dgmacarthur | November 5, 2008In addition to the African and Asian genome studies I discussed in my last post, Nature's latest issue is completely dominated by the topic of personal genomics.
Erika Check Hayden has a nice piece on methods to squeeze the most out of your own personal genomic data, including a profile of the Promethease analysis tool developed by SNPedia's Mike Cariaso and Greg Lennon, which allows personal genomics customers to match their own genetic data against the SNPedia database.
Hayden also gives me my first ever mention in Nature - unfortunately, it's in the context of the unflattering comments I…
dgmacarthur | November 5, 2008
The latest issue of Nature is just as it should be: nearly wall-to-wall human genomics, with a special focus on personal genomics (more on that later).
The main event is a potential historical milestone: quite possibly the last two papers ever to be published in a major journal describing the sequencing of single human genomes from healthy individuals1. The papers, which both appear to be open access (kudos to Nature for that decision) describe the analysis of the first Asian genome by researchers at the Beijing Genomics Institute, and the sequencing of the first African genome by a cast of…
dgmacarthur | November 3, 2008One of the major challenges of the personal genomic era will be knowing exactly which (if any) of the millions of genetic variants present in your genome are likely to actually have an impact on your health. Such predictions are particularly problematic for regulatory variants - genetic changes that alter the expression levels of genes, rather than the sequence of the protein they encode. A paper out in PLoS Genetics this week goes some way towards solving this problem by giving researchers a much better idea of exactly where they need to look for these variants.
The paper
The paper draws on…
dgmacarthur | November 2, 2008Dienekes takes a critical look at 23andMe's new "global similarity" tool (requires a 23andMe login or a demo account to view), which allows you to visually place your own genetic data in the context of genome-wide SNP data from over 1,000 individuals from around the world. The take-home message: the feature is an improvement over previous versions of 23andMe's genetic ancestry tool, but it still needs plenty of work.
dgmacarthur | October 30, 2008Retail DNA tests - personified by personal genomics company 23andMe - have been named Time magazine's Invention of the Year. The fairly lengthy citation notes that "[a]lthough 23andMe isn't the only company selling DNA tests to the public, it does the best job of making them accessible and affordable."
It's yet more public exposure for the personal genomics industry, pushing recreational genetic testing closer towards becoming a mainstream pursuit.
I note that 23andMe has wasted no time giving the award a central position on their home page and their corporate blog.
HT: the ever-readable…
dgmacarthur | October 30, 2008One of the ethical quandaries raised by direct-to-consumer genetic testing is the possibility that customers may send in DNA samples for analysis from other people who haven't provided informed consent - prospective spouses, for instance, a la Gattaca - and then use that genetic information for nefarious purposes. In the past, personal genomics company 23andMe has responded to this possibility by arguing that it's not really the company's responsibility to prevent its customers from performing illegal acts; they have also (quite convincingly) pointed out the difficulties of extracting 2 mL of…
dgmacarthur | October 29, 2008Over at Think Gene, Drew Yates has a fine rant about the notion that using unsupported genomic information to make medical decisions is better than simple voodoo.
dgmacarthur | October 24, 2008Over at PolITiGenomics, Washington University's David Dooling discusses his work as part of the Tumor Sequencing Project. The TSP and a variety of other groups (like The Cancer Genome Atlas) are using large-scale sequencing to create comprehensive maps of the genetic changes that underlie cancer formation.
The cancer genome sequencing community have already made impressive headway - Dooling notes two papers in this week's edition of Nature, one from the TSP on lung adenocarcinoma, and another from The Cancer Genome Atlas on glioblastoma (which received extensive media attention when it was…
dgmacarthur | October 23, 2008When James Watson's genome sequence was publicly released earlier this year, Watson famously kept only one region of his DNA a secret - the region encoding the APOE gene, which contains common variants that contribute substantially to the risk of late-onset Alzheimer's, and also affect predisposition to other diseases.
A recent article in the European Journal of Human Genetics shows something that shouldn't have come as a surprise to anyone familiar with human genetics: simply removing the APOE gene was not enough to prevent someone from inferring whether or not Watson carries the riskier…
dgmacarthur | October 23, 2008The promise of release of raw sequence data files from the first 10 Personal Genome Project volunteers certainly caused a media stir (see the round-up by the PGP's own Jason Bobe), but the actual released data are pretty underwhelming.
So far raw sequence data files have been posted on the PGP profile sites of only four of the ten volunteers: George Church, John Halamka, Esther Dyson and James Sherley. The files are the result of targeted resequencing of a proportion (perhaps 20%) of the protein-coding regions of the genome (called exons, collectively the exome). Although a relatively small…
dgmacarthur | October 20, 2008The first 10 participants of the ground-breaking Personal Genome Project (PGP) will be receiving a hefty chunk of data today: the sequence of the protein-coding regions from many of their genes (collectively known as the "exome"). And if all goes according to plan, they'll soon be dumping all of that data on the web for anyone to access.
The PGP is an audacious endeavour led by Harvard's George Church (recently profiled in Wired). The ultimate goal of the Project is to sequence the entire genomes of 100,000 volunteers, and release both genetic and medical data from those volunteers to the…
dgmacarthur | October 14, 2008Navigenics has announced in the industry publication In Sequence (subscription only) that it plans to add gene sequencing to its personal genomics service. This would make it the first of the "Big Three" personal genomics companies (Navigenics, 23andMe and deCODEme) to offer analysis of rare as well as common genetic variants.
The move into sequencing has always been inevitable for the personal genomics industry. Currently all three of the major players in the affordable personal genomics field (as opposed to Knome's high-end service) use chip-based technology to analyse up to a million…
dgmacarthur | October 14, 2008From a geneticist's point of view, male pattern baldness - also known as androgenic alopecia - is a tempting target. Baldness is common in the general population, with a prevalence that increases sharply with age (as a rule of thumb, a male's percentage risk of baldness is approximately equal to his age, e.g. 50% at age 50, and 90% at age 90), so there are no shortage of cases to study. It's also a strongly heritable trait, with about 80% of the variation in risk being due to genetic factors. Finally, baldness has been reported to be associated with a wide range of diseases such as prostate…
dgmacarthur | October 12, 2008
Nature News has an intriguing article
on the next three decades of reproductive medicine: essentially a
series of short musings from scientists working in the field about the
issues we will be facing in 30 year's time.
It's worth reading through in full, but this statement from Susannah Baruch at Johns Hopkins caught my eye:
There's
speculation that people will have designer babies, but I don't think
the data are there to support that. The spectre of people wanting the
perfect child is based on a false premise. No single gene predicts
blondness or thinness or height or whatever the 'perfect…
dgmacarthur | October 6, 2008The already frantic DNA sequencing market just got a little bit more crowded, with the dramatic entrance of a new competitor called Complete Genomics. The newcomer brings new technology to the table, as well as big promises: namely the commercial provision of whole-genome sequencing for a bargain $5,000, beginning in mid-2009.
It's still unclear whether the company has the capability to make good on such a promise, but its claims have certainly gained it some attention - the story was broken in the NY Times, Bio-IT World and MIT's Technology Review today (see also coverage from The Genetic…
dgmacarthur | October 4, 2008Anyone who has walked past a TV set over the last few days will have seen footage of the remarkable Jamaican sprinter Usain Bolt, who comfortably cruised to victory (and a world record) in the Olympic 100 metre sprint, and as I write this has just done precisely the same thing in the 200 metre sprint. The interest in Bolt stems not from the fact that he wins his races, but rather from the contemptuous ease with which he does so.
And Bolt is not the only Jamaican to impress in short distance events in Beijing: the country's women's sprint team took all three medals in their 100 metre dash.…
dgmacarthur | September 19, 2008Google co-founder Sergey Brin has discovered that he carries a genetic variant associated with a fairly serious increase in Parkinson's disease risk.
Brin found out about the variant through a 23andMe genome scan (Brin is married to 23andMe co-founder Anne Wojcicki, so I'm sure he gets to play with the company's toys as much as he wants). He announced his result on his new personal blog, TOO; 23andMe's blog The Spittoon has some additional details.
The variant in question is a mutation called G2019S in the LRRK2 gene, which has been reported in a large number of families with members…
dgmacarthur | September 19, 2008
This will probably only be of interest to population genetics afficianados, but I just noticed that the HapMap project has made its phase 3 data available through its browser (the data were previously available for download, but are much more accessible - especially to non-bioinformaticians - through the browser interface).
The HapMap project is a massive international collaboration collecting information on common sites of genetic variation (called single nucleotide polymorphisms, or SNPs) in anonymised individuals from a variety of human populations. Phase 3 has data on about 1.5 million…
dgmacarthur | September 16, 2008The genome-wide association study has been the technique du jour in human genetics for much of the last two years. It's a pure brute force approach, surveying up to a million sites of common variation throughout the genomes of thousands of people at a time, some of whom suffer from a particular disease, and some of whom are healthy controls. The underlying principle is simple: if a genetic variant increases the risk of the disease in question, it will be more common in patients than in controls.
The whole exercise is predicated on one major assumption: that common diseases, such as type 2…
dgmacarthur | September 15, 2008The successes of genome-wide association studies (GWAS) in identifying genetic risk factors for common diseases have been heavily publicised in the mainstream media - barely a week goes by these days that we don't hear about another genome scan that has identified new risk genes for diabetes, lupus, cardiac disease, or any of the other common ailments of Western civilisation.
Some of this publicity is well-founded: for the first time in human history, we have the power to identify the precise genetic differences between human beings that contribute to variation in disease susceptibility. If…