tag:blogger.com,1999:blog-36768584.post144878118846811364..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: Nanopores: Fission or Fusion?Keith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-36768584.post-75974338939817931572012-11-05T19:45:20.427-05:002012-11-05T19:45:20.427-05:00Wanunu paper is available from his web site:
http:...Wanunu paper is available from his web site:<br />http://nuweb9.neu.edu/wanunu/wp-content/uploads/wanunu_article_plrev.pdf<br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-58157833360922004832012-10-30T11:58:41.446-04:002012-10-30T11:58:41.446-04:00If you read the paper based on the new Genia licen...If you read the paper based on the new Genia licensed tech, it's a lot of proof of concept hand waving. They use PEG-bases with varying pegylation. They show that the polymerase can incorporate the base and spit off the PEG, but then say that the leftover triphosphate is too charged. So they replace it with an NH2 using alkaline phosphatase and pass THAT through the pore. But instead of linking all of these steps together, they chemically synthesize the PEG by-products and pass those through the pore. Of course, they say in the future they can link all of these steps together, but the technical hurdles seem much greater than a 2 year solution even for this technology.<br /><br />The Wanunu review is pretty good, although, of the 30 pages, only about a paragraph is spent on nanopore DNA sequencing. The review wasn't dismissive at all, but said that even after decades of research the tech is still in its infancy and needs to overcome many hurdles.Brian Kruegerhttps://www.blogger.com/profile/13456672262242780223noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-45767247072255781022012-10-24T22:41:56.023-04:002012-10-24T22:41:56.023-04:00There's a company in Seattle called Stratos Ge...There's a company in Seattle called Stratos Genomics. I saw they announced a financing based on achieving some level of sequencing on WT alpha hemolysin pores and claim to have a solution for homopolymers. If the animation on their site is accurate this could be the path to commercial nanopore sequencing. I hadn't heard anything about these guys until their press release, anyone have more on them?sciengrnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-44493557438186288832012-10-23T11:03:53.237-04:002012-10-23T11:03:53.237-04:00Few comments on this:
1. The Wanunu paper is a fe...Few comments on this:<br /><br />1. The Wanunu paper is a few months old (I read it back in June I think). I wonder why the publisher chose to highlight it now? <br /><br />As it is, the review is nowhere close to being as dismissive of nanopore sequencing as suggested in the press release. As pointed out in the first comment, the review mostly deals with the biophysical aspects of nanopores. The paper also describes some of the drawbacks that could be associated with the enzymatic slowing of DNA - ie similar to the approach taken by ONT (though ONT is supposedly using a motor protein). These drawbacks have been pointed out by a number of people over the years at conferences and forums.<br /><br />2. While ONT has not released any data, but has received all the hype, very few people paid attention to the work of the Gundlach lab. They are using polymerase to slow down the DNA -which indeed has some disadvantages - but have been very successful in demonstrating single base discrimination for long DNA molecules. This is not actual sequencing, but the closest published result out there validating the nanopore approach. <br /><br />(I can send you pdfs of both the papers if you are interested. please email at nanoporous at omespeak dot com). <br /><br />Overall I agree with your post about wrongly dismissing the technology as 'perpetual motion machines of our age'. <br /><br />[Full disclosure: I work for a company developing nanopore sequencing that is not named Genia, ONT, or Nabsys; nor am I associated with the Gundlach group in nay manner.]Nanoporoushttp://omespeak.comnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-14279472381384600122012-10-22T16:20:02.747-04:002012-10-22T16:20:02.747-04:00Keith -
I asked them to lecture to a class on thei...Keith -<br />I asked them to lecture to a class on their basic technology, and received polite refusals, as they were working "on the final development of GridION and MinION in preparation for commercialization, which has us all fully committed."Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-18170475976095335622012-10-22T13:27:41.067-04:002012-10-22T13:27:41.067-04:00It seems worth pointing out that contrary to the i...It seems worth pointing out that contrary to the impressions of some of threads linked above, this review doesn’t have any particularly radical opinions that need to be disputed. Prof. Wanunu is a very well-regarded researcher and most of this paper highlights interesting biophysical experiments that have been done with nanopores, despite the fact that nanopore DNA sequencing has been slower to arrive than everyone might have hoped.Jacob Rosensteinnoreply@blogger.com