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Uncharted Territory

自分が読んで興味深く感じた英文記事を中心に取り上げる予定です

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Natureも取り上げていました

 
$1,000でゲノム解析が可能になってきたことは大きなマイルストーンなんでしょうね。正直今でもそのインパクトの大きさを理解できていませんが。。。(汗)今週のNatureでも取り上げていました。こちらは、プログラムを支援する側の政府の役割の大きさを評価するものでした。まず社説で成功要因として以下の6つを挙げています。

How to get ahead
The success of the $1,000 genome programme offers lessons for fostering innovation.
19 March 2014

Set a clear goal.
Set the bar high, but not too high.
Spur competition.
Foster cooperation.
Seed a broad range of ideas.
Be flexible.

詳しい経緯については別途記事になっています。これだけの短期間で値段を下げられたのはMoore's lawを超えるすごいことのようです。

Technology: The $1,000 genome
With a unique programme, the US government has managed to drive the cost of genome sequencing down towards a much-anticipated target.

Erika Check Hayden
19 March 2014
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In dozens of presentations over the past few years, scientists have compared the slope of Moore's law with the swiftly dropping costs of DNA sequencing. For a while they kept pace, but since about 2007, it has not even been close. The price of sequencing an average human genome has plummeted from about US$10 million to a few thousand dollars in just six years (see ‘Falling fast’). That does not just outpace Moore's law — it makes the once-powerful predictor of unbridled progress look downright sedate. And just as the easy availability of personal computers changed the world, the breakneck pace of genome-technology development has revolutionized bioscience research. It is also set to cause seismic shifts in medicine.

In the eyes of many, a fair share of the credit for this success goes to a grant scheme run by the US National Human Genome Research Institute (NHGRI). Officially called the Advanced Sequencing Technology awards, it is known more widely as the $1,000 and $100,000 genome programmes. Started in 2004, the scheme has awarded grants to 97 groups of academic and industrial scientists, including some at every major sequencing company.

当時主流だったSanger sequencingはslow, labour-intensive processだったこともあり、別のやり方を模索することに決めたそうです。

The dominant technology at the time was Sanger sequencing, an inherently slow, labour-intensive process that works by making copies of the DNA to be sequenced that include chemically modified and fluorescently tagged versions of the molecule's building blocks. One company, Applied Biosystems in Foster City, California, provided the vast majority of the sequencers to a limited number of customers — generally, large government-funded laboratories — and there was little incentive for it to reinvent its core technology.

Still, researchers had seen some advances, including robots that replaced some human work and improvements in devices capable of handling small amounts of liquid. At a 2002 meeting convened by the NHGRI, scientists predicted that such developments would drive costs down at least 100-fold over the next five years. But that was not enough.

They debated what price target would make human genome sequencing routine, the kind of thing a physician might order to help diagnose a patient — on a par with a magnetic resonance imaging scan. “Somebody threw out, to great rolling of eyes, 'a thousand dollars',” recalls Schloss.

ある方法だけを一方的に支援するというのではなく、競合する側にも支援したそうです。

So Schloss and the NHGRI stepped in and began to fund basic research on entirely new methods of sequencing, as well as industrial research to develop these technologies for commercial use. The mixture of applied and academic research within a single programme was uncommon at the National Institutes of Health (NIH), the NHGRI's parent agency. The project was also more nimble than the typical NIH grant programme because it allowed the agency to make small awards for work considered promising but risky. “That flexibility is unusual for the NIH,” says Schloss.

Furthermore, the programme provided support to sequencing companies that could compete with Applied Biosystems. One of the companies funded in the first round of grants, 454 Life Sciences of Branford, Connecticut, was the brainchild of entrepreneur Jonathan Rothberg. It aimed to develop a method that was faster and cheaper than Sanger sequencing by using a much simpler sample-preparation procedure and running many sequencing reactions simultaneously on a solid surface. But as he tried to round up funding, Rothberg heard the same refrain over and over from investors. “People said, 'Why would you want to sequence DNA fast? We've already done the Human Genome Project.'”

Illumina社の登場は、このような流れの中で可能になったようです。

The $1,000 genome project seeded so many companies and labs that it populated the entire industry with expertise, say sequencing researchers. One of the beneficiaries of that is Illumina in San Diego, currently the market leader in sequencing machines. Illumina, whose technology reads out many short stretches of DNA, has acquired multiple companies and many scientists who were once supported by the NHGRI. “It's through acquisitions that Illumina has become stronger and stronger,” says Mostafa Ronaghi, the company's chief technology officer.

But Schloss's programme also forced competitors to exchange expertise at an annual progress meeting that has become a must-attend event. “That meeting is one of the most important venues for keeping an eye on what's happening in sequencing technology development,” says Turner. “There's a tremendous amount of altruistic sharing of knowledge that occurs.”

資金を支援していたNHGRIは直接関与するのではなく、場作りに徹したということでしょうか。正解が分からない場合の方法としては賢明なのかもしれません。

“One of our challenges is to figure out what is the right role for the government; to not get in the way, but feed the pipeline of private-sector technology development,” he says.

*********

“The NHGRI funded smaller companies and academic groups to create a pipeline of technologies,” says Ronaghi. “They didn't decide which technologies to bet on.”

安価にゲノム解析できたとしても、臨床に使用するまでにはまだ越えなくてはいけないハードルがあるそうです。

Genome sequencing stumbles towards the clinic
Technology can uncover disease risks but faces technical and scientific hurdles.
Erika Check Hayden
11 March 2014

The team of doctors, genetic counsellors and scientists report today in the Journal of the American Medical Association that it sequenced the whole genomes of 12 people with no diagnosed genetic diseases, looking for genetic mutations that might cause disease. Every patient was found to have 2–6 such mutations, and one woman found out that she carried a mutation in the gene BRCA1, which is linked to greater risk of ovarian and breast cancer. She opted to have her ovaries removed as a result.

But the researchers, led by cardiologists Euan Ashley and Thomas Quertermous, also found that between the two genome sequencing services they used — Illumina, based in San Diego, California, and Complete Genomics, based in Mountain View, California — 10–19% of genes known to be linked to disease were not adequately sequenced. So doctors might have missed finding harmful mutations in these genes. The two services also disagreed two-thirds of the time about the presence of a particularly worrisome type of mutation — the addition or deletion of parts of genes linked to disease.

Deciding what these results meant for patients was not easy. The study clinicians often disagreed about what patients should do in light of the findings about their genomes — for instance, whether a particular mutation meant that the patient should undergo further testing.

解析したデータをどのように読み取り、診療に生かしていくのか、ビッグデータと同じような悩みを抱えているようですが、新しいフェーズに来ているのは確かなようです。
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