of fields, including science, law and public health, who hold a range of opinions. Some of us are very gung-ho about direct-to-consumer genetics, and enthusiastic about the benefits, while others are sceptical, and more in favour of regulation. While we’ve been putting together the blog, we’ve had many meetings between contributors, and with outside advisers (such as ethicists), and I have already learned so much before anything has been published. So, needless to say, I am pretty excited about the whole project.

The current blog is in the beta stage at the moment; this is because what you see now is not yet the finished version. Soon, the project will expand in scope; stay tuned for more announcements.