Comments on: Up Next: Outsourcing for Sequencing

By: Jeanne Loring

Jeanne Loring — Tue, 23 Feb 2010 02:20:58 +0000

Will Chinese scientists be able to form hypotheses? Absolutely. Many of the key researchers have returned to China after many years of experience with the Western research system. I would not make the mistake of underestimating the abilities of Chinese researchers.

Will they find drug reaction and disease-associated genetic or epigenetic variants? No doubt. For an overview of some variants that are already known, see the 23andme site: https://www.23andme.com/

As an example, I learned from genotyping that I am likely to have a very bad reaction if I take statins (like Lipitor), but I will have a normal response to Warfarin. That alone was worth the price of being genotyped.

By: Michael F. Sarabia

Michael F. Sarabia — Sun, 14 Feb 2010 08:49:13 +0000

Yes, I know some DNA segments define some drug composition that is used for something but, we have no clue on what the something ¨was¨or ¨may have been¨or not.

By: Michael F. Sarabia

Michael F. Sarabia — Sun, 14 Feb 2010 08:45:27 +0000

But, are they only ¨data collecting¨, what will they do with that data? Will they come out with a Hypothesis that if such and such is true the following diseases will follow? Of course Not!
After all the promises made when the first gnome sequence was completed, the only thing I read was all the imperfactions in the DNA secquence they left behind, if that is what they are. We don´t even know enogu to say a variation is due to a disease or genetic or something else.
Would you support the view that if DNA cannot provide proof of a valuable critical drug that was developed based on the knowledge of the Gnome Sequence, we should convert the machines into something useful?

By: Tom Nichols

Tom Nichols — Thu, 11 Feb 2010 23:14:34 +0000

I think that this says in more than words what President Obama was trying to convey in his State Of The Union Speech….China wants these jobs and we are falling behind unless we begin to invest immediately.

By: Dieter ERNST

Dieter ERNST — Thu, 11 Feb 2010 22:23:00 +0000

The speed of China’s learning and catching-up in leading-edge research and innovation is mind-boggling. Who would still stick to the claim that China can only copy? Thsi raises questions for public policy:
- What can we in the West learn from China’s approach?
- How should we respond?
- What does this require in terms of science, technology and innovation policy, and the reform of the education system?
- And what policies could foster US-China scientific cooperation?
dieter ernst,EWC

By: Andrew Plemmons Pratt

Andrew Plemmons Pratt — Thu, 11 Feb 2010 14:16:42 +0000

mballon–

Thanks for the correction. The image appears on both the DOE Joint Genome Institute and LBNL flickr streams–hence the confusion.

By: mballon

mballon — Wed, 10 Feb 2010 17:27:51 +0000

Quick correction: the image above is of Illumina sequencers at the DOE Joint Genome Institute, not at LBNL.

By: David Dooling

David Dooling — Wed, 10 Feb 2010 15:02:14 +0000

Illumina actually does do contract sequencing and NIH, specifically NHGRI, does coordinate significant sequencing capacity through its Large Scale Sequencing grants which currently go to Baylor, Broad, and Washington University in St. Louis (a total of about 140 Illumina GA IIx, 10 SOLiD, and 24 454).

By: Jeanne Loring

Jeanne Loring — Tue, 09 Feb 2010 23:11:38 +0000

This is a response to GreggT. The issue here is not how many instruments there are scattered across the U.S. or in the world. What matters is whether they are coordinately managed. In the U.S., they are not.

Most research institutions have one or a few instruments. We have one Illumina sequencer here at Scripps. In my neighborhood there are about 10 more (excluding Illumina itself, which does not do service sequencing). The instruments are used by whoever bought them, and no effort is made to coordinate use among institutions (the NIH would have to drive that), so some groups are working at far less than capacity, and others are longing for more machines. The group I worked with in Singapore for my recent epigenome paper has about 20, along with some very good collaborative scientists. That’s why I worked with them.

The Broad Institute has more sequencing capacity than any other US institution, but it’s a private, not national resource. Having 157 instruments under management by one institution makes BGI a juggernaut.

By: GreggT

GreggT — Tue, 09 Feb 2010 20:54:34 +0000

Based on James Hadfield’s map & DB of next-gen sequencers available at http://pathogenomics.bham.ac.uk/hts/, the US appears to have a sizable lead on China in terms of NGS instruments. A quick count based on these data indicate at least 325 institutional instruments in the US and 59 in China. This does not include the commercial capacity of companies like Complete Genomics, Illumina, etc.