Tag Archive for 'sequencing'

Complete Genomics to sequence 1500 whole genomes for pre-term birth study

15/09/2011
Categories: In The News
Written by Daniel MacArthur

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.
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Cracking non-coding variation, carrying cystic fibrosis, and more Alzheimer’s prediction

20/05/2011
Categories: Friday Links
Written by Luke Jostins

Daniel and Luke attended the Biology of Genomes conference at Cold Spring Harbour last week. The talks did not have a huge amount of direct relevance to personal genomics, but did show some real quantum leaps in understanding the function of the non-coding DNA that makes up most of our genomes. Understanding mutations that lie outside of coding DNA is largely a prerequisite for transitioning to whole-genome sequencing for personal genomics, as most of the variation that drives genetic differences between people appears to lie there. As we’ve said before, one of the powerful aspects of sequencing is that it allows you to get at the aspects of your DNA that are unique to you, but that is only really useful (and a lot cooler) if we know what this unique variation does. Biology of Genomes showed us that that dream is closer now than it has ever been before.

For a (somewhat technical) account of some of the conference talks, you can read Luke’s blog posts over at Genetic Inference (along with a signficiantly less technical post about chipmunks and wood cabins), and Matthew Herper has a lay-friendly post on his Forbes blog. As has become standard, Twitter was an important way of disseminating knowledge live during talks, and Keith Bradnam and EpiExperts wrote about this aspect. [LJ]

Since GNZ started, Luke has actually been holding back writing about his many and varied genomics woes, and his resulting quest for bodily health, mostly for lack of time. However, one part of this has leaked out somewhat: he has recently given an interview to fellow blogger Elaine Westwick about being one of the two cystic fibrosis carriers in Genomes Unzipped. Read the interview at Elaine’s blog The Stuff of Life. [LJ]

On a similar subject to our recent post about calculating Alzheimer’s risk, over at Genomics Law Report Dan has written a detailed post about the regulatory challenges ahead for both direct-to-consumer and clinical tests for Alzheimer’s. [LJ]

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Defining a complete genome, innovative sequencers, and the mess ahead for personalised medicine

25/02/2011
Categories: Friday Links
Written by Daniel MacArthur and Luke Jostins

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:
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A decade of genomics, 60 new genomes, parenthood and sharing genetic data, and more on data return

04/02/2011
Categories: Friday Links
Written by Luke Jostins and Katherine Morley

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]

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Cluster Sequencing with Oxford Nanopore’s GridION System

28/01/2011
Categories: Technology
Written by Luke Jostins

More on nanopore sequencing this week. I mentioned in my Genetic Future post that the UK sequencing company Oxford Nanopore is somewhat of a dark horse, and an agreement with Illumina has required complete silence about their potential DNA sequencing machines. However, this wasn’t strictly true; Illumina has signed an agreement for the exonuclease sequencing technology, and on that we aren’t likely to hear anything until it is ready.

However, Oxford Nanopore still can, and does, talk about other aspects of their technology. And today, they have released information on their website on the GridION platform, which will be used to run all their nanopore technology (including DNA sequencing and protein analysis). In effect, these are details about the sequencing machine, but with no new specifics about the sequencing process itself.

Here are a few first impressions.

Sequencing in Clusters

The machines are small and low-cost; I expect they will cost the same or less than an Ion Torrent machine. Like the Ion Torrent, MiSeq and GS Junior, the Nanopore machines should be suitable to sit on the bench of a small lab, running small projects and with small budgets and floorspace.

However, this isn’t the full story. Each individual machine is rocking the VCR-machine-circa-1992 look, and the reason for this becomes clear when you see many of them together. The boxes are designed to fit together in standard computing cluster racks, and Oxford Nanopore refer to each of the individual machines as “nodes”. The nodes connect together via a standard network, and can talk to each other, as well as reporting data in real time through the network to other computers. When joined together like this, one machine can be designated as the control node, and during sequencing many nodes can be assigned to sequence the same sample.

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HiSeq doubles its output, a next-gen sequencing primer, and return of genetic data to patients

28/01/2011
Categories: Friday Links
Written by Katherine Morley, Daniel MacArthur, Jeff Barrett, and Dan Vorhaus

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.

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Sequencing DNA with Nanopores

24/01/2011
Categories: Technology
Written by Luke Jostins

As we have already mentioned, Daniel has recently moved his blog Genetic Future over to the Wired science blogging network. While Daniel is off flying around Europe introducing his newborn to mozzarella and skiing, I have written a guest post for Genetic Future entitled An Introduction to Nanopore Sequencing.

I have been meaning to write about nanopore sequencing for quite a while (if you don’t know what nanopore sequencing is at all, go read the post!). What prompted me to write this was a CGI video made by Oxford Nanopore that managed to sum up nicely some of the basic theory behind nanopore sequencing:

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Are synthetic associations a man-made phenomenon?

19/01/2011
Categories: Journal Club and Opinion
Written by Jeff Barrett and Carl Anderson

Early last year David Goldstein and colleagues published a provocative paper claiming that many GWAS associations are driven not by common variants of modest effect (the canonical common disease – common variant hypothesis underpinning GWAS) but instead by a local cluster of lower frequency  variants that have much bigger effects on disease risk. They dubbed this hypothesized phenomenon “synthetic association” and the term quickly became a genetics buzzword. The paper was widely discussed in both the specialist and mainstream media, and caused quite a stir among academic statistical geneticists.

That debate has been re-opened today by a set of Perspectives in PLoS Biology: a rebuttal by us (Carl & Jeff) and our colleagues at Sanger, a rebuttal by Naomi Wray, Shaun Purcell and Peter Visscher, a rebuttal to the rebuttals by David Goldstein and an editorial by Robert Shields to tie it all together.

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A Googol of Genomes?

12/01/2011
Categories: In The News and Technology
Written by Dan Vorhaus

[Editor's Note: this was originally posted over at the Genomics Law Report but we'd like to survey Genomes Unzipped readers as well. How many complete genomes do you think will be sequenced in 2011? Poll is at bottom.]

Earlier this week we took a look back at 2010 and offered our projections for the coming year in personal genomics. Topic #1, just as it was last year: the $1,000 genome.

In hindsight, it might have been ill-advised to offer predictions about the near-term future of genome sequencing during the same week in which one of the year’s major industry conferences (the JP Morgan annual Healthcare Conference) is taking place.

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Solving Medical Mysteries Using Sequencing

12/01/2011
Categories: Journal Club
Written by Luke Jostins

There is a real “wow” paper out in pre-print at the journal Genetics in Medicine. It is a wonderful example of the application of cutting edge sequencing technology to solve a medical mystery. Even better, the authors also include an auxiliary discussion about the medical and ethical issues surrounding the diagnosis, which raises some interesting issues about the transition from research to clinical sequencing.

The Case

A child manifested severe inflammation of the bowel at 15 months; antibiotics failed to clear it up, and he started to lose weight. Standard treatments seemed to have only sporadic effects, and only severe treatment with immunosuppressants, surgery and full bowel clearing could slow down the disease, which is not a long term solution. No cause could be found; the patient’s active immune system seemed to be acting abnormally, but all tests for the known congenital immune deficiencies came back negative. The doctors could try a full bone-marrow transplant, but without knowing what was causing the disease, and where it was localised, they had no way of knowing if such an extreme intervention would be successful.

Such a severe and early onset disease is likely to be genetic, but testing immune genes at random to find the mutation could take years before it turned anything up. Meanwhile, the child was seriously malnourished, and at times required daily wound care under general anaesthetic. A few years ago this might have been the end of the story.

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