Tag Archive for 'blogs'

Identical twins usually do not die from the same thing

Over at Nature News, Erika Check Hayden has a post about a recent Science Translational Medicine paper by Bert Vogelstein and colleages looking at the potential predictive power of genetics. The take-home message from the study (or at least the message that has been taken home by, e.g., this NYT article) is that DNA does not perfectly determine which disease or diseases you may get in the future. This take home message is true, and to me relatively obvious (in the same way that smoking doesn’t perfectly determine lung cancer, or body weight and dietary health doesn’t perfectly determine diabetes status).

A lot of researchers have had a pretty negative reaction to this paper (see Erika’s storify of the twitter coverage). There are lots of legitimate criticism (see Erika’s post for details), but to be honest I suspect that a lot of this is a mixture of indignation and sour grapes that this paper, a not particularly original or particularly well done attempt to answer a question that many other people have answered before, got so much press (including a feature in the NYT). A very large number of people have tried to quantify the potential predictive power of genetics for a number of years – why was there no news feature for me and Jeff, or David Clayton, or Naomi Wray and Peter Visccher, or any of the other large number of stat-gen folks who have been doing exactly these studies for years. ANGER RISING and so forth.

But of course, the reason is relatively obvious. Continue reading ‘Identical twins usually do not die from the same thing’

Making sequencing simpler with nanopores

The Advances in Genome Biology and Technology (AGBT) conference, one of the main go-to destinations for those who get excited by DNA sequencing technology, is currently going down in Florida. Sadly, no-one from GNZ could make it this year, but we are keeping up with the various announcements about new genomics tech as best we can. One that caught our attention was the announcement of a brand new sequencing machine from a company that has previously kept very quiet about its technology.

Oxford Nanopore, who we have written about before, today announced two new sequencing machines to come out this year. The announcement has caused quite a buzz amoungst, well, everyone. Nature, New Scientist, GenomeWeb, BioIT World and Forbes all have reported on it, and bloggers Nick Loman and Keith Robison have also had a chance to talk to some of the Oxford Nanopore peeps about their new toys.

A lot of the interest has come from the (very cool) MinION, a tiny, disposable USB-key sequencer (shown in the picture above) that can sequence about a billion base pairs of DNA, and cost around $500-$900 each. The applications of this are endless – the ability to pick up a bit of biological matter, mix it with a few chemicals, and read whatever DNA is in it, could help with diagnostics, epidemiology, ecology, forensics. It is also (though not quite) the price where hobbyists could consider having a play; perhaps in a few years plug-and-play DIY genetics could be a possibility.

Less immediately striking, but still just as interesting, is the GridION sequencing machine. This is the work-horse of the nanopore sequencing world, made for reading lots of DNA, and scaling up to massive sequencing centers. Obviously, many scientists are going to be very interested in many of the features (notably, the ability to read very long pieces of DNA, a trick that has previously been more-or-less impossible to do reliably). However, what will this announcement mean for those of us who are interested in personal genomics?

Continue reading ‘Making sequencing simpler with nanopores’

Predicting lupus outcomes, US biomedical funding battles and telling children about genetic disease

There are a pair of papers in PLoS Genetics that shine some light on the effect of common GWAS variants on complex traits. The first investigates the effect of 22 common variants on sub-phenotypes of systemic lupus erythematosus, in how well a model including clinical measures plus GWAS variants can predict specific complications of lupus, over a model including just clinical outcomes. In some cases, there is little improvement (GWAS variants add nothing to prediction of renal failure, for instance), but in many there is a measurable improvement (such as for hameatological disorder and oral ulcers, the former of which is largely unpredictable from clinical outcomes). The second paper is a breakdown of the effect of the common obesity-associated variant FTO on BMI across age ranges; we see an interesting effect, whereby the variant that causes an increase in BMI in older children actually causes a fall in BMI in children under the age of 2. [LJ]

It’s budget battle season in the United States, and biomedical research funding looks likely to be caught in the crossfire. President Obama has proposed a $745 x 106 increase in the NIH budget, bringing it to $31.8 x 109 in total. This wouldn’t quite keep up with inflation, leading to a slight decrease in grant success rates from America’s largest biomedical research funder. The Republican-controlled House of Representatives, by contrast, has slashed the NIH budget by $1.6 x 109 in their proposed budget (bill HR1), which would be a heavy blow to research funding. Of course, scientists, non-crazy editorial writers and activist groups have been rallying around protecting research funding (in the NIH and beyond). Unfortunately I wouldn’t expect a speedy resolution, as veteran US politics blogger Nate Silver likens the whole situation to Zugzwang. [JCB]

Continue reading ‘Predicting lupus outcomes, US biomedical funding battles and telling children about genetic disease’

Friday Links

Nature ran an excellent story on the rise of genetic hobbyist-bloggers, featuring our own Joe Pickrell’s discovery of his Jewish heritage as well as the impressive efforts of bloggers Dienekes and David Wesolowski to explore human ancestry using publicly available large-scale genetic data, which finishes with a comparison by George Church between genomics blogging and the early days of social networks:

Church argues that better access to high-quality data could help this kind of informal bioinformatics to flourish, enabling computer-savvy people to make important contributions to genomics, just as they have with online businesses such as Facebook. “It didn’t take that much training to become a social-networking entrepreneur. You just had to be a good coder,” he says. With bioinformatics, “I think we’re in a similar position.”

Ion Torrent logoDNA sequencing news this week was dominated by the commercial launch of the fancy new machine from Ion Torrent and the announcement of $1 million prizes for home-brew improvements to the work-flow, throughput and accuracy of the embryonic platform. Nick Loman cast a skeptical eye over the output from the Ion Torrent PR machine, and particularly the competition, asking “Is this helping democratise sequencing, or is it a cynical tactic to get cheap R&D?” At the other end of the cynicism-naivete spectrum, Harvard molecular biologist Gary Ruvkun pondered sending an Ion Torrent to Mars to sequence the (hypothetical) DNA sprinkled across its dusty terrain.

Continue reading ‘Friday Links’

Estimating heritability using twins

Last week, a post went up on the Bioscience Resource Project blog entited The Great DNA Data Deficit. This is another in a long string of “Death of GWAS” posts that have appeared around the last year. The authors claim that because GWAS has failed to identify many “major disease genes”, i.e. high frequency variants with large effect on disease, it was therefore not worthwhile; this is all old stuff, that I have discussed elsewhere (see also my “Standard GWAS Disclaimer” below). In this case, the authors argue that the genetic contribution to complex disease has been massively overestimated, and in fact genetics does not play as large a part in disease as we believe.

The one particularly new thing about this article is that they actually look at the foundation for beliefs about missing heritability; the twin studies of identical and non-identical twins from which we get our estimates of the heritability of disease. I approve of this: I think all those who are interested in the genetics of disease should be fluent in the methodology of twin studies. However, in this case, the authors come to the rather odd conclusion that heritability measures are largely useless, based on a small statistical misunderstanding of how such studies are done.

I thought I would use this opportunity to explain, in relative detail, where we get our estimates of heritability from, why they are generally well-measured and robust, and real issues need to be considered when interpreting twin study results. This post is going to contain a little bit of maths, but don’t worry if it scares you a little, you only really need to get the gist.
Continue reading ‘Estimating heritability using twins’

Friday Links

This will be somewhat of an introspective Friday Links, looking at what other people have had to say about our recent announcement. We’ll resume our regular programming next week.

It’s been a big week here at Genomes Unzipped, with the announcement that all of the group members have released their genetic data publicly. The announcement was accompanied by a story by Mark Henderson in The Times (subscription only, unfortunately, but also syndicated here) along with commentary from Misha Angrist, Linda Avey and Christine Patch.

You can also listen to Daniel talk about the project on the BBC World Service (starts 19m30s), and Carl on BBC Radio Scotland (starts 38m). Finally, Luke and Daniel were on CBC Radio’s The Current today.

Continue reading ‘Friday Links’

Friday Links

Two exciting-looking new science blogging collectives have been announced this week. The Public Library of Science launched a new blogging collective, including personal genomics blogger Misha Angrist, and the Guardian newspaper has launched its Guardian Science Blogs network, including Dr Evan Harris, ex-MP for Oxford West and long time supporter of the role of science in public policy. I’m pretty excited about these new blogs, but it does stand to increase my RSS load significantly. [LJ]

In this month’s issue of European Journal of Human Genetics, Yang, Visscher and Wray contribute to the discussion around the aetiology of common complex diseases.  They demonstrate that the existence of a large number of sporadic cases (instances where a patient has no first, second, or third-degree relatives with the disease) is not incompatible with a polygenic model of disease.  A little less hot-off-the-press are two opinion pieces on genetic testing regulation from the August issue of Nature.  Arthur Beaudet argues that stringent government regulation should be applied to genotyping/sequencing, and interpretation should be the exclusive domain of the medical profession.  Gail Javitt takes a different view, arguing that genetic tests to be treated in the same way as other medical tests and that the level of regulation imposed should be determined by medical relevance of the outcome. [KIM]

Finally, Procreation News; our very own Daniel MacArthur and Ilana Fisher have recently given birth to a baby boy (the picture to the left may be a little out of date). Daniel made the announcement on Twitter, and also had this to say:

After careful inspection, I’ve decided that my six-day-old son is the most remarkable human being to have ever lived.

Due to double blinding, neither we nor Daniel know whether he has an actual or placebo baby, so we can’t yet assess the significance of this claim. Watch this space! [LJ]


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