dgmacarthur | December 8, 2008In my previous post on Finnish population clustering I should have emphasised that the map was constructed only from individuals who had both parents from the same geographic/linguistic region; this obviously provides a lot more power to detect a correlation.
The close match between genetic and geographic ancestry in these selected individuals indicates that there hasn't been a huge amount of long-range admixture between Finnish populations over quite a long period of time - if there had been, there would be no reason to expect much correlation between the two maps. However, data in the…
dgmacarthur | December 8, 2008Personal genomics company 23andMe is now offering a discount of $200 for customers who buy three or more kits before December 31st.
In a press release the company explains the reasoning behind the price cut:
By offering this discount, 23andMe hopes to encourage families, in particular, to explore the unique features of the 23andMe Personal Genome Service⢠that are of special interest to people who are related. These features allow family members to learn how genetically similar they are and how genes were passed down from grandparents to grandchildren.
Still unconvinced? Just imagine the…
dgmacarthur | December 8, 2008Here's a figure from a brand new paper on the genetics of metabolic traits in a large Finnish cohort (which I'll be posting about in more detail shortly):
On the left is a map of the counties the samples were collected from, colour-coded by geographical/linguistic group; on the right is the genetic clustering of the samples using the same colour scheme. For anyone who's been reading Razib's posts on genetic maps of Europe and East Asia, the clear message here won't come as a surprise: once you have a sufficiently large sample of markers, genes correlate with geographic ancestry with…
dgmacarthur | December 8, 2008Think Gene's Andrew Yates has posted generic responses for medical professionals to use when dealing with patients who come armed with their results from 23andMe or Navigenics.
They're probably quite useful little tools for busy doctors without the time to brush up on the field of personal genomics, but - seeing as this is Andrew Yates - they're also a dig at the careful "medicine but not medicine" stance of personal genomics companies.
An excerpt:
Thus, applying 23andMe to your health care would be a violation of the 23andMe terms of service and, as stated, it "cannot be relied upon at this…
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 6, 2008I'm in the middle of a longer post on a recent paper on the effects of genetics on gene expression differences in African-Americans, which has also been well-covered by p-ter at Gene Expression. I wanted to post this section separately to avoid detracting from the issues in that post.
This figure will not provide any big surprises for those who have been following developments in human genetics over the last five years - but it still provides a compelling illustration of the power of genetics to predict individual ancestry:
The figure shows the results obtained when the European, Nigerian…
dgmacarthur | December 4, 2008David Dooling from PolITiGenomics has put together a handy little table for genomics nerds like me: statistics on the output of the various iterations of the three major competing second-generation DNA sequencing platforms (Roche's 454, Illumina's Solexa/Genome Analyzer and ABI's SOLiD).
It's a little inscrutable for non-genomicists, but it helps to provide some insight into the sheer scale of the DNA sequence data currently being produced by large-scale sequencing facilities. A single Illumina GA II machine, for instance, churns out at least 8 gigabases of sequence (that's almost three human…
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…
dgmacarthur | December 3, 2008Chris over at A Free Man has done a great job putting together the latest issue of genetics blog carnival Mendel's Garden - check it out.
dgmacarthur | December 2, 2008Reposted with a new title and minor corrections.
A sorry saga in Australian commercial genetics has apparently drawn to a close - just as another one looks set to begin.
Let's start from the beginning. Back in 2003, Australian biotech Genetic Technologies bought acquired the rights to a patent on testing of the breast cancer genes BRCA1 and BRCA2 from Myriad Genetics (see comments for details). In the face of massive public opposition to restrictions on public testing for the genes, the company announced that it wouldn't be enforcing the patent as a "gift to the people of Australia and New…
dgmacarthur | November 30, 2008Disclaimer: I was one of the authors on a 2003 study reporting a link between ACTN3 and athletic performance, but I have no financial interest in ACTN3 gene testing. The opinions expressed in this post are purely my own.
An article in the NY Times yesterday describes the launch of the grandiosely named Athletic Talent Laboratory Analysis System (ATLAS). The ATLAS test looks at a common genetic variation within the ACTN3 gene, which has been associated in numerous studies with elite athlete status and with variation in muscle strength and sprint ability in the general population. The company…
dgmacarthur | November 20, 2008At Gene Expression, p-ter points to two studies in this week's New England Journal of Medicine examining the predictive value of known genetic markers for type 2 diabetes.
Both studies find the additional predictive power of the genetic markers beyond traditional predictors (like age, sex, family history, body-mass index, fasting glucose levels, systolic blood pressure, high-density lipoprotein cholesterol levels, and serum triglyceride levels) to be extremely small, to the point of complete clinical insignificance. Thus while massive genome-wide association studies for T2D have been…
dgmacarthur | November 20, 2008Pharmacogenomics Reporter (subscription required) describes an intriguing twist in the ongoing struggle between the nascent personal genomics industry and regulatory bodies: apparently the FDA is exploring the possibility of collaborating with consumer genomics providers to track adverse drug reactions:
Lawrence Lesko, director of FDA's Office of Clinical Pharmacology, said the agency has already begun preliminary discussions with some undisclosed personal genomics firms "to evaluate the feasibility" of forging such alliances.
In marketing ancestry and disease-predisposition genetic testing…
dgmacarthur | November 19, 2008
A Nature News article describes the growing availability of technology that allows the screening of human embryos for hundreds of different genetic disorders prior to implantation.
The technology is based on the same type of chips used by personal genomics companies like 23andMe, but the chips used for embryo screening would initially be used to target known rare disease-causing mutations or large chromosomal abnormalities rather than performing a genome-wide scan for common variants (in the article, a screening company director describes the targeted diseases as "nasty, early-onset and…
dgmacarthur | November 18, 2008A Nature News article discusses the ongoing 1000 Genomes Project, an international effort planning to sequence 1,200-1,500 human genomes. The discussion springs from project co-chair David Altshuler's update at last week's American Society of Human Genetics meeting on the progress of the project (in brief: 3.8 terabases down, 996.2 terabases to go).
The article provides a generally positive overview of the project's historical context, goals and progress. The one contrary note comes from Duke University's David Goldstein, who has previously publicly expressed skepticism regarding the value of…
dgmacarthur | November 15, 2008Blaine Bettinger at the Genetic Genealogist has an extensive and thoughtful critique of the American Society of Human Genetics' recently released statement on genetic ancestry testing (pdf). (You can read about the Society's statement at GenomeWeb News and Science Now; 23andMe also comments from the point of view of a company engaged in ancestry testing.)
If you have comments on the issues surrounding genetic ancestry testing I'd encourage you to add them to Blaine's post.
dgmacarthur | November 14, 2008Last week I posted on the publication of three papers in Nature describing whole-genome sequencing using next-generation technology: one African genome, one Asian genome, and two genomes from a female cancer patient (one from her cancer cells and one from healthy skin tissue). At the end of that post I noted that the era of the single-genome publication is drawing to a close as the age of population genomics commences.
Today GenomeWeb News reports from the American Society of Human Genetics meeting on the biggest current foray into the field of population genomics: the 1000 Genomes Project.…
dgmacarthur | November 11, 2008
Reports in Australian papers the Age and the Brisbane Times note the impending arrival of a newcomer to the personal genomics scene: Lumigenix, a home-grown offering cooked up by Sydney entrepreneur Romain Bonjean.
The new arrival will face several major obstacles to establishing itself in the market. Firstly, 23andMe has been offering its well-established and well-publicised service in Australia since October 3rd (announced on Twitter). There's no obvious home-ground advantage for an industry where the service requires only a postal address and an internet connection, so Lumigenix will…
dgmacarthur | November 10, 2008Note: I'm introducing Do It Yourself as a new and hopefully semi-regular section on Genetic Future. The aim is to provide readers with instructions on how to access online resources for sequence analysis - an activity traditionally restricted to researchers, but one that will no doubt become more common as more and more people begin to access and interpret their own genetic data.
In this post I'll introduce the brand new HGDP Selection Browser, a tool for exploring traces of recent positive selection in the human genome produced by researchers at the University of Chicago.
Introduction: the…
dgmacarthur | November 7, 2008deCODE CEO Kari Stefansson on the recent award of Time magazine's "Invention of the Year" to personal genomics competitor 23andMe:
Despite the fact that we launched our test first - so we basically invented this, and also 23andMe is using a substantial number of sequence variants that we discovered. So we feel flattered by the fact that our test was selected as the invention of the year by Time magazine. We are amused by the fact that they decided to ascribe the invention to 23andMe, probably because its founder is associated with the rich and famous.
From an article in Bio-IT World on deCODE…