genetics of normal variation
dgmacarthur | April 29, 2010A paper just released in the Lancet describes a thorough and integrated approach to squeezing as much clinically relevant information as possible out of a genome sequence. However, despite a state-of-the-art clinical interpretation pipeline, the major message from the paper is just how far we still have to go before we can make full use of our genetic information.
The paper is based on the genome of Stephen Quake (right), which was sequenced using the single-molecule platform developed by Helicos (I wrote about Quake's genome publication at the time). This is a rather curious choice: of all…
dgmacarthur | November 11, 2009Medland et al. (2009). Common Variants in the Trichohyalin Gene Are Associated with Straight Hair in Europeans. The American Journal of Human Genetics DOI: 10.1016/j.ajhg.2009.10.009
A couple of weeks ago I reported on a presentation by 23andMe's Nick Eriksson at the American Society of Human Genetics meeting in Honolulu, in which Eriksson presented data on a series of genome-wide association studies performed by the company using genetic and trait data from its customers.
Along with genetic analysis of a variety of other traits (such as asparagus anosmia and photic sneeze) Eriksson…
dgmacarthur | October 25, 2009It's been an intensive week of genomics here at the American Society of Human Genetics meeting, and I haven't been able to grab time to blog as much as I'd have liked. In fact there's a whole load of genomics news I'll be trying to cover in some detail over the next couple of weeks; for the moment, though, I couldn't let today's presentation from personal genomics company 23andMe go by without at least some comment. (For other coverage of the conference, do check out Luke Jostins' blog coverage and the stream of live analysis on Twitter.)
The 23andMe presenter (Nick Eriksson) delivered an…
dgmacarthur | August 6, 2009CNN reports:
At the Chongqing Children's Palace, experts are hoping to revolutionize child-rearing with the help of science. About 30 children aged 3 to 12 years old and their parents are participating in a new program that uses DNA testing to identify genetic gifts and predict the future.
The test is conducted by the Shanghai Biochip Corporation. Scientists claim a simple saliva swab collects as many as 10,000 cells that enable them to isolate eleven different genes. By taking a closer look at the genetic codes, they say they can extract information about a child's IQ, emotional control,…
dgmacarthur | April 28, 2009Cho, Y., Go, M., Kim, Y., Heo, J., Oh, J., Ban, H., Yoon, D., Lee, M., Kim, D., Park, M., Cha, S., Kim, J., Han, B., Min, H., Ahn, Y., Park, M., Han, H., Jang, H., Cho, E., Lee, J., Cho, N., Shin, C., Park, T., Park, J., Lee, J., Cardon, L., Clarke, G., McCarthy, M., Lee, J., Lee, J., Oh, B., & Kim, H. (2009). A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits Nature Genetics, 41 (5), 527-534 DOI: 10.1038/ng.357
A paper just released in Nature Genetics takes the most comprehensive look yet at the genetic factors…
dgmacarthur | April 2, 2009GenomeWeb Daily News points to a new funding opportunity from the US National Institutes of Health (NIH) for researchers interested in studying the link between genetic variants and variation in the expression levels of genes.
This is an incredibly important area of research. Genome-wide association studies have recently uncovered vast numbers of DNA regions linked to common diseases (the latest estimate I've heard suggests around 400 common genetic variants associated with 75 different diseases or traits) - but we still don't have a clue how the majority of these regions actually alter…
dgmacarthur | March 25, 2009Neuroscientists Sam Wang and Sandra Aamodt have a guest post on Olivia Judson's NY Times blog discussing the complex interplay between genes and environment in the determination of personality traits. A taste:
So some of the effects that we call "genetic" (or "nature") are the
indirect result of people being drawn to particular environments
because of their personality. Or to put it another way, some
"environmental" (or "nurture") effects are actually attributable to
genetic tendencies.
It's worth noting that similar effects can occur for other traits: for instance, a genetic variant that…
dgmacarthur | March 12, 2009I posted a while back on two duelling essays in Nature on the intensely controversial subject of whether scientists should be permitted to study group differences in cognition. Nature now has a series of correspondence on the topic in its latest issue.
Firstly, there are rebuttals from the authors of the two original essays: Steven Rose argues that the debate is dead and that reviving it serves no purpose, while Ceci and Williams argue (substantially more convincingly, in my opinion) that Rose's declaration of these areas of research as invalid is premature.
Some of the other opinions are…
dgmacarthur | March 10, 2009Fan Liu, Kate van Duijn, Johannes R. Vingerling, Albert Hofman, André G. Uitterlinden, A. Cecile J.W. Janssens, Manfred Kayser (2009). Eye color and the prediction of complex phenotypes from genotypes Current Biology, 19 (5) DOI: 10.1016/j.cub.2009.01.027
In a recent post I noted that genetic tests to predict adult height are still a long way off being accurate; currently, known genetic variants can predict just over 5% of the variance in height, as opposed to 40% predicted using a simple algorithm based on the heights of both parents. The genetic complexity of height means that trying to…
dgmacarthur | March 3, 2009Yurii S Aulchenko, Maksim V Struchalin, Nadezhda M Belonogova, Tatiana I Axenovich, Michael N Weedon, Albert Hofman, Andre G Uitterlinden, Manfred Kayser, Ben A Oostra, Cornelia M van Duijn, A Cecile J W Janssens, Pavel M Borodin (2009). Predicting human height by Victorian and genomic methods European Journal of Human Genetics DOI: 10.1038/ejhg.2009.5
Human height is a strongly genetic trait: in well-nourished Westerners somewhere in the vicinity of 80-90% of the variation in height is due to genetic factors; if your parents are tall, there's a very good chance you will be too. That means…
dgmacarthur | February 21, 2009An article on GenomeWeb Daily News discusses some tantalising but still unpublished data from a team at Penn State University led by Mark Shriver:
The team has already found a handful of genes that seem to influence
different facial features. "I think we've got compelling evidence for
six genes that we tested," Shriver said. The team's data also suggests
that different parts of the face are influenced by different genes.
Variation in face shape is certainly strikingly heritable (all you need to do is look at any family photo to see that), but there's currently little known about the genetic…
dgmacarthur | January 19, 2009
Welcome to the 42nd edition of Gene Genie, the blog carnival of clinical genetics and personalised medicine.
Most of the entries in this edition fall under the broad umbrella of personalised genetics, with posts emphasising both the pros and cons of the emerging consumer genetic testing industry.
The promise and perils of personalised genetics
Hsien-Hsien Li from Eye on DNA warned about the potential dangers of pressuring kids to compete in athletic events based on genetic testing results, citing the suicide of a 15-year-old Singaporean boy. Alberto from Medical Pills used Hsien's post as a…
dgmacarthur | January 19, 2009Well, it's a little late, but I finally have a list of what I see as some of the major trends that will play out in the human genomics field in 2009 - both in terms of research outcomes, and shifts in the rapidly-evolving consumer genomics industry.
For genetics-savvy readers a lot of these predictions may seem, well, predictable, so I want to emphasise that my purpose here is not really to make risky forecasts; I'm more interested in laying out what I see as the major big picture trends for the year to come, with a few specific predictions about unknowns thrown in. In any case (as you will…
dgmacarthur | January 13, 2009Following the dramatic appearance of the field of personal genomics just over a year ago the major players in the field have worked hard to distinguish themselves from their competition: 23andMe has emphasised the intellectual joy of learning about genetics, and also attempted to actively engage its customers in the company's research projects; deCODEme has leaned heavily on the impressive academic credentials of its parent company, deCODE Genetics; Navigenics has committed itself utterly to an image of sober, responsible reflection on the medical information present in its customers' genomes…
dgmacarthur | January 12, 2009Steven Pinker's recent article in the NY Times is a rich source of insight into the field of personal genomics and the experience of personal genomics customers - if you haven't read it already, you really should.
This paragraph, for instance, seems to perfectly encapsulate the experience of the average intellectually curious personal genomics customer:
It became all the more confusing when I browsed for genes beyond those on the summary page. Both the P.G.P. and the genome browser turned up studies that linked various of my genes to an elevated risk of prostate cancer, deflating my initial…
dgmacarthur | December 15, 2008Willer et al. (2008). Six new loci associated with body mass index highlight a neuronal influence on body weight regulation Nature Genetics DOI: 10.1038/ng.287
Thorleifsson et al. (2008). Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity Nature Genetics DOI: 10.1038/ng.274
There are two massive studies now online in Nature Genetics looking at the genetic architecture of body mass index (BMI). Body mass index is a widely-used measure of body fat levels, calculated by dividing a subject's weight (in kg) by the sqare of their height (in…
dgmacarthur | December 10, 2008I posted last week on a paper purporting to identify a genetic variant influencing the placebo response. The main message of my post was that given the terrible history of small candidate gene association studies, a paper describing an association with a sample size of just 25 individuals should be simply ignored - and certainly not described in the popular science press as "a milestone".
Now Neuroskeptic has a detailed critique of the paper up in which he argues that the problems in the study go much deeper than inadequate sample size - in fact, the study wasn't measuring the placebo effect…
dgmacarthur | December 8, 2008Nature Genetics has just released six advance online manuscripts on the genetic architecture of complex metabolic traits. The amount of data in the manuscripts is overwhelming, so this post is really just a first impression; I suspect I'll have more to say once I've had time to dig into the juicy marrow of the supplementary data.
The general approach of exploring the genetic architecture of quantitative disease-associated traits (often called intermediate phenotypes or endophenotypes) rather than categorical case-control analyses of disease status raises some interesting questions, but I'm…
dgmacarthur | December 8, 2008I was planning to write a long article on this recent paper in PLoS Genetics, but p-ter at Gene Expression and G at Popgen ramblings have both covered the central message very well.
So if you haven't read those articles, already, go and do so now - when you come back, I want to talk about the potentially worrying implications of this paper for the future of personal genomics.
There's really only two pieces of jargon you need to know to follow this story, and those are the two classes of genetic variants that alter the expression levels of genes: cis and trans variants. To put it simply, cis…
dgmacarthur | December 3, 2008New Scientist trumpets the discovery of "the first placebo gene". The study in question is here.
I usually don't comment on this type of study, but this time the hype is just too much for me: New Scientist describes the study as "a milestone in the quest to understand" the placebo effect; an article in ScienceNow quotes a psychiatrist saying that "the findings could have major implications for research design". The article itself certainly doesn't talk down its results, with the first sentence of the discussion stating:
The present study demonstrates that the magnitude of the placebo response…