tag:blogger.com,1999:blog-6334453475526523597.post2967422763269884730..comments2023-11-07T10:31:25.370+00:00Comments on CoreGenomics: Extracting cell-free DNA from plasmaJames@cancerhttp://www.blogger.com/profile/02825715598810395734noreply@blogger.comBlogger21125tag:blogger.com,1999:blog-6334453475526523597.post-16410205883612501022017-05-24T18:18:31.253+01:002017-05-24T18:18:31.253+01:00donde puedo comprar los tubos soy de la cd de mexi...donde puedo comprar los tubos soy de la cd de mexico helpmeAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-18227241569393845152017-05-15T03:21:41.352+01:002017-05-15T03:21:41.352+01:00I am now doing automation extraction of Ct DNA, us...I am now doing automation extraction of Ct DNA, using the kit of Epigenomics, produced by Biochain which is authorized by EPIGENOMICES, after cf DNA is isolated, it will be bisulfit converted and used the bisDNA as colorectal cancer screening test (Septin 9 methylation). I found that the amount of bisDNA which is extracted using automation is less than using hand protocol. Are there any one can give me some suggestion?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-32915734313851894962017-04-13T20:32:36.118+01:002017-04-13T20:32:36.118+01:00It depends from the sample. Its very important to ...It depends from the sample. Its very important to exclude gDNA. From my esperience the average yield is 800pg/1ng per ul. <br />Anonymoushttps://www.blogger.com/profile/01193746674045492013noreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-62846019256970891492017-04-04T13:56:39.294+01:002017-04-04T13:56:39.294+01:00I am currently trying to extract cfDNA from plasma...I am currently trying to extract cfDNA from plasma. We get 8ml blood and spin for plasma (3-5ml) which we then freeze at -80 until extraction by QIAamp circulating nucleic acid kit. We determine concentration by Qubit dsDNA High Sensitivity but the amounts are very low. I elute in 20ul and the concentration is around 4ng/ul. Can anyone tell me if this is average for cfDNA?Melody Cnoreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-10292283344668223122016-11-30T19:24:17.951+00:002016-11-30T19:24:17.951+00:00They do publish data but all the samples are plasm...They do publish data but all the samples are plasma, not blood. I think it's misleading to claim direct cfDNA extraction from whole blood in this case. There is clearly a blood/plasma separation step upfront : "Blood-drop cellfree DNA was enriched from 20 uL of plasma using Circulogene proprietary technology"Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-3054557638221058792016-09-02T15:53:30.818+01:002016-09-02T15:53:30.818+01:00In the list there are automated and manual systems...In the list there are automated and manual systems. Among the automated you could mention<br />Maxwell® RSC ccfDNA Plasma KitAnonymoushttps://www.blogger.com/profile/01193746674045492013noreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-58013128538111493522016-09-02T15:52:31.943+01:002016-09-02T15:52:31.943+01:00This comment has been removed by the author.Anonymoushttps://www.blogger.com/profile/01193746674045492013noreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-39398126232762324512016-07-10T17:56:31.727+01:002016-07-10T17:56:31.727+01:00Thank you very much.. that was very helpful Thank you very much.. that was very helpful Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-71021655277687321952016-07-02T12:09:33.290+01:002016-07-02T12:09:33.290+01:00Circulogene publishes data! See more at https://ww...Circulogene publishes data! See more at https://www.genomeweb.com/sequencing/circulogene-publishes-first-patient-data-liquid-biopsy-testJames@cancerhttps://www.blogger.com/profile/02825715598810395734noreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-11751338532182801262016-06-30T19:28:45.001+01:002016-06-30T19:28:45.001+01:00Have you, by chance, developed a spreadsheet of te...Have you, by chance, developed a spreadsheet of techniques and quantitative results? Great paper. Thank you!Anonymoushttps://www.blogger.com/profile/02447950744922520689noreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-5879410385610309222016-05-27T22:57:13.477+01:002016-05-27T22:57:13.477+01:00I checked Circulogene papers and even if they ment...I checked Circulogene papers and even if they mention blood as initial sample in them, the materials and methods clearly always state that they separate plasma from blood by centrifugation.<br />I am not sure that they get their technology to work yet with blood. But that'd be great if they can get there.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-61113659417727235102016-04-20T16:52:00.261+01:002016-04-20T16:52:00.261+01:00I work at Norgen. The author may have missed it b...I work at Norgen. The author may have missed it but we are not limited to 400uL of plasma. We do have micro, mini, midi and maxi kits to isolate cfDNA from as little as 10uL of plasma up to 10mL+.<br /><br />Here is a new publication where Norgen performed very well compared to the other cfDNA isolation kits.<br /><br />Comprehensive evaluation of methods to isolate, quantify, and characterize circulating cell-free DNA from small volumes of plasma.<br />Mauger F, et al. Anal Bioanal Chem. 2015.Anonymoushttps://www.blogger.com/profile/09527197361953905885noreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-48881581907021426192016-01-20T01:14:06.539+00:002016-01-20T01:14:06.539+00:00Which SPRI technology are you using? And are you t...Which SPRI technology are you using? And are you trying lysis before binding? Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-20977867009723111442015-11-16T20:43:57.726+00:002015-11-16T20:43:57.726+00:00Hi Anonymous,
I am currently trying to determine t...Hi Anonymous,<br />I am currently trying to determine this, and will let you know when I have a better idea. A larger problem that I've been encountering with adapting the SPRI beads for a large scale cf-DNA isolation is the protein/peg/lipid precipitation that occurs during the process. The isolation is successful, but there's so much junk that comes out it inhibits downstream applications. Would anyone have any suggestion on how to remove these impurities?<br />Thanks!<br />Anonomoushttps://www.blogger.com/profile/03835493398603569108noreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-9069827639579537632015-10-13T15:13:25.907+01:002015-10-13T15:13:25.907+01:00Hi,
So far I have seen most of the work is with CF...Hi,<br />So far I have seen most of the work is with CF DNA from serum/plasma. Nothing is being published for CF RNA from serum/plasma by QiaAmp circulating nucleic acid. Did anybody come across that?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-70107612099785046632015-09-22T19:14:06.438+01:002015-09-22T19:14:06.438+01:003.2ng of gDNA is about 1000 copies of DNA. To get ...3.2ng of gDNA is about 1000 copies of DNA. To get accurate assessment of mutations, copy numbers, large number of copies of DNA is needed from large volume of plasma. If you are dealing with large number of plasma samples, I think Aline biosciences plasma DNA kit is the option as it can handle large volume of plasma sample in a 96 well plate format with magnetic beadsAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-15619615349422089342015-07-01T15:42:37.538+01:002015-07-01T15:42:37.538+01:00if you're doing cfDNA research at academic ins...if you're doing cfDNA research at academic institute, and biobank is precious to you especially those associated with clinical data, you don't want 2-5 mL plasma for extraction of cfDNA because you could run out of your biobank very quick!! I found out that now CirculoGene Diagnostics can do droplet volumes of blood to recover cfDNA for cancer monitoring by NGS (2015 ASCO abstract)..its so cool!!.before only Theranos can do it in a drop of blood and mostly they do chemistry testing, not genetic test.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-36122040515893245392015-02-04T06:36:03.072+00:002015-02-04T06:36:03.072+00:00Thank you for the nice post.Thank you for the nice post.용준https://www.blogger.com/profile/02522719241113298854noreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-85322781993310204522015-01-09T16:01:59.136+00:002015-01-09T16:01:59.136+00:00I anticipate using Streck tubes for a study, based...I anticipate using Streck tubes for a study, based on their properties of preserving cfDNA and ability to ship ambient without first processing by centrifugation. However, I will also require some buffy coat DNA (to make sure any mutations of ctDNA are not germline) based on your research, is another tube (ie regular EDTA) necessary? or can the buffy coat from the streck tubes be used?Distillment18https://www.blogger.com/profile/06928122025741245498noreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-19970630133728361772014-12-25T11:08:42.583+00:002014-12-25T11:08:42.583+00:00Thank you very much for this timely appeared doc!Thank you very much for this timely appeared doc!Anonymoushttps://www.blogger.com/profile/11907352444483636507noreply@blogger.comtag:blogger.com,1999:blog-6334453475526523597.post-15733777898149351112014-12-22T12:14:14.035+00:002014-12-22T12:14:14.035+00:00Nice Work Dr H! Very useful.Nice Work Dr H! Very useful.Anonymousnoreply@blogger.com