Genome sequencing provider Complete Genomics has announced a deal with the non-profit Inova Translational Medicine Institute, under which the company would sequence 1,500 complete human genomes to help explore the genetic basis of premature birth.
The Inova collaboration is one of many large-scale genome sequencing studies currently being planned and performed around the world. In some respects the study is actually quite a small one – only 250 “cases” (i.e. premature babies) are being sequenced, along with 250 normal-term control babies, which means the researchers will have low statistical power by the standards of modern genomics. However, sequencing this number of complete genomes to high depth is (as far as I know) unprecedented, and the inclusion of the parents of all of the children in the study will provide the team with the ability to do some very interesting analyses – for instance, looking at “de novo” mutations that arise in the babies but weren’t present in either parent, as well as exploring potential effects of the maternal genome. Maternal genetics are known to be important in determining the risk of premature birth: girls born prematurely have a higher risk of delivering a pre-term baby themselves (with twin studies suggesting between 15 and 40% of the risk is heritable), while paternal genes seem to have almost no effect.
Continue reading ‘Complete Genomics to sequence 1500 whole genomes for pre-term birth study’
The Archon X Prize for Genomics offers a $10 million prize to to the first team that can sequence 100 human genomes within 10 days or less at a total cost of $10,000, with strict criteria for accuracy and completeness. However, given that there aren’t currently any gold standard genomes that could be used to confirm that a team has met the Prize’s requirements, and the complexity of judging the winner is far greater than for any previous award from the X Prize Foundation. To help refine the validation process, the Prize Foundation has just announced a collaboration with Nature to crowd-source ideas, which can be submitted via comments on the current plan over at Nature Precedings. If you’re interested in helping to define the state of the art in human genome construction, head over and have your say. [DM]
This week MIT’s Technology Review released this year’s TR50, a list of the 50 most innovative companies. Biomedical companies make a good showing, with 8 in total. Excitingly, three of these companies have been chosen for innovations in DNA sequencing technology; Complete Genomics, for developing the service approach to sequencing human genomes, Life Technologies for aquiring the new Ion Torrent machine, and Pacific Biosciences for their single-molecule sequencing machines. [LJ]
Over at Forbes, Matthew Herper pointed out the announcement of an exciting new targeted drug for cystic fibrosis that showed greater than expected results in clinical trials, as well as the announcement by Life Technologies of an impending upgrade to their Ion Torrent sequencing platform (also comprehensively dissected by Keith Robison here and here). This all sounds like good news, but Herper warned in a separate post that the implications of recent developments in genomics and pharmaceuticals might be heading towards a chaotic impact:
Continue reading ‘Defining a complete genome, innovative sequencers, and the mess ahead for personalised medicine’
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’