personal genomics
sporte | October 2, 2011For the past few days I've been avidly following Daniel MacArthur's tweets from the Personal Genome Conference at Cold Spring Harbor(@dgmacarthur #cshlpg).
The Personal Genomics tweets aren't just interesting because of the science, they're interesting because MacArthur and others have started to take on the conventional dogma in genetic ethics.
For years, there has been a strong message from the clinical genetics and genetics education community that genetic information is dangerous.
Unlike the other medical tests we're continually urged to get (mammograms, blood pressure readings, sugar…
sporte | February 14, 2011This morning I attended a "bloggers-only" conference call with Dr. Eric Green and the folks from the NIH Human Genome Research Institute (NHGRI) to hear about NHGRI's new strategic plan. The new plan represents a shift away from viewing the genome through a lens marked "for research use only" and towards the goal of making the genome useful as a clinical tool. As a consequence, we will see a greater emphasis on funding activities that support clinical work. For example, it's not always clear how variations in the genome are related to disease. NHGRI might fund projects that help sort and…
sb admin | January 7, 2011As part of his Gene Week celebration over at Forbes, Matthew Herper has a provocative post titled "Why you can't have your $1000 genome". In this post I'll explain why, while Herper's pessimism is absolutely justified for genomes produced in a medical setting, I'm confident that I'll be obtaining my own near-$1000 genome in the not-too-distant future.
Matt's underlying argument is that while sequencing costs will continue to drop, obtaining a complete genome sequence that is sufficiently accurate for medical interpretation will require additional expenses (increased sequence coverage to…
dgmacarthur | January 7, 2011As part of his Gene Week celebration over at Forbes, Matthew Herper has a provocative post titled "Why you can't have your $1000 genome". In this post I'll explain why, while Herper's pessimism is absolutely justified for genomes produced in a medical setting, I'm confident that I'll be obtaining my own near-$1000 genome in the not-too-distant future.
Matt's underlying argument is that while sequencing costs will continue to drop, obtaining a complete genome sequence that is sufficiently accurate for medical interpretation will require additional expenses (increased sequence coverage to…
sb admin | December 15, 2010Late last week I stumbled across a press release with an attention-grabbing headline ("The Causes of Common Diseases are Not Genetic Concludes a New Analysis") linking to a lengthy blog post at the Bioscience Resource Project, a website devoted to food and agriculture. The post, written by two plant geneticists, plays a tune that will be familiar to anyone who has encountered the rhetoric of GeneWatch UK: basically, modern genomics is pure hype perpetuated by scientists seeking grant money and corporations seeking to absolve themselves of responsibility for environmental disasters.
The…
sb admin | December 3, 2010A reminder to anyone who reads my other blog Genomes Unzipped that we have a reader survey underway there now, which includes some questions about genetic testing experiences and attitudes towards genetics. We're closing the survey to responses this weekend, so if you're an Unzipped reader but haven't had a chance to fill in the survey, please do so now.
dgmacarthur | November 24, 2010Update 30/11/10: 23andMe has extended their 80% discount until Christmas, without a need for a discount code.
Personal genomics company 23andMe has made some fairly major announcements this week: a brand new chip, a new product strategy (including a monthly subscription fee), and yet another discount push. What do these changes mean for existing and new customers?
The new chip
23andMe's new v3 chip is a substantial improvement over the v2 chip that most current customers were run on (the v2 was introduced back in September 2008). Firstly, the v3 chip includes nearly double the number of…
sb admin | November 24, 2010Update 30/11/10: 23andMe has extended their 80% discount until Christmas, without a need for a discount code.
Personal genomics company 23andMe has made some fairly major announcements this week: a brand new chip, a new product strategy (including a monthly subscription fee), and yet another discount push. What do these changes mean for existing and new customers?
The new chip
23andMe's new v3 chip is a substantial improvement over the v2 chip that most current customers were run on (the v2 was introduced back in September 2008). Firstly, the v3 chip includes nearly double the number of…
sb admin | October 12, 2010
Back in June I launched a new blog, Genomes Unzipped, together with a group of colleagues and friends with expertise in various areas of genetics. At the time I made a rather cryptic comment about "planning much bigger things for the site over the next few months".
Today I announced what I meant by that: from today, all of the 12 members of Genomes Unzipped - including my wife and I - will be releasing their own results from a variety of genetic tests, online, for anyone to access. Initially those results consist of data from one company (23andMe) for all 12 members; deCODEme for one…
dgmacarthur | August 5, 2010Two days ago I reported a rumour that the FDA might have convinced genotyping chip provider Illumina to stop providing its products to direct-to-consumer genetic testing companies - a move that would effectively prevent these companies from being able to operate.
The rumour seemed plausible at the time, based on two pieces of evidence. Firstly, a letter sent to Illumina by the FDA in June warned the company that the use of its chips by personal genomics companies appeared to violate FDA regulations:
Although Illumina, Inc. has received FDA clearance or approval for several of its devices,…
dgmacarthur | August 4, 2010Following up on the rumours I posted about yesterday regarding a potential bid by the FDA to choke of direct-to-consumer genetic testing companies' supply of genotyping chips, I received the following statement by email from 23andMe's PR firm:
23andMe is engaged in an ongoing process with the FDA.
23andMe understands that Illumina is also engaged in such a process.
23andMe has no reason to believe there will be an interruption in the supply of Illumina chips at this time.
I understand we'll have some more clarity on this issue from the FDA tomorrow.
dgmacarthur | July 30, 2010This week was pretty hectic, so there were plenty of useful or interesting links from the personal genomics world that I didn't have time to write about in detail. Feel free to share your own suggestions in the comments.
Responses to the Congress/FDA crack-downAs all of you will be aware, the big news this week revolved around the debate over the regulatory future of the direct-to-consumer (DTC) genetic testing industry, following a brutal Congressional hearing into the industry last Thursday that featured a scathing report by the US Government Accountability Office.
Over at Genomes Unzipped…
dgmacarthur | July 29, 2010(This is an edited excerpt from an op-ed piece I just wrote for Xconomy, posted here as I think it provides some nuance on my views on regulation of genetic testing that was lacking from my post last week.
Some context for new readers: a Congressional investigation into the direct-to-consumer (DTC) genetic testing industry last week left a sour taste in the mouths of many observers of the embryonic industry; it was a vicious, one-sided affair, starring a biased report on a "sting" operation performed by the US Government Accountability Office. Along with other recent moves by the FDA, it…
dgmacarthur | July 22, 2010(Cross-posted to Genomes Unzipped.)
Today's US Congress Committee on Energy and Commerce hearing into the direct-to-consumer genetic testing industry was a vicious affair. Representatives from testing companies 23andMe, Navigenics and Pathway faced a barrage of questions about the accuracy and utility of their tests, made all the worse by the fact that many of the Committee's members seemed unable to distinguish between the more responsible companies in the field and the scammers and bottom-feeders. (I watched by web-cast, which I can't yet track down a copy of online; you can read the…
dgmacarthur | July 21, 2010
I mentioned last week on Genetic Future that a reporter with the Washington Post, Rob Stein, had emailed the National Society of Genetic Counsellors to search specifically for people with negative experiences of personal genomics for an upcoming article on the industry. At the time I called for personal genomics customers with positive experiences to email Stein, to ensure that he had a balanced view of the industry's impact.
Stein's article came out a couple of days ago, presumably timed for maximum impact in advance of the FDA's meeting on lab-developed tests over the last two days.…
dgmacarthur | July 13, 2010The first ever post on the new group blog I announced yesterday, Genomes Unzipped, is now live: it's Luke Jostins of Genetic Inference talking about the importance of sequencing for the future of personal genomics. Here's a taste:
There is a particular type of variation that genotype chips can never get at, the type of variation that most people will find most interesting: variation that is unique to you, or to your family. If you get sequenced now, about 200,000 single-base variants in your genome will never have been seen before, ever. These are likely to include changes that modify…
dgmacarthur | July 12, 2010
I'm pleased to announce the beta launch of a new group blog on personal genomics, Genomes Unzipped.
I've been working with a group of scientific colleagues and fellow bloggers on this project for quite a while now. Some of the group members will be familiar to regular readers: Dan Vorhaus from Genomics Law Report, Luke Jostins from Genetic Inference, and Caroline Wright from the PHG Foundation. Others are new to blogging, but have backgrounds in genomic analysis, statistical genetics and other fields that allow them to bring valuable insight into the scientific, ethical and social issues…
dgmacarthur | June 25, 2010An excerpt from an article I co-wrote for Xconomy with Genomics Law Report's Dan Vorhaus - link to the full article below.
Are you ready for consumer genetics? Is your government?
Recent announcements of federal investigations into the budding direct-to-consumer (DTC) genetic testing industry suggest that authorities are preparing to increase regulation of companies offering consumers access to their own genetic data. However, rather than rushing in to clamp down on the industry, regulators should slow down and focus, first, on understanding this complex field.
An increasing number of…
dgmacarthur | June 25, 2010In October last year I reported on a presentation by direct-to-consumer genetic testing company 23andMe at the American Society of Human Genetics meeting in Honolulu, in which the company described results of genetic association studies performed using combined genetic and survey data from their customers. The results of their study include replication of several known associations for traits like hair colour, eye colour and freckling, as well as the discovery of previously unpublished associations for things like asparagus anosmia (the ability to smell urinary breakdown products after eating…
dgmacarthur | June 24, 2010Blogging time has been pretty scarce for me lately, mainly due to the impending submission of the 1000 Genomes Project pilot paper (more on my involvement in that project later). Sadly, personal genomics has not done me the favour of sitting still while I'm busy. Here are some of the more interesting recent bits and pieces from the personal genomosphere:
Speaking of the 1000 Genomes Project, the consortium has formally announced the release of data from its three pilot projects. The pilot data include low-coverage whole-genome sequences from 180 individuals, high-quality whole-genome…