Tag Archive for '$1000 genome'

Making sequencing simpler with nanopores

The Advances in Genome Biology and Technology (AGBT) conference, one of the main go-to destinations for those who get excited by DNA sequencing technology, is currently going down in Florida. Sadly, no-one from GNZ could make it this year, but we are keeping up with the various announcements about new genomics tech as best we can. One that caught our attention was the announcement of a brand new sequencing machine from a company that has previously kept very quiet about its technology.

Oxford Nanopore, who we have written about before, today announced two new sequencing machines to come out this year. The announcement has caused quite a buzz amoungst, well, everyone. Nature, New Scientist, GenomeWeb, BioIT World and Forbes all have reported on it, and bloggers Nick Loman and Keith Robison have also had a chance to talk to some of the Oxford Nanopore peeps about their new toys.

A lot of the interest has come from the (very cool) MinION, a tiny, disposable USB-key sequencer (shown in the picture above) that can sequence about a billion base pairs of DNA, and cost around $500-$900 each. The applications of this are endless – the ability to pick up a bit of biological matter, mix it with a few chemicals, and read whatever DNA is in it, could help with diagnostics, epidemiology, ecology, forensics. It is also (though not quite) the price where hobbyists could consider having a play; perhaps in a few years plug-and-play DIY genetics could be a possibility.

Less immediately striking, but still just as interesting, is the GridION sequencing machine. This is the work-horse of the nanopore sequencing world, made for reading lots of DNA, and scaling up to massive sequencing centers. Obviously, many scientists are going to be very interested in many of the features (notably, the ability to read very long pieces of DNA, a trick that has previously been more-or-less impossible to do reliably). However, what will this announcement mean for those of us who are interested in personal genomics?

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Responsible and effective use of personal genomes

This is the final of three posts from panellists in the Race to the $1000 Genome session today at the Cheltenham Science Festival – this time by Genomes Unzipped’s own Caroline Wright.

As the previous posts from Clive Brown and Adam Rutherford have indicated, there has long been enormous hype and hope surrounding the human genome project and the prospect of a $1000 genome. But what do these developments really mean for the general public? What do we need to know – either as individuals or as health care providers – before we can decide whether it’s worth having a genome sequenced?

Before starting to unpick some of the issues involved in the responsible and effective use of personal genome sequences, it’s worth reviewing how, where and why someone might actually have their genome sequenced. There are currently essentially three different and nonequivalent contexts in which an individual could have their genome sequenced:
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Guest post by Adam Rutherford: Unknown unknowns and the human genome

This is the second of three guest posts from panellists in the Race to the $1000 Genome session tomorrow at the Cheltenham Science Festival. Yesterday we heard from Oxford Nanopore‘s Clive Brown about the disruptive effects of genomic technology; today’s instalment is from science broadcaster Adam Rutherford, presenter of the recent BBC series about the genome, The Gene Code. Tomorrow we’ll hear from Genomes Unzipped’s own Caroline Wright.

There are known knowns; there are things we know we know. We also know there are known unknowns; that is to say we know there are some things we do not know. But there are also unknown unknowns – the ones we don’t know we don’t know. —Donald Rumsfeld.

The expectations of the Human Genome Project were Rumsfeldian. This much-mocked statement that the then US Secretary of Defense Donald Rumsfeld made in response to the continued absence of evidence for weapons of mass destruction was made almost exactly a year after the publication of the first results of the Human Genome Project (HGP). His oddly profound cod-philosophy resonates with that grand endeavour. The announcement, initially in June 2000, and the publication, were met with triumphalism in the media, fanned by our and its glorious leaders. President Clinton stood on a platform, flanked by Craig Venter and Francis Collins at the White House, and declared that:

Without a doubt this is the most important most wondrous map produced by human kind…

Today we are learning the language in which God created life.

Whatever your religious disposition, that is a bold statement. He and others went on to speculate that soon we would understand and be on the path to curing many, if not all, diseases. Geneticists bristled at this hubris. The fundamental problem was unknown unknowns. It turned out that humans have far fewer genes than we expected. The vast majority of the genome does not contain genes. So what is it doing?
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Guest post by Clive Brown: the disruptive power of cheap DNA sequencing

In advance of the Cheltenham Science Festival session on the race for the $1,000 genome this Wednesday, panel participant Clive Brown agreed to write a guest post on the importance of advances in genomic technology. Clive is Chief Technology Officer at Oxford Nanopore Technologies, where he leads the specification and design of the Company’s nanopore based sensing platform, including strand DNA/RNA sequencing and protein sensing applications, which we’ve written about previously here at Genomes Unzipped.

Incidentally, the other panel members will be Adam Rutherford, presenter of the excellent recent genetics documentary series The Gene Code, and Genomes Unzipped’s very own Caroline Wright, and the session will be chaired by Times Science Editor Mark Henderson – so if you’re anywhere near Cheltenham, you should definitely check it out.

When the final Human Genome Project publication was published in 2004, hundreds of scientists from 18 different institutions from the UK to the US, China and Japan authored the paper. The cost of this phenomenal collaborative project has been estimated at more than $3 billion from its initiation, a ‘moon-shot’ that was necessary to step onto the path of improving the process of obtaining and understanding genetic information. In 2004 the cost of sequencing a whole (haploid) human genome was still in the region of tens of millions of dollars. In 2008 this dropped through $1 million, in 2009 through $100k and in 2011 the cost is approaching $10k.

Many people have criticised the fact that the Human Genome Project did not in itself deliver a new era of personalised medicine, without realising that the project was just the first hurdle which facilitated major steps forward in the basic scientific understanding of genomics – for example, understanding the basic structure of the genome or mapping the variation between different peoples’ genomes. Importantly, the foundations were laid for understanding the very complex mechanisms behind how the genetic code relates to the expression of a protein and therefore the ‘phenotype’ – how those genetic differences are manifested whether it is a trait or disease-causing malfunction.
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Cluster Sequencing with Oxford Nanopore’s GridION System

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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A Googol of Genomes?

[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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Friday Links

The Genomes Unzipped team has been quiet for the last few weeks as we prepare for a major announcement – stay tuned next week to find out more. In the meantime, here are a few things we found around the web this week.

China’s sequencing powerhouse BGI collaborated with Danish researchers to analyse the exomes (the sequences of all protein-coding genes) of 200 individuals from Denmark, in a study published in Nature Genetics. The researchers took an approach similar to that adopted by the 1000 Genomes Project, sequencing each of the individuals at fairly low depth (with each base in the exome being covered on average by 12 sequencing reads, as compared to at least 30 for a “high quality” genome), but then using a statistical approach to identify variants and infer their frequency within the population. The headline finding was that the sequenced individuals carry more rare protein-altering polymorphisms than expected; the authors conclude:

Based on our findings, we support the idea that much of the heritable variation affecting fitness is caused by low-frequency mutations, which are often overlooked in studies based on genotyping rather than resequencing.

The conclusion that much of the “missing heritability” for disease is driven by rare protein-altering mutations is plausible, but this study in and of itself doesn’t provide compelling evidence in support of it. Fortunately, more definitive studies are underway: as tens of thousands of exomes from disease patients and controls accumulate over the next two years, the contribution of rare protein-coding variants to disease (or surprising lack thereof) will soon be fairly definitively established. [DM]

Bio-IT World has an excellent special issue on “The Road to the $1000 Genome”, highlights include an article pondering the often underestimated costs of analysis of genome sequences, and an update on Hugh Reinhoff’s personal quest to find the mutation underlying his daughter’s genetic disease. The issue coincides with the launch of editor Kevin Davies’ new book The $1000 Genome, which was favourably reviewed this week at 23andMe’s blog The Spittoon. [DM]

In Science this week, John Travis takes a look at the technically and ethically challenging world of Native American genetics, focusing on the effort to sequence the nuclear genome of Lakota warrior Sitting Bull from snippets allegedly taken from the man’s hair. The story includes the unusual method by which the main researcher in the project gained approval to study the Native American’s remains:

LaPointe said the basement ceremony was required to get permission from Sitting Bull himself, who was killed in 1890. Willerslev says something odd happened at the ceremony, recalling a blue-green light that ran across his body and into his mouth. LaPointe says the spirit of Sitting Bull tested the geneticist and approved. As a result, LaPointe allowed Willerslev to cut a short section from a long braid of Sitting Bull’s still-shiny black hair and fly it back to the University of Copenhagen for analysis.

If only all ethics committee meetings were livened up by pyrotechnics… [DM]

A piece in Fortune tells the remarkable story of Hugh Martin, CEO of the massively-funded third-generation sequencing startup Pacific Biosciences, who has battled openly with cancer while guiding the company through funding rounds and towards a public share offering. [DM]

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