tag:blogger.com,1999:blog-36768584.post230509531841649778..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: Ion's S5Keith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger8125tag:blogger.com,1999:blog-36768584.post-44602060046546262002017-03-10T17:56:13.975-05:002017-03-10T17:56:13.975-05:00Has the S5 been released already?
Thank you very m...Has the S5 been released already?<br />Thank you very muchAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-78086579426493159912016-04-19T19:14:28.824-04:002016-04-19T19:14:28.824-04:00Dont forget Illumina's massive lawsuit against...Dont forget Illumina's massive lawsuit against Nano-pour which will prevent them form ever getting a product to market without giving illumina nearly all their profit in royalty paymentsAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-17302041211993987442015-09-23T06:20:57.942-04:002015-09-23T06:20:57.942-04:00Nick, looks like an interesting product, especiall...Nick, looks like an interesting product, especially the deamination-of-cytosine-to-uracil- and nicks-and-gaps repair part. But it will not give longer reads, of course. <br /><br />I don't really see how ONT will be terribly useful in FFPE tumor sample analysis. Maybe handling will be easier, but unless you can afford and do whole genome analysis with it (certainly not with a MinION), you will still need some enrichment, which really is most work (and cost) on any platform. <br />Biggest plus for nanopore sequencing seems to me the ultralong haplotyping. But if you have short fragments to start with, that won't play out. Also, the error rate apparently is still quite high in nanopore sequencing. Especially if you want to look into rare somatic mutations, high error rates are problematic.<br /><br />Cheers,<br />LarsAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-56419523617418690182015-09-09T15:01:25.306-04:002015-09-09T15:01:25.306-04:00Saw a vendor talk at Genome Science 2015 that sugg...Saw a vendor talk at Genome Science 2015 that suggested that FFPE damage can be repaired with a kit from NEB (https://www.neb.com/products/m6630-nebnext-ffpe-dna-repair-mix). It was also suggested it was compatible with long read instruments (maybe not actually generating long reads).<br />Nick Lomanhttps://www.blogger.com/profile/12121179953421841062noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-45224206650495137162015-09-02T22:04:02.049-04:002015-09-02T22:04:02.049-04:00I don't know of any datasets yet from FFPE for...I don't know of any datasets yet from FFPE for MinION -- given its propensity to detect any sort of deviation from standard DNA, straight FFPE may be nightmarish. On the other hand, even limited PCR would generate unmodified copies, so that could be a quick workaround.Keith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-45566416601122978012015-09-02T21:55:19.428-04:002015-09-02T21:55:19.428-04:00What's Oxford Nanopore sequencing look like on...What's Oxford Nanopore sequencing look like on DNA derived from FFPE? Lots of these ion ampliseq panels target tumors preserved with formalin. DNA quality may be a huge challenge for the nanopore devices in the future.Brian Kruegerhttps://www.blogger.com/profile/13456672262242780223noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-61677582573419273682015-09-02T09:24:50.186-04:002015-09-02T09:24:50.186-04:00Hi Keith,
nice summary. As for the diagnostic set...Hi Keith,<br /><br />nice summary. As for the diagnostic setting of clinical genetics looking for germline mutations, I still like the "no homopolymer issue by design" aspect of Illumina. Errors are just not allowed in that field. For somatic mutations in cancer and for bug identification, that is not so much of an issue and as far as I can tell, that's what most Ion users do. These are also the fields that can be time sensitive.<br /><br />Looking at list prices here in Europe, it seems like run prices don't really change much. 8 runs using Chef with 318 and HiQ come down to 6842.88 Euros, but that's only 200bp, if you need 400bp you have to add 488.16 Euros for the 400 supplies kit.<br />8 runs with 520 are 7390 Euros, but that already includes 400pb. So PGM runs are pretty much same price when looking at basically the same output. <br /><br />However, there are people who need low output runs, e.g. because they can't wait for more samples to come in. So if a 314 or 316 is all you need, your runs will be substantially cheaper with the PGM.<br /><br />For those who could use a little more output like very large gene panels, the 530 chip is really what is completely new here. 15-20 million reads is around 4x the 318 chip, while hopefully offering the same quality incl. 400bp reads. Personally, I would have prefered to see this chip as a "320" for PGM, if at all technically possible.<br /><br />Too bad they still cannot produce quite the same quality incl. 400bp in the higher output arena. That would make e.g. their AmpliSeq Exome kit a lot better. AmpliSeq panels have profited quite a bit from 400bp and HiQ. Less amplicons and higher specificity. Ampliseq is really a large plus for the Ion platform. Works very good, very high coverage and high uniformity.<br /><br />Handling seems a little easier, but most Ion users will agree that handling of PGM/Proton is not that much of an issue, Templating/loading with Chef was more of a leap forward.<br /><br />So yes, it is a nice evolution and they clearly target the diagnostics market where things need to be simple and robust. Adding low output chips to the line might be a good idea.Geneticshttps://www.blogger.com/profile/03293264010948215031noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-69119674468019644082015-09-01T09:56:05.654-04:002015-09-01T09:56:05.654-04:00Hi Keith, thanks for this write-up! A great perspe...Hi Keith, thanks for this write-up! A great perspective on where we are today - Ion Torrent / Thermo Fisher going after a market where they can excel.<br /><br />Now a bit over three months moving onto SeraCare, I wonder how long it'll be before vendors give me a 'sneak peek' at their new wares... :)<br /><br />All the best!<br /><br />DaleAnonymoushttps://www.blogger.com/profile/06793338970769363594noreply@blogger.com