tag:blogger.com,1999:blog-4457216402399127579.post3526041440052693528..comments2024-03-13T11:06:06.997-04:00Comments on Next-Gen Sequencing: Targeted ResequencingAnonymoushttp://www.blogger.com/profile/14602560263535951430noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-4457216402399127579.post-30130831071946346972010-09-20T06:01:20.885-04:002010-09-20T06:01:20.885-04:00Yah. i am completely satisfy with this is that the...Yah. i am completely satisfy with this is that the NG seq methods showed distinct bias favoring the ends of PCR products, and required very high coverage (34-fold, 110-fold and 101-fold for Roche 454, Illumina GA, and ABI SOLiD, respectively) to achieve a 10% false positive rate - false negative rates were much lower.bioinformatics traininghttp://www.genebyte.firm.in/noreply@blogger.comtag:blogger.com,1999:blog-4457216402399127579.post-70419160272689971452010-06-08T07:52:29.452-04:002010-06-08T07:52:29.452-04:00Capture technology is NOT what it is cracked up to...Capture technology is NOT what it is cracked up to be and I don't think ieven the big 3 US centers know why. But there's incredible problems with the inability to comprehensively cover using capture since, well, the sequence is only as good as the capture and capture is extremely inefficient.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4457216402399127579.post-88191635918988602302010-05-21T01:44:04.825-04:002010-05-21T01:44:04.825-04:00How do you account for the cost of the 12x librari...How do you account for the cost of the 12x libraries into your per run equation? Understand that sequencing reagent costs go down. But you still have to now make 12 libraries. Naturally if you are only planning on running 12 samples then that's one thing. But with multiplexing wouldn't you find ways to perform more runs?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4457216402399127579.post-44486608983775950672009-10-08T06:37:03.317-04:002009-10-08T06:37:03.317-04:00we (at BMR GENOMICS - ITALY) are trying to prepare...we (at BMR GENOMICS - ITALY) are trying to prepare a service of target resequencing targeting the 10 most interesting (as spread on the population) autosomal recessive genetic disease. <br />We have a 454 and will are probably going to use target enrichment systems such as dna microarrays. <br />Combimatrix's arrays are under test right now.<br /><br />p.s. ( the 1000 $ of total costs is not far from the true costs adding reagents, labour costs and instruments. We have ~ 70/80kb of target to sequence)Unknownhttps://www.blogger.com/profile/14553159009997910084noreply@blogger.comtag:blogger.com,1999:blog-4457216402399127579.post-74216703672884366832009-06-09T07:47:56.958-04:002009-06-09T07:47:56.958-04:00Hello,
Could you explain the without-a-NGS-instrum...Hello,<br />Could you explain the without-a-NGS-instrument-yet that I am, how do you achieve the $1000 cost you are mentioning?<br /><br />My gues is that you'll need to order more than $1000 of reagents from illumina (or the others) to run the experiment you are describing.<br /><br />Also, what is the level of multiplexing that is commercialy available from illumina? I heard AB has a 20 barcodes kit available.<br /><br />Thanxx for your very interesting blog.<br />Best.The DNAcowboyhttps://www.blogger.com/profile/12751840095860771080noreply@blogger.comtag:blogger.com,1999:blog-4457216402399127579.post-38928006377705292812009-05-22T21:32:23.772-04:002009-05-22T21:32:23.772-04:00I wonder if the trouble with overrepresentation of...I wonder if the trouble with overrepresentation of the PCR product ends is just showing that these very short fragments don't shear well. I think in the <A HREF="http://www.ncbi.nlm.nih.gov/entrez/utils/fref.fcgi?PrId=3094&itool=AbstractPlus-def&uid=19182786&db=pubmed&url=http://dx.doi.org/10.1038/nbt.1523" REL="nofollow">Broad group's sequence capture paper (using Agilent chips)</A> at one phase they concatenated the fragments with intervening linkers and then fragmented that product.<br /><br />You might also want to read the <A HREF="http://www.the-scientist.com/templates/trackable/display/article1.jsp?type=article&o_url=article/display/55645&id=55645" REL="nofollow">article in The Scientist on capture methods</A>; the last two described seem to be appropriate for the level of multiplexing described in this paper, which is perhaps where you are looking for something.Keith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.com