genetic ancestry testing
dgmacarthur | March 8, 2010Dan Vorhaus pointed me to this review of the recent PBS series Faces of America. I haven't seen the series myself, but I found this segment of the review hilarious:
The element of the last PBS episode I found most intriguing was Gates' interview with novelist Louise Erdrich, who declined to have her DNA tested because her identity as a descendant of the Chippewa Native American tribe is so important to her. She said that she felt her tribe and family were what made her who she was. And, as she explained to Gates, she "didn't want to add any confusion to it."
Erdrich, in other words, didn't…
dgmacarthur | October 6, 2009
Last week I noted a highly controversial plan by the UK Border Agency to begin using DNA and isotope testing to help determine the geographical origins of refugees, for use in making decisions about whether or not to grant asylum.
A reader has just pointed me to this recent post on ScienceInsider indicating an apparent change in policy: the Border Agency has now stated that the trial will be "proof of concept" only, and that "no decisions on individual cases will be made using these techniques, and they will not be used for evidential purposes". As ScienceInsider notes, this represents a…
dgmacarthur | September 29, 2009ScienceInsider reports that plans by the UK Border Agency to employ DNA and isotope testing to test the origins of asylum seekers are being met with outrage by scientists and refugee advocates.
There's not much information about the precise tests that will be employed, but what information has been made available has horrified a number of scientists including the University of Leicester's Alec Jeffreys:
After reviewing the Border Agency's plans, Jeffreys echoed those criticisms in an e-mail to Science: "The Borders Agency is clearly making huge and unwarranted assumptions about population…
dgmacarthur | March 12, 2009Genetic genealogist Blaine Bettinger explores the results of his ancestry testing from 23andMe, and compares it to previous results from a much lower-resolution test.
The main message: the hundreds of thousands of genetic markers used by 23andMe (and other personal genomics companies, e.g. deCODEme) to infer genetic ancestry provide a much more detailed and accurate picture of the geographical origins of your genome.
No surprises here. The power of the type of genome-wide genotype data generated by 23andMe for ancestry prediction has been compellingly illustrated by a series of recent…
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 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 | December 12, 2008There's a new paper in the American Journal of Human Genetics following on from the paper on the genetics of metabolic traits that I posted on earlier in the week. This study explicitly focuses on the population structure of the Finns, and includes these maps showing the correlation between geography and genetics within Finland and related populations:
(Image from Jakkula et al. (2008) The Genome-wide Patterns of Variation Expose Significant Substructure in a Founder Population The American Journal of Human Genetics, 83 (6), 787-794 DOI: 10.1016/j.ajhg.2008.11.005)
More details below the fold…
dgmacarthur | December 8, 2008A few days ago I posted a picture depicting the genetic ancestry of African-Americans modelled as a linear combination of European and Nigerian genetic clusters (reproduced below). Dienekes has some thoughtful comments on the same picture.
Meanwhile, Razib comments on a post from Ed Yong discussing the social flexibility of race. Ed cites a survey showing that people change their self-described race with surprising frequency, with about one in five respondents changing their description at least once over a nineteen year period (with some intriguing correlations with incarceration and…
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, 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, 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 | 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 2, 2008Dienekes takes a critical look at 23andMe's new "global similarity" tool (requires a 23andMe login or a demo account to view), which allows you to visually place your own genetic data in the context of genome-wide SNP data from over 1,000 individuals from around the world. The take-home message: the feature is an improvement over previous versions of 23andMe's genetic ancestry tool, but it still needs plenty of work.