dgmacarthur | February 5, 2009Just a quick pointer to a new paper in American Journal of Human Genetics with my office-mate Bryndis Yngvadottir as lead author, which I see has already received some well-deserved coverage from ScienceDaily and GenomeWeb Daily News. The paper shows that specific types of genetic variants that inactivate genes - called nonsense SNPs - are surprisingly common in the human population.
Here's the abstract:
Nonsense SNPs introduce premature termination codons into genes and can
result in the absence of a gene product or in a truncated and
potentially harmful protein, so they are often considered…
dgmacarthur | February 5, 2009Regular readers will know that I'm at the Advances in Genome Biology and Technology (AGBT) meeting this week, one of the most highly-awaited meetings on the genomics calendar.
There's a huge amount of fascinating data being presented (anyone interested in a blow-by-blow account should follow Anthony Fejes' live-blogging), but there's definitely an overarching theme: the evolving battle between the new-technology sequencing companies. This is a competition that most researchers in genomics are watching with great interest, because it promises to bring about very rapid advances in the speed,…
dgmacarthur | February 4, 2009The view from my back door in Cambridge on Monday:
The view from my hotel balcony in Marco Island this afternoon:
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dgmacarthur | February 2, 2009Helix Health's Steve Murphy rather breathlessly announces the launch of the Coriell Personalized Medicine Collaborative website (for the uninitiated: you can tell Steve is really excited when he uses five exclamation marks at the end of a sentence rather than four.)
To be fair, it is big news. Coriell is offering a free service - a full genome scan, plus a genetic health report and genetic counselling - that would cost you at least $500 from Navigenics. The pay-off to them is a massive database to mine for new gene-disease associations and information about patient responses to genetic…
dgmacarthur | February 1, 2009Francis Collins, former Director of the National Human Genome Research Institute, in a presentation last week (as reported by GenomeWeb Daily News):
He also said that he is "delighted" that direct-to-consumer genetic
testing services are being offered, even though the field "has become a
favorite whipping boy for some of us." He said it is good "that the
public is having the chance to learn about their genomes if they think
they want to know ... and that companies are doing this in a responsible
way. But, of course, there are some things on the web that are not
responsible."
In addition,…
dgmacarthur | February 1, 2009Edited 2/2/09: The cited study discusses pre-natal genetic screening, not only embryo screening; I've updated some wording to reflect this, but it doesn't have any major impact on the overall message.
Razib points to an article suggesting that Australian couples are "flocking" to a US fertility clinic that allows them to screen their potential IVF embryos for sex and even cosmetic traits like skin and eye colour, in addition to variants that predispose to severe disease risk. ("Flocking", in this context, means about 14 couples a month.)
This follows on the heels of a fairly widely-publicised…
dgmacarthur | February 1, 2009Complete Genomics is a DNA sequencing company that launched back in October, and has been creating a buzz in the genomics community ever since.
The company's business model is based around a novel technology for rapidly generating DNA sequence data; but rather than make its money by selling its platform to genomics facilities and biotech companies (as do its competitors, such as Illumina and ABI), Complete will be offering its technology only through its own purpose-built service facilities.
The buzz has focused on whether Complete's technology will be accurate and powerful enough to meet…
dgmacarthur | January 28, 2009Nearly five months after 23andMe dropped the price of its genome scan service from $1000 to $400, personal genomics competitor Navigenics has made its own foray into the lower-cost genetic testing market.
Navigenics has always been the most expensive of the three mainstream genome-scan companies, despite offering essentially the same product as competitors 23andMe and deCODEme: a genome scan examining between 500,000 and a million sites of common genetic variation, known as SNPs. While its competitors charge a one-off fee of $400 (23andMe) or $1,000 (deCODEme), Navigenics whacks its customers…
dgmacarthur | January 27, 2009Misha Angrist passes on a call from Case Western University for personal genomics customers to participate in a study of the experience of getting your genome scanned. If you've paid money to 23andMe, deCODEme or Navigenics, consider getting involved - Misha assures us that the process was relatively painless.
By the way, if you happen to be that most elusive of creatures - a happy customer of Navigenics - Drew Yates has been waiting to hear from you for a long time.
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dgmacarthur | January 26, 2009I'll be at the Advances in Genome Biology and Technology meeting next week - this will be my my first experience of this annual conference on Florida's picturesque Marco Island, but I already have high expectations based on reports from previous years. The programme is packed with cutting-edge genomics, and to be honest after a few months of Cambridge weather I'm craving even a brief glimpse of blue sky and salt water.
I'll be giving a talk myself on some fairly preliminary data emerging from work I've been doing with the Sequencing R&D team at my new home, the Wellcome Trust Sanger…
dgmacarthur | January 22, 2009New Scientist has an investigation into companies offering surreptitious genetic testing - basically, providing analysis of DNA samples obtained without permission from others. Currently popular uses are searching for evidence of non-paternity or infidelity (by testing underwear for strange DNA), but obviously the potential exists to also look for markers of potential disease risk, a la Gattaca - an attractive prospect for employers, insurers, or those hunting for the flaw-free spouse.
Human nature being what it is, there's little doubt that a considerable market for non-consensual genetic…
dgmacarthur | January 21, 2009Keith Robison from Omics! Omics! has a fun nostalgia piece looking back on his days in the midst of the genomics bubble of the late 90s.
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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 19, 2009Well, it's a little late, but I finally have a list of what I see as some of the major trends that will play out in the human genomics field in 2009 - both in terms of research outcomes, and shifts in the rapidly-evolving consumer genomics industry.
For genetics-savvy readers a lot of these predictions may seem, well, predictable, so I want to emphasise that my purpose here is not really to make risky forecasts; I'm more interested in laying out what I see as the major big picture trends for the year to come, with a few specific predictions about unknowns thrown in. In any case (as you will…
dgmacarthur | January 16, 2009A new paper in Bioinformatics describes an efficient compression algorithm that allows an individual's complete genome sequence to be compressed down to a vanishingly small amount of data - just 4 megabytes (MB).
The paper takes a similar approach to the process I described in a post back in June last year (sheesh, if only I'd thought to write that up as a paper instead!). I estimated using that approach that the genome could be shrunk down to just 20 MB - compared to about 1.5 GB if you stored the entire sequence as a flat text file - with even further compression if you took advantage of…
dgmacarthur | January 16, 2009Razib has an excellent discussion of a brand new paper in PLoS Genetics, which uses DNA samples from medieval Icelandic skeletons to explore the genetic history of the Icelandic population.
This population is of course of great interest to human geneticists: the Icelandic company deCODE (the home of over half the authors on this paper) has used its exclusive access to the DNA and genealogical and health records of Icelanders to publish vast numbers of studies on the genetic basis of human disease and other complex traits. In addition, deCODE's consumer genetics division deCODEme provides one…
dgmacarthur | January 14, 2009Still quite a way, based on this survey of second-generation sequencing users (subscription only, I think) conducted by the industry publication In Sequence.
Along with a range of other questions, the survey asked users about the cost to generate one billion base pairs (one gigabase, or Gb) on their platform at the end of 2008, which is about as current as we're likely to get. I've estimated below the total cost to sequence a complete* human genome, assuming an overall depth of coverage** of 30x, for the three most widely-used second-generation platforms:
The fine print
Note that the number…
dgmacarthur | January 14, 2009
Olivia Judson's blog has a guest post by Aaron Hirsh that got me thinking about a topic that will be familiar to most scientists: the transition of research towards Big Science. Big Science basically includes any project involving a large consortium of research groups working together on a tightly-defined problem, usually with a very specific goal in mind (e.g. sequence and analyse a genome, or build a big machine to smash particles together at high speed).
Hirsh only mentions genetics in passing, but this field - and particularly human genetics - is an area where the trend towards Big…
dgmacarthur | January 13, 2009
A very belated note to say that I'll be hosting the 42nd Gene Genie blog carnival here this weekend. Gene Genie showcases the best of the blogosphere on any topic pertaining to genes and gene-related diseases.
Due to the late announcement I'll be accepting submissions up until Saturday night (whatever your time zone). Please submit your favourite gene-related posts by emailing them to me directly.
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…