Razib Khan, more known for his detailed low-downs of population biology and history, has written an important post on Gene Expression, explaining in careful detail exactly how to run some simple population genetic analysis on public genomes, as well as on your own personal genomics data. The outcome of the tutorial is an ADMIXTURE plot (like the one to the left), showing what proportion of your genome comes from different ancestral populations. This sort of analysis is not difficult, but it can often be hard to know how to start, so Razib’s post gives a good landing point for people who want to dig deaper into their own genomes.
This tutorial also ties in to some political ideas that Razib has been talking about since the recent call to allow access to genomic information only via prescription. If you are worried about losing access to your genome, one option is to ensure that you do not require companies to generate and interpret your genome. As sequencing, genotyping and computing prices fall, DIY genetics becomes more and more plausible. Learn to discover things about your own genome, and no-one will be able to take that away from you. [LJ]
Continue reading ‘Analysing your own genome, bloggers respond to the FDA and more reporting on bogus GWAS results’
To celebrate 10 years since the back-to-back publications of complete human genomes in Science and Nature, Science has published series of articles looking back at the last 10 years of genomics, and forward to the future. The article contains short essays from Francis Collins and Craig Venter, the former talking about some of the successes of medical sequencing (including giving a name and photograph to the exome-sequenced IBD patient I discussed a few weeks ago), and the latter discussing how far we still have to go before genomics can reach its potential. Baylor’s Richard Gibbs talks about how the large-scale technical discipline of genomics and the biological subject of genetics are starting to re-merge, after the Human Genome Project saw the two diverging, and there is an oddly inspiring comment from theologian Ronald Cole-Turning about how genomics is redefining our vision of humanity.
Of particular interest is an article by Eliot Marshall on why genomics hasn’t yet had a large effect on medical practice, and what needs to be done to allow the genomic revolution to trickle into medical care. He argues that scientists and doctors need to meet each other half way; scientists need to focus more on showing the direct clinical utility of genomics, whereas doctors need to be more ready to accept new technologies and discoveries, and adapt the way they practice medicine to make full use of them. [LJ]
Continue reading ‘A decade of genomics, 60 new genomes, parenthood and sharing genetic data, and more on data return’
Illumina CEO Jay Flatley announced that an upgrade to their HiSeq 2000 platform expected this spring will allow users to generate 600 gigabases of sequence (the equivalent of 5 high quality human genomes) per one-week run of the machine. This would essentially double the current throughput of the platform and propel Illumina even further ahead in the arms race of delivering vast quantities of low cost sequence data. [JCB]
Over at Golden Helix, Gabe Rudy has just completed a three-part series introducing readers to the promise and challenges of new DNA sequencing technologies, which is well worth a read for those just starting out in the analysis of next-gen sequence data or who have a more-than-casual interest in the current state of the field. [DM]
This month’s edition of Trends in Genetics includes a review article on the ethical issues raised by the feedback of individual genetic data to research participants by Bredenoord and colleagues. This has long been a subject of debate, but the recent increase in studies that assay a large number of genetic variants (such as genome-wide association studies and whole-genome sequencing studies) has brought this issue to the fore. There is currently no consensus on how to deal with this, and in my experience the approach favoured has varied both between projects and between the ethics committees that have assessed them.
Continue reading ‘HiSeq doubles its output, a next-gen sequencing primer, and return of genetic data to patients’
Last year, at the American Society of Human Genetics meeting in Hawaii, Nick Eriksson gave a talk on 23andWe, the scientific arm of 23andMe. He reported a series of genetic association studies that used their customer base as a pool of active participants, by asking them to fill out questionnaires, and correlating their answers with their genotypes. They reported a few novel genes that were associated with semi-amusing/semi-serious traits, including a variant associated with curly hair, and the olfactory receptor variant that predicts whether or not you can smell asparagus in your own urine; these associations have since been published in PLoS Genetics.
This is all very interesting, but that’s not really what I want to talk about here. What I do want to talk about is the effect that knowledge of these results can have on the users of personal genomics, and how this could feed back into genetics research. Stay with me, I’m going somewhere with this.
Continue reading ‘Personal genomics and genetic feedback loops’
The work of geneticists, a category that includes the majority of Genomes Unzipped contributors, typically consists of analyzing DNA sequences from large collection of individuals and this constant flow of data gives us an overview of the diversity of human genotypes. And while in most cases these mutations do not have any functional impact, some rare cases are well documented and have important adverse effects.
A famous example is the BRCA2 gene for which rare mutations have been linked to an increase prevalence of breast and ovarian cancer. Another example: multiple rare variants have been linked to various forms of familial hypercholesterolemia, a condition that significantly increases heart disease risk. I picked these examples because for both cases the identification of carriers of these rare mutations in the general population could improve health: aggressive detection of breast cancer, and use of relevant treatments (such as statins) if you are a familial hypercholesterolemia patient, can make a real difference.
The fact that, in some cases at least, something can be done can put geneticists in a difficult situation. Indeed, we often come across known disease related mutations in the DNA from patients who were not recruited for anything linked to that disease. And it is not clear how this information should be handled. On one hand, we cannot assume that the patient has any desire of knowing anything about his/her disease risk. On the other hand, while analysts always work on anonymous genetic data, the medical staff that collected the sample could potentially get back in touch with the patient who donated his/her DNA. Letting DNA donors know may actually make a difference in their lives (again, this situation is rare but it happens).
Continue reading ‘Communicating genetic data to DNA donors’