Category Archives: Uncategorized

ICHG2011: Epigenetic inheritance and rare variants in skin and inflammatory disorders

Yesteray was the first full day of the 2011 International Congress on Human Genetics in Montréal. This is the largest gathering of human geneticists in history, with over 7000 of us here to see over 350 talks by presentors from over 25 countries, along with thousands of posters. Exciting times all round.

As always, I aim to report on this blog at least one thing that I found interesting for every day of the conference. Also as always, I will be tweeting the odd thing of interest from my twitter feed @lukejostins, and you can get more in-depth coverage on the hashtag #ICHG2011.

This year I am also giving a talk. In fact I am giving one of the closing talks of the conference! (to put an overly positive spin on the graveyard slot). I’ll be talking at 3.15pm on Saturday in the Statistical Genetics IV session (room 517BC), so if anyone is interested in seeing a little something on disease risk prediction in families, come along!

Continue reading

BG2011: Geography and recent human evolution

The second to last day of Biology of Genomes is now over, and instead of the usual late night set of talks, last night we were treated to a “lobster buffet”, followed by “all genome-nerd band” Ethidium Spill, lead by Francis Collins. As always, you can follow live coverage via twitter at #BG2011, and you can also read Matthew Herper’s thoughts at the Forbes blog.

The quality of all the talks remains very high, but today I am only going to write about two. What I liked about both of these talks was the link between recent human evolution, geography and phenotype-associated traits, despite being two very different methodologies.
Continue reading

BG2011: Things to do with a genome

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

BG2011: The diverse life of non-coding DNA

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.

Continue reading

BG2011: High-Throughput Genomics Goes Mainstream

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.

Continue reading

BG2011: Wood cabins and chipmunks

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: Doing it with exomes

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.

Continue reading

ASHG: Getting At Low-Frequency Variants

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%.

Continue reading

ASHG: Genewise Assocation and Sequencing Families

All the ASHG talks that I have had to do analysis for have now been given, so today I’ve managed to dedicate my full attention to the sessions. Also a good day for tweeting; I managed to live-tweet quite a few talks on @lukejostins, and the #ASHG2010 hashtag has been totally rammed.

Larry Parnell over a Varigenome has been putting his ASHG notes up, if you are still hungry for details. Daniel Macarthur has promised a post on the “Identifiability in the Era of Genome-Scale Research” session for Genomes Unzipped, and I saw him getting pretty worked up about Jim Evan’s talk on his twitter feed, so hopefully we’ll see something from him as soon as he’s done being dead of plague.

Two sessions today, “Statistical Analysis of Human Sequence Variation” and “Finding High-Risk Susceptibility Gene Variants”, seem to encapsulate the cutting-edge of disease gene association, and illuminate where disease genetics is heading in the immediate future.

Continue reading

ASHG: Diploid Assembly and Low-Key Personal Genomics

Unfortunately, I’ve had a bit of a distracted day today; some analysis that is being presented tomorrow failed, and as a result I dropped off the radar somewhat trying to put it right.

I sat in the “Lessons from High-Throughput Sequencing” session, and picked up bits of it, but was generally distracted. Zam Iqbal presented some very impressive work on assembling genome sequence as diploid individuals, which will be extremely important in the future. The main reason for this is that it allows accurate HLA typing from whole-genome sequencing; HLA typing costs hundreds of dollars, so getting it for free as part of the genome is a major win for personal genomics.

Low-Key Personal Genomics

An interesting, though not new, story came in the form of back-to-back talks by Euan Ashley and Russ Altman on the disease and pharmacogenomic work on Steve Quake’s genome.

Continue reading