disease genetics
dgmacarthur | January 13, 2011In the last century infant mortality has declined precipitously in the Western world, thanks in large part to the development of antibiotics and vaccination. Yet as the suffering and death from infectious disease has reduced, the burden from genetic disease has become proportionately greater: currently around 20% of all infant deaths in developed countries are a result of inherited Mendelian (single-gene) disorders.
What can be done to reduce this burden? Increasingly sophisticated methods for detecting disease in embryos during pregnancy will help, and these have recently taken another step…
sb admin | January 11, 2011Software company 5AM Solutions has just launched a neat little FireFox plug-in for customers of consumer genomics company 23andMe.
The idea is very simple:
Download your raw data from 23andMe (or use one of the files from me or my colleagues at Genomes Unzipped);
Install the plug-in from here and point it to your 23andMe data;
Browse to a website discussing one of the genetic variants included on the 23andMe chip, and you'll see highlights around the rsID of any variant on the page (rsIDs are unique codes assigned by dbSNP to most of the common variants targeted by personal genomics…
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…
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.
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 | March 31, 2010
Wellcome Trust Case Control Consortium. (2010). Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls Nature, 464 (7289), 713-720 DOI: 10.1038/nature08979
The Wellcome Trust Case Control Consortium has just published the results of a massive survey of common, large DNA duplications and deletions (collectively termed copy number variation, or CNVs) in 16,000 patients suffering from complex diseases and 3,000 controls. The results come as no surprise, but are nonetheless disappointing: the study identified absolutely no novel CNVs…
dgmacarthur | March 10, 2010Lupski, J.R., et al. (2010). Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. New England Journal of Medicine advance online 10.1056/nejmoa0908094
Roach, J.C., & et al. (2010). Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science : 10.1126/science.1186802
Two new papers out today - the first ever studies to employ whole-genome sequencing for disease gene discovery - neatly illustrate both the promise and the challenges lying ahead both for clinical and personal genomics.
The first paper presents the final - and successful…
dgmacarthur | January 7, 2010Genetic 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…
dgmacarthur | November 3, 2009New-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:
The Institute for Systems Biology (ISB) and Complete Genomics Inc. announced today that they are embarking on a large-scale human genome sequencing study of Huntington`s disease (HD). ISB has engaged Complete Genomics to sequence 100 genomes,…
dgmacarthur | July 17, 2009Purcell et al. (2009). Common polygenic variation contributes to risk of schizophrenia and bipolar disorder Nature DOI: 10.1038/nature08185
Neil Walker has been doing a spectacular job of serving up useful information in the comments recently, so I asked him to write the first ever guest post on Genetic Future - something that (as I will be announcing shortly) I intend to do fairly regularly over the next couple of months.
The topic is a paper that has created a rather perplexed buzz recently in the complex disease genetics community: the genome-wide association study (GWAS) for…
dgmacarthur | July 7, 2009The UK House of Lords Science and Technology Committee has published the long-awaited report (PDF) from its inquiry into genomic medicine.
Mark Henderson at The Times has been busy today, putting out three excellent pieces on the report: a summary of the major implications, an opinion piece pushing the need for the health service to respond quickly to the arrival of genomic medicine, and a lengthy blog post praising the report and providing his views in more detail.
I find little to disagree with in Henderson's coverage, and certainly agree with his overall opinion of the report: this…
dgmacarthur | May 3, 2009I'll be spending the next few days at the Biology of Genomes meeting at Cold Spring Harbor, NY - one of the most awaited events on the genomics calendar. I plan to blog here about the major themes emerging from the meeting; you can also follow me on Twitter if you want shorter, punchier updates, and I've set up a FriendFeed group for more complex topics.
The meeting kicked off last night with a session on cancer genomics that gave a sense of the serious amounts of data currently being generated on the genetic origins of tumour development. Most of the work in this area has a fairly…
dgmacarthur | April 28, 2009A new paper in Nature reports the results of a large genome-wide association of autism. After some fairly heroic data analysis, the researchers have managed to tag one region of the genome as containing a common variant that contribute to the disease, with odds ratios on the order of 1.2 (the paper actually reports six variants in the same region, but these all appear to be tagging the same underlying causal variant).
The finding is getting fairly glowing press coverage, but let's keep it in context: an odds ratio of 1.2 means that individuals carrying the variant have their risk of the…
dgmacarthur | April 21, 2009A paper just published online in Nature Genetics describes a brute force approach to finding the genes underlying serious diseases in cases where traditional methods fall flat. While somewhat successful, the study also illustrates the paradoxical challenge of working with large-scale sequencing data: there are often too many possible disease variants, and it can be extremely difficult to work out which are actually causing the disease in question.
The authors looked at 208 families where multiple members suffered from mental retardation and where the family history was consistent with the…
dgmacarthur | April 21, 2009I wrote a few days ago about a debate in the New England Journal of Medicine over the value of data emerging from recent genome-wide studies of the role of genetic variation in common human diseases and other traits. David Goldstein argued that genome-wide association studies (GWAS) have generated disappointing results, and should be scaled back in favour of whole-genome sequencing; Joel Hirschhorn responded with an upbeat piece emphasising the insights generated by GWAS into the molecular basis of common diseases.
Now geneticist Steve Jones has an opinion piece in the Telegraph that…
dgmacarthur | March 24, 2009Pickrell, J., Coop, G., Novembre, J., Kudaravalli, S., Li, J., Absher, D., Srinivasan, B., Barsh, G., Myers, R., Feldman, M., & Pritchard, J. (2009). Signals of recent positive selection in a worldwide sample of human populations Genome Research DOI: 10.1101/gr.087577.108
I pointed yesterday to a new paper in Genome Research taking a genome-wide look at the signatures of recent natural selection in a worldwide sample of humans.
I promised a more thorough analysis of this paper today, but I see Razib at Gene Expression has already done a fine job of that. Razib's post covers the bulk of…
dgmacarthur | March 23, 2009This casual aside on a recent post on personal genomics company 23andMe's corporate blog caught my eye:
Mutations in several other genes have also been associated with
Parkinson's disease, but these are extremely rare. Many have been found
only in one or two families. While these mutations are so rare that
they are not covered by 23andMe (to date we have found no customers
with any of them), studying them could help scientists better
understand the mechanisms of Parkinson's generally... [my emphasis]
In other words, the company already has probes on its custom chip targeting these variants,…
dgmacarthur | March 21, 2009A couple of weeks ago I pointed to an article by bioethicist Jacob Appel arguing that genetic screening for severe disease mutations should be mandatory for parents undergoing IVF, and that not doing so is tantamount to child abuse.
Today the same theme is taken up by New Scientist biology editor Michael Le Page, but extending the process to all parents-to-be via carrier testing:
All would-be parents should be offered screening to alert them to any
genetic disorders they risk passing on to their children. Those at risk
should then be offered IVF with pre-implantation genetic diagnosis
(IVF-…