Friday Links

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A couple of interesting articles this week on the Personal Genome Project and public genomics in general. Mark Henderson at the Times has an opinion piece (behind a paywall, I’m afraid) about Misha Angrist‘s book Here Is A Human Being (see also this review from The Intersection), and in the Duke Magazine Mary Carmichael has an in-depth feature on the work of George Church, with some interesting history of the early days of the PGP.

One aspect that comes out of these articles is how those who take part in public genomics projects are starting to own the unknown unknowns. They accept that they cannot anticipate all the risks of making their data public, but are willing to take the risk of exposing themselves to these unknown risks, and in doing so turn them into knowns. Another aspect is the sheer number of individuals who want to sign up to have their data published online: 15,000 people have expressed interesting in being part of the PGP, despite initial NIH concerns the no-one would want to take part at all. This also chimes with research presented at ASHG this year, showing that members of the public are more concerned with contributing to scientific knowledge, and, crucially, getting access to their own genetic data than they are about the potential risks that such data could expose them too. [LJ]

Kevin Mitchell at Gene Expression has a nice post discussing two recent papers on Rett syndrome, a developmental disorder caused by mutations in the MECP2 gene. The papers describe a clever approach to studying a neurological disease–taking skin cells from patients and converting them into neurons in the lab. [JP]

An article that is currently advanced online at Nature Genetics shows that GWAS don’t only identify genetic variants with small effect on disease risk. A study of around 800 cases with hypospadia (malformation of the male urethral opening) and over 1000 controls found significant association to variants within the DGKK gene on chromosome X. The odds ratios associated with the minor allele at the most associated SNP (rs1934179: allele A) ranged from 2.5-4 and the authors estimate that the causal variant underlying the association at DGKK accounts for around a third of all dysplasias (a metric known as the population attributable fraction or PAF). To put this into context the PAF of APOE in alzheimer’s disease is 0.26. However, it is probably worth pointing out that the APOE4 allele is much more predictive of Alzheimer’s than rs1934179 is of hypospadia. As always, further studies are needed to confirm the odds ratios reported in the study and thus support the PAF, and I am pleased to report the authors stressed this point in their article. [CAA]

Over at Genomics Law Report, UNC’s Jim Evans argues that the abolition of gene patents like those held by Myriad Genetics over breast cancer genes would be a net benefit to the biotech industry. [DM]

Finally, the most recent issue of Stanford Medicine is devoted to personalised medicine, and includes several articles that would be of interest to Genomes Unzipped readers. A particular highlight is the piece on the ground-breaking course offered to Stanford medical students, which included the option to purchase a discounted personal genome scan and sparked enormous controversy among Stanford faculty before being allowed to proceed. [DM]