Genetic Future

Blogging hiatus

Fri, 22 Jan 2010 18:00:00 -0500

Blogging on Genetic Future will be pretty much non-existent for the next three weeks.

Personal genomics is getting serious: Counsyl emerging from stealth mode

Fri, 22 Jan 2010 17:00:00 -0500

Disclaimer: my wife and I have both received and used free testing kits from Counsyl.

Counsyl is a rather enigmatic player in the personal genomics field: apart from a brief mention in Steven Pinker's excellent NY Times piece over a year ago and an even briefer post on a Newsweek blog late last year, the company has been in determined stealth mode for much of the last two years.

All that was publicly known about the company when I wrote about them last year was that they will be offering a large-scale carrier screening test: basically, allowing couples who are considering having a baby to test their genomes for a wide range of severe mutations that might - if both potential parents carry copies in the same gene - result in severe disease in their children. Couples who discover these types of variants could then arrange for pre-implantation genetic screening to be performed during the process of IVF.

While other companies (notably 23andMe and Pathway Genomics) do offer limited carrier testing in addition to their more "recreational" tests (things like ancestry and complex trait prediction), Counsyl's offering is intensely focused: the goal is simply to pick up as many known serious disease-associated mutations as possible.

There are two things I find particularly intriguing about the Counsyl approach.

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Weekly Twitter summary

Fri, 15 Jan 2010 12:15:00 -0500

Continuing my new tradition, here are some of the genomics-related links and information I posted on Twitter this week:

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Will new sequencing technology kill arrays

Fri, 15 Jan 2010 11:35:00 -0500

Keith Robison has a perceptive piece riffing off the recent Illumina instrument launch, and ponders whether 2010 will be the year that array-based genomic technologies finally start to die off with the rise of sequencing.

The market certainly seems to think so. Check out the immediate effect on stock prices for Illumina (ILMN) and array manufacturer Affymetrix (AFFX) following the Illumina announcement (both normalised to 0 at the start of the graph):

This comes in the context of long-term stagnation of AFFX stock, while Illumina has exploded over the last five years. Illumina made plenty of money from the array market, but it also established itself as a key player in the emergence of next-generation sequencing. Affymetrix was not as far-sighted.

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Illumina announces new arrival in the sequencing arms race

Tue, 12 Jan 2010 20:00:00 -0500

The big news from the JP Morgan investment conference today is the announcement of a brand new shiny sequencing machine from Illumina, the HiSeq 2000. The new machine boasts an impressive set of statistics, and looks likely to gradually replace Illumina's GAIIx as the workhorse of most modern sequencing facilities.

So, how excited should we be?

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Weekly Twitter summary

Fri, 08 Jan 2010 12:15:00 -0500

Some of you may know that I post many links of interest that don't make it into a full blog post via Twitter. Since I know there are a number of blog readers who haven't yet made the move to Twitter, I'm going to follow in Dan Vorhaus' footsteps by posting a weekly roundup of useful links here on Genetic Future.

Here's episode 1, encompassing the first week of 2010:

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Personal genomics links of note

Thu, 07 Jan 2010 17:45:00 -0500

Several articles with a personal genomics theme popped up today.

Most importantly, this piece in the Times by Mark Henderson is a superb analysis of the current state and likely future of the personal genomics industry, and a must-read for anyone interested in the field.

Henderson notes that despite the turmoil in the industry in 2009, it's still unclear which of the disparate models adopted by competitors in the industry (e.g. 23andMe's curiosity-driven "genomics is fun" approach, or Navigenics' sombre, paternalistic, health-focused image) will prove the most successful in the long run:

The success or failure of these competing visions will do much to determine the patient experience of the genetic age, and whether direct-to-consumer genomics becomes more than a passing phase. Will we take control of our DNA as individuals, to explore our inheritance, to meet new friends and relatives, and to participate in research? Or will DNA become just another kind of routine medical information, such as cholesterol or blood pressure, which we get through a GP? A lot will depend on which model proves more popular.

The article contains plenty of juicy detail, so go read it all.

Henderson also has two other articles out today that are well worth checking out: a piece exploring the implications of David Goldstein's recent prediction in Nature that genetic research findings will "substantially increase interest in embryonic and other screening programmes"; and another brief piece on growing concerns about the privacy of personal genomic data.

In New Scientist, Peter Aldhous reviews Francis Collins' new book on personalised medicine, taking issue with Collins' more vague descriptions of the benefits of personalising treatment and describing the NIH head as "a cheerleader for a revolution that hasn't arrived quite yet".

Finally, Genomics Law Report's Dan Vorhaus asks five questions for personal genomics in 2010 - and nails several of the key areas yet to be resolved as the industry stumbles into its third year, under an economic cloud and facing tremendous financial and regulatory uncertainty.

Enjoy!

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Blogger shares his increased type 2 diabetes risk with the world

Thu, 07 Jan 2010 10:45:00 -0500

Genetic genealogist Blaine Bettinger has a fantastic post dissecting and contextualising a rather worrying result from his personal genomic analysis: a 50-60% increased lifetime risk of type 2 diabetes.

Blaine is unfortunate enough to be among the 1-2% of individuals who carry two risky versions at each of three major risk variants for the disease. (It's worth noting that type 2 diabetes risk is determined by many different genetic variants, most of which remain unknown, as well as environmental factors - so Blaine's discovery is very far from a certain diagnosis of the disease.)

Blaine's attitude towards the results is admirably pragmatic:

I, personally, am not afraid of my genetic information. I'm not afraid of any potential psychological effects it might have, nor am I afraid of any repercussions of sharing my genetic information with others. It is certainly clear that I lost the genetic lottery when it comes to diabetes risk, but there is no genome so perfect that it lacks at least one serious risk.

[...]

For me personally, interpreting my genotype is no more dangerous than the receiving the results of a home glucose test. Indeed, the results of the glucose test represent a current reality while the genotype merely suggests a future possibility.

I also applaud his decision to share this information with the world, a very personal way of demonstrating the spirit of openness to genetic data that he has consistently advocated in his posts. I completely agree with his reasoning here:

Although I won't go so far as to say that there is never any danger to anyone upon receiving genetic information, I will go so far as to say that it should be the individual, not the government, that decides whether the danger exists.

Amen.

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Will the Archon X Prize for genome sequencing be won in 2010?

Mon, 04 Jan 2010 07:00:00 -0500

The Gene Sherpa predicts that Complete Genomics will win the Archon X Prize in Genomics in 2010. In the comments, Keith Robison is wisely skeptical. I agree with Keith - it's unlikely that the X Prize will be won this year, and if it is the winner is unlikely to be Complete Genomics.

For those who don't know the prize, here's the brief summary: the X Prize Foundation will give US$10 million to the first team to satisfy the following conditions:

sequence 100 human genomes within 10 days or less, with
an accuracy of no more than one error in every 100,000 bases sequenced [note that the stated error rate on this page is mistakenly quoted as one in 10,000 bases], with
sequences accurately covering at least 98% of the genome, and
at a recurring cost of no more than $10,000 per genome.

Sequencing technology is developing fast, but it seems unlikely that these conditions will be successfully met in 2010. Here's why:

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"New" features in the deCODEme interface

Tue, 22 Dec 2009 11:00:00 -0500

I'm currently playing around with my 23andMe data in the deCODEme browser.

deCODEme's (apparently new?) Relationship Check feature, which appears to be a targeted version of 23andMe's Relative Finder algorithm, allows users to compare their genetic data to other profiles in the database and calculate the probability of a familial relationship.

My comparison with notoriously cranky deCODE CEO Kari Stefansson (pictured, left) gave me this reassuring result:

Phew!

On Twitter, genetic genealogist extraordinaire Blaine Bettinger noted that deCODEme appears to have also introduced a brand new community section containing forums (all currently looking rather empty). A reader also recently noted via email the introduction of research questions asked when users consent to examining their results for each different disease.

It looks to me as though the offer of free analysis has been timed to expand the (by all accounts previously fairly tiny) pool of deCODEme users in time for the launch of these new features, all of which rely on a critical mass of users to be of much interest.

It's an interesting approach, but unfortunately thus far all of deCODEme's improvements look very much like attempts to clone innovations previously developed by 23andMe - which I suspect is not really a viable long-term strategy. We'll see what they come up with next.

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deCODEme's embarrassing data processing glitches - lessons for companies and customers

Tue, 22 Dec 2009 07:15:00 -0500

Late last week I noted an intriguing offer by personal genomics company deCODEme: customers of rival genome scan provider 23andMe can now upload and analyse their 23andMe data through the deCODEme pipeline.

On the face of it that's a fairly surprising offer. As I noted in my previous post, interpretation is what generates the real value for personal genomics companies, so giving it away for free seems a bizarre approach to business - especially for a company living on the edge of a financial precipice. However, I also argued that the intention here is likely to be to generate an opportunity for deCODEme to display its interpretation skills to otherwise entrenched 23andMe customers, in preparation for the upcoming battle for interpretation supremacy in the whole-genome sequencing era.

In digging back through my archives I realised that this isn't actually the first time that this strategy has been employed in the personal genomics game: back in June this year, 23andMe offered its interpretation service free to customers of Illumina's freshly-launched $48,000 whole genome sequencing service (the original source is this subscription-only article in industry publication In Sequence).

It's nonetheless the first time that a personal genomics company has opened itself up to genome scan customers, and it's certainly a disruptive (and potentially game-changing) move. AccessDNA's Jordanna Joaquina even goes as far as to speculate that this may herald a shift in deCODEme's strategy towards pure data interpretation. I personally think this is unlikely for deCODEme itself, but I wouldn't be shocked to see a proliferation of multi-platform interpretation services over the next 12 months (Knome's recently announced discovery service is a step in that direction).

But creating an interpretation service that can deal seamlessly with data provided in a multitude of formats from different providers can be a challenging task, as deCODEme learnt in a particularly embarrassing manner this week:

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deCODEme opens its doors to free data upload from 23andMe customers

Thu, 17 Dec 2009 08:45:00 -0500

A curious tweet this morning from personal genomics company deCODEme, barely a few weeks after the declaration of formal bankruptcy of parent company deCODE Genetics:

@decodegenetics: Migrate to deCODE this winter! Upload your genetic data for free. http://www.decodeme.com/data-upload

Here's a description of the service from the URL in the tweet:

deCODEme wants to give even more people the chance to enjoy the best in personal genomics. Our bioinformatics team has just launched a simple system to enable existing customers of 23andMe™ to migrate their data into deCODEme and to join our growing community. If you already have a 23andMe genetic scan, just click on the button below to begin the upload process and start to view your genome using deCODEme's many advanced features.

This service is available to existing 23andMe customers and for a limited time only.

Enjoy and spread the word!

Basically, the company seems to be providing its interpretation service free to customers who have already had their genome scanned by competitor 23andMe.

That's a bold and initially rather puzzling move. Those of you who've been following the personal genomics industry will know that the value of genome scans is not in the actual generation of the data (this is a straightforward procedure), but in the breadth and quality of the interpretation service.

Converting a series of half a million or so genetic data points into predictions of ancestry and disease risk is a non-trivial exercise, and requires the creation and constant, painstaking maintenance of a database of genetic associations. Parsing the literature to extract the required information can be a frustrating exercise, made even more difficult by the sheer rate that new associations are being generated.

Why, then, would deCODEme choose to give away its hard-won interpretation to customers of its most successful competitor?

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A short but glorious rant

Tue, 24 Nov 2009 18:30:00 -0500

Misha Angrist has a very brief but eloquent rant in response to the genomics nay-sayers in this Nature News piece on the bankruptcy of deCODE Genetics.

Here's a taste:

I agree: GWAS is of limited value and this probably contributed to deCODE's demise. But whatever deCODE's fate, if whole human genomes can be sequenced for < $2000, isn't it about time we stopped kicking GWAS's ever-stiffening corpse? Second, just because something is not a medical necessity, does it follow that it is worthless?

Here's the rest.

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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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