Genetic Future

My Gene Profile: the lamest genetic testing scam on the internet?

Thu, 19 Nov 2009 19:00:00 -0500

Pharyngula, via a reader, points me to the most aggressively bad attempt at a genetic testing product I have ever encountered, coupled with a truly horrific attitude to parenting.

The tag line alone is hilariously inept:

"Our Technology Spawned from Human Genome Project led by US Scientists. The Industry is Featured by CNN, CBS News"

The idea that is being spruiked here is that genetic testing can help you determine your child's "inborn talents", which you can then use to ruthlessly jam them into whatever career the test results suggest.

The presenter notes that he "wasted a lot of time exposing my children to as many extracurricular activities as possible" - how fortunate that he can now give us access to genetic testing technology to save us the money and effort involved in letting children choose their own favourite activities!

For anyone uncertain about this: the test is a scam. It is impossible to predict which career your child is best suited to using any genetic test. Don't buy it. That is all.

Here's a screen-shot that tells you everything you need to know:

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DIY ancestry inference from personal genomic data

Wed, 18 Nov 2009 07:15:00 -0500

European Genetics and Anthropology has a neat little tutorial that may be of interest for genetic hobbyists: it provides instructions on how to run the program STRUCTURE on your own genetic data generated by a personal genomics company such as 23andMe or deCODEme.

STRUCTURE is an extremely popular tool among researchers working in population genetics, which allows you to generate plots showing estimates of the proportion of an individual's genome belonging to different population clusters.

The tutorial on the blog shows you how to run your analysis using a subset of just 125 markers selected from your genetic data. That's enough to get a sense of what's going on, but of course having access to more than 500,000 markers from a genome scan theoretically allows you to perform a more powerful analysis using a much larger set of markers (and comparing to, say, the freely available SNP data from the Human Genome Diversity Panel).

It's great to see tools developed by academia being democratised by personal genomics hobbyists. One major benefit: if your personal genomics company does go bankrupt, so long as you've downloaded your data you can still analyse your genetic ancestry...

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Details on the future of the deCODEme service

Tue, 17 Nov 2009 05:00:00 -0500

I was just sent this email by a deCODEme customer:

As a valued subscriber to deCODEme, we wanted to write to you directly to let you know about some important developments in the company and how we believe these will underpin our ability to continue to keep you in the forefront of understanding what the latest advances in genetics mean to you.

For the past several months, deCODE has been working on restructuring its operations. One of the principal goals of this effort has been to enable us to find new investment that will continue our work in human genetics and to offer to our customers the products and services that are based upon our expertise and capabilities. Today we have announced concrete steps in that direction. This morning deCODE genetics, Inc. filed a voluntary petition for Chapter 11 protection in the United States. At the same time, there has also been filed with the court an offer by Saga Investments LLC to purchase deCODE's Icelandic subsidiary, Islensk Erfdagreining (IE). IE, which is not declaring bankruptcy, carries out all of deCODE's human genetics work and and provides deCODEme.

We believe this offer provides a firm foundation for continuing to offer you the same path breaking science and service you expect from deCODEme. Saga is led by Polaris Venture Partners and Arch Venture Partners, two leading technology investors who were involved in the founding of deCODE. While other higher bids may be made for IE under the Chapter 11 process, this offer, even if no others are forthcoming, provides resources for us to continue operations without interruption during the Chapter 11 proceedings, and would provide up front funds sufficient to support operations for two years. With the filing today, deCODE has also asked the Court for the customary authority to continue to manage its operations and serve its customers during the proceedings. [my emphasis]
For this reason, we do not expect this to have any impact on your deCODEme account. As ever, our commitment at deCODEme is to keep you in the forefront of progress in understanding the human genome and what it means for you and your health.

Please don't hesitate to get in touch with our customer support team if you have any questions.

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deCODE Genetics declare bankruptcy, will sell core business to US investors

Tue, 17 Nov 2009 04:45:00 -0500

Struggling Icelandic biotech deCODE Genetics has finally reached the point of formal insolvency. A press release today announces that the company has filed for chapter 11 bankruptcy in a US court:

In a filing with the U.S. Bankruptcy Court for the District of Delaware late on Monday, deCODE listed total assets of $69.9 million and total debt of $313.9 million, as of June 30.

deCODE launched in 1996, basing its business plan on its unique access to biological samples and genealogical and medical records from the small, homogeneous Icelandic population. Since its launch it has proved wildly successful as a research institute, generating an astonishing number of high-profile publications on the genetics of common traits and diseases. Unfortunately it has also been a complete disaster as a commercial venture, haemorrhaging away over $700 million while failing to generate a single quarterly profit.

As I understand it, following the filing deCODE will continue to operate its business, just in a different form: the company has entered into an agreement with a US investment firm to sell off its subsidiary Islensk Erfdagreining (IE), which "conducts deCODE's human genetics research, manages its population genetics resources and provides its personal genome scans, DNA-based risk assessment tests, and genomics services for contract customers". In other words, pretty much all of the core business that deCODE does will continue, simply under a different name.

While deCODE will limp on for a couple more years under this agreement, this is very much a temporary fix. The core problem for the company - figuring out how it can use its expertise and unique resources to generate an actual profit, rather than simply more Nature Genetics paper - remains. Until that problem is solved the company's future, and that of its superb genetic resources and databasem remains in doubt.

What would happen to the genetic data from customers being held by deCODEme if the company goes under for the final time? Three very timely recent guest posts from Dan Vorhaus and Lawrence Moore here on Genetic Future provide a solid basis for speculation, here, here and here.

We'll have to wait and see what the future holds for deCODE's database, and cross our fingers that it doesn't simply slip under the Icelandic permafrost.

For the financially cognisant, I've added more details from Stockhouse:

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23andMe raises prices, splits its health and ancestry analyses

Sun, 15 Nov 2009 08:15:00 -0500

Added in edit: for superb analysis of the announcement from multiple angles, you should also check out Dan Vorhaus' three incisive articles on Genomics Law Report.

Personal genomics company 23andMe announced yesterday on its blog (and in an email to customers) of impending changes to its product line. Until now 23andMe has offered only two products: its $399 full scan, and a $99 Research Revolution product that offers limited functionality and a focus on common disease risk prediction.

There are two major components of the altered product line. Firstly, customers will now be able to purchase separate products focusing on health and ancestry: the Ancestry Edition ($399) will focus on ancestry and genealogy analyses, while the Health Edition ($429) will provide risk predictions for common diseases and provide an updated line of carrier testing for rare, severe, recessive mutations relevant to reproductive decisions. It sounds as though 23andMe plans to move more extensively into the carrier testing market:

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23andMe gets scooped on hair curl genes

Wed, 11 Nov 2009 19:15:00 -0500

Medland 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 presented data on two novel regions significantly associated with hair curl, one close to the TCHH gene and a second near WNT10A (see the abstract for details). I noted at the time that 23andMe appears to be doing a pretty good job of running genome-wide association studies, although of course the real test of this is independent replication.

Well, now we have replication (of a sort) for at least two of 23andMe's novel findings - but unfortunately for the 23andMe crew the "replication" study has beaten them into print.

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More on return of research data to participants from Genomics Law Report

Wed, 04 Nov 2009 13:15:00 -0500

Yesterday I posted a brief rant about the need for researchers to think about the best way to return genetic research data to participants, spinning off an equally brief opinion piece I wrote for the ongoing ELSI series at Genomics Law Report.

Today Dan Vorhaus has posted an excellent piece on the same topic over at GLR, triggered by an exchange between 23andMe's Anne Wojcicki and Kaiser Permanente. Go check it out.

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Research subjects should have access to their own data

Tue, 03 Nov 2009 10:15:00 -0500

My contribution to Genomics Law Report's superb "What ELSI is New" series is up now.

The gist of my argument: as we move into an era of large-scale whole-genome sequencing studies and the utility of genomic information grows, researchers will increasingly frequently be faced with the discovery of highly medically relevant information within their subjects' genomes. Yet under the consent procedures established for most modern genetic research projects the anonymised subjects would never have a chance to learn about this information.

As such, people will die from breast cancer and other diseases even though someone out there possesses genetic information ~~they would have needed to avoid this~~ that could have been used to guide additional screening to detect such cancers early.

Throwing medically actionable data away without the subjects ever having a chance to learn about it is unconscionable - we need to start changing the way we think about the rights of research subjects to their own data.

It's important not to understate the challenges posed by returning research data to research subjects - such as balancing against the need for privacy and data security, or unduly alarming people with inaccurate results - but these are not reasons to avoid data return. They are simply obstacles we need to overcome.

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First ever association study using whole genome sequences

Tue, 03 Nov 2009 07:30:00 -0500

New-technology DNA sequencing provider Complete Genomics will provide near-complete genome sequences of 100 individuals to the Institute for Systems Biology, driving the first ever association study for a complex trait using whole-genome sequencing. Here's the press release, and GenomeWeb has some additional information.

This is pretty exciting stuff:

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What happens when a DTC genomics company goes bust? Follow up post on Genomics Law Report

Tue, 27 Oct 2009 12:00:00 -0500

A while back Dan Vorhaus and Lawrence Moore wrote a fantastic series of guest posts here on Genetic Future on the issue of what would happen to customer data in the event that a direct-to-consumer genetic testing company went bankrupt - here's the introduction, a detailed analysis of the implications of bankruptcy law, and a summary of the implications for consumers.

Lawrence Moore and Emily Sherlock now have a follow-up post over at Genomics Law Report digging into the implications of federal privacy regulations in the event of a DTC genomics company collapse.

The rather worrying conclusion is that "at present it does not appear that there is any federal regulation--including HIPAA--that clearly restricts the transfer of customers' information as part of a sale of assets by a troubled DTC genomics company." Given that uncertainty, Moore and Sherlock conclude:

...the most practical advice at this time, for existing and potential customers, continues to be to understand the terms and conditions offered by each individual DTC genomics company with respect to their customers' information--and to recognize that, in bankruptcy, genomic data may be transferred to a similar company without regard to those terms and conditions.

There's also a tantalising promise of posts to come in the near future exploring the implications if impending regulatory changes in the DTC genomics area push testing companies firmly into the realm of clinical diagnostics.

Genomics Law Report continues to impress with the quality and diversity of its posts - if you haven't already added it to your RSS reader (and added @genomicslawyer to your Twitter feed) you should go and do so without delay.

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23andMe presents novel genetic associations at American Society of Human Genetics meeting

Sun, 25 Oct 2009 05:30:26 -0500

It'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 overview of the potential of the 23andMe cohort for association studies: all 23andMe customers have genetic information for over 500,000 common genetic variants, and they are also encouraged to provide self-reported phenotype data on a wide range of traits ranging from the presence of detached earlobes to longitudinal tracking of Parkinson's disease symptoms. Eriksson reported that the company now had sufficient numbers of returned surveys to perform genome-wide association studies for 22 traits, with sample sizes ranging between 2500 and 6000 individuals - reasonable sample sizes for an initial look at the genetic architecture of a complex trait.

The company seems to be doing a reasonable job of identifying and controlling for the various potential confounders that plague genome-wide association studies, such as population structure. However, 23andMe faces an unusual challenge that standard academic GWAS consortia don't: the possibility that a subject will give a biased trait report after seeing their own genetic data.

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Off to Hawaii... and looking forward to new associations from 23andMe

Wed, 14 Oct 2009 19:15:00 -0500

I'll be away for the American Society of Human Genetics meeting in Hawaii for most of the next couple of weeks - I'll be covering the conference primarily via Twitter, and you can follow all of the tweets from the conference using the #ASHG2009 hashtag.

Genetics bloggers/tweeters should also pencil in the "tweetup" on Thursday 22nd from 4:30 to 5:15 in the ASHG Press Office (Room 318 in the Convention Center), organised by Chris Gunter; anyone interested should RSVP via email. This should be a good chance to put faces to many of the names in your Twitter and RSS feeds.

There's a lot of talks I'm looking forward to, but here's one of particular interest to those who follow the personal genomics industry (and a useful counterpoint to my critique of 23andMe's NFL genetics press release yesterday):

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23andMe performs genome-wide association study on NFL players, fails to find athlete genes

Tue, 13 Oct 2009 12:30:00 -0500

Details are pretty sketchy, but a press release announced today suggests that personal genomics company 23andMe has performed a genome-wide association study comparing 100 current or former professional NFL players with a set of controls of unspecified sample size.

The shocking result:

The study did not find the tested players to be genetic outliers, suggesting that genetics may not be a good predictor of athletic success.

It's unsurprising that the results of this study are negative (more on this below), but the conclusions they draw from this are fallacious. In fact we know from twin and family studies that many (but not all) traits related to athletic performance are highly heritable; researchers just haven't been able to track down the vast majority of the genetic variants responsible yet, and this study is no exception.

What 23andMe have actually shown here is that the limited subset of genetic variation captured by their genotyping chip (which almost exclusively targets genetic variants with a frequency of greater than 5%) doesn't include any variants with an extremely strong association with NFL prowess.

That shouldn't come as a surprise to anyone who's been following advances in human genetics for the last few years; a genome-wide association study on a highly complex trait with a sample size of 100 has, historically speaking, a vanishingly small chance of yielding any positive results at all. (Yes, there are exceptions, but I don't think a sensible prior expectation would be that athletic performance has a similar genetic architecture to macular degeneration.)

The press release argues that the results "speak to the breadth of the genetic research the company is undertaking". That may be so, but I certainly hope they aren't indicative of the general quality of 23andMe's research program. Much as I hate to say it about a company whose work I generally admire, this study carries all the hallmarks of being pure PR fluff. If you want to do a GWAS for athletic performance, at least wait until you have a homogeneous sample that's well-powered enough to have a fighting chance of detecting real associations.

On the bright side, 23andMe has been building up much more sensible sample sizes for other projects, including 4,500 older amateur athletes and over 3,000 Parkinson's disease patients. I'm hopeful that we'll see something a little more interesting than this NFL story roll out of the company over the next few months.

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Scientists call for changes to personal genomics based on comparison of test results

Wed, 07 Oct 2009 21:20:00 -0500

Four scientists - including the omnipresent J. Craig Venter (left) - have penned an opinion piece in the latest issue of Nature based results from five individuals genotyped by two separate personal genomics companies. The article highlights some deficiencies in the way that genetic data are currently used by direct-to-consumer companies to generate risk predictions and to present them to customers.

The identity of the tested individuals isn't made explicit in the article, except to note that there were two males and two females from the same family and one unrelated female. All of the individuals were tested by the companies 23andMe and Navigenics, which examine ~580,000 and ~923,000 sites of common genetic variation (SNPs), respectively. It's worth noting that in both cases the scans were performed before the companies were required to comply with CLIA standards (meaning that genotyping accuracy may have improved somewhat since these scans were done).

The first result is reassuring: the concordance between the genotype calls from the companies was excellent, with disagreements at fewer than one in every 3,000 sites. Previous comparisons (see comments on this article) between 23andMe and deCODEme have found even smaller discrepancy rates, closer to one error in every 25,000 sites - the difference appears to be due to a substantially higher error rate on the Navigenics platform compared to 23andMe (compared to research-quality typing performed on the same samples, Navigenics had a 0.29% discordance compared to 0.01% for 23andMe). Overall, though, it's clear that the levels of technical accuracy being achieved by the genotyping platforms used by major personal genomics companies are perfectly acceptable.

The real challenge is not with generating the raw genetic data, but rather with converting it into disease risk predictions - and here, the authors argue, the results of the comparison are less than ideal:

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Nature special issue a treasure trove for personal genomics fans

Wed, 07 Oct 2009 18:30:00 -0500

The latest issue of Nature contains an embarrassment of riches for those of us interested in personal genomics, and indeed I'm having trouble figuring out which article to write about first.

Just look at the options: there's a review on approaches to tracking down the missing heritability of common diseases; there's a potentially highly controversial plea from Chicago researcher Bruce Lahn for acknowledgment that "genetic diversity contributes to variation across numerous physical, physiological and cognitive domains" between human populations; and there's an advance online publication describing the highest-resolution survey yet performed of large-scale structural variation in the human genome (on which I am proud to be fifteenth author!), accompanied by a tidy News and Views piece from John Armour.

Any of these would provide ample fodder for a post, but right now I only have time to write about one. Hmmm...

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