Q: UMI and software? Barry: Have a version of Picard to mark duplicates #AMP2016
2:18pm November 9th 2016 via Hootsuite
Q: Tried lower input? Barry: 100ng input rec'd. Have good understanding of performance. Can go down to 10ng, but for cf 100ng #AMP2016
2:17pm November 9th 2016 via Hootsuite
Barry: Since pre-synthesized, can relatively quickly put it together. Currently in early-access. #AMP2016
2:15pm November 9th 2016 via Hootsuite
Barry: Showed 2% to 100% MAF linearity; shows sensitivity, spec and uniformity compared to others. Have baits for 450 genes, 1MB #AMP2016
2:14pm November 9th 2016 via Hootsuite
Barry: Bases <33x of the mean is 1.5%; side-by-side competition is much higher (measuring specificity of capture) #AMP2016
2:13pm November 9th 2016 via Hootsuite
Barry: Target size optimized for 2x75 PE (ILMN). Shows % mappability across fresh-frozen, cell-free and FFPE samples #AMP2016
2:11pm November 9th 2016 via Hootsuite
Barry: Shows tiling across KIT; nice coverage plot. Able to scale from 17kb to 360kb targets w/o alignment and % on-target loss #AMP2016
2:10pm November 9th 2016 via Hootsuite
Barry: Same-day sample-to-seq; no lo-vol transfers; no heated buffers. UMI is 12bp. #AMP2016
2:08pm November 9th 2016 via Hootsuite
Barry: They do hyb upfront; then convert to library. Hyb targets both strands at 3' end; after strepavidin pull-down bait stays on #AMP2016
2:07pm November 9th 2016 via Hootsuite
Barry: Needs: low input (<100ng); FFPE / blood / cfDNA); UMI's, sens. spec. uniformity; flexibility; automatable #AMP2016
2:05pm November 9th 2016 via Hootsuite
Andrew Barry (New England Biolabs, product manager) A unique method for target enrichment: NEBNext Direct #AMP2016
2:04pm November 9th 2016 via Hootsuite
SeraCare Life Sciences collaborates with ArcherDX on RNA Fusion Reference Standards PR Newswire https://t.co/77IfI656Oa #AMP2016
1:34pm November 9th 2016 via Hootsuite
Q: Amount of blood? (Personal GenomeDx): 2 or 3 10mL tubes. #AMP2016
1:33pm November 9th 2016 via Hootsuite
(Personal GenomeDx): EDTA can be kept at 4C; equivalent results to Streck BCT at RT. Hospitals may not be able to fractionate #AMP2016
1:32pm November 9th 2016 via Hootsuite
(Personal GenomeDx): Showed effect of storage - EDTA increases at RT, but 4C is fine over 2d. But EDTA 4C shows dec in MAF #AMP2016
1:26pm November 9th 2016 via Hootsuite
(Personal GenomeDx): Kinetic stability study at RT; storage tested 4C EDTA and RT Streck. Tested via ddPCR #AMP2016
1:24pm November 9th 2016 via Hootsuite
(Personal GenomeDx): Studied sample prep: 15 ca pts w/known tissue mutations. 5x in EDTA, 5x in Streck. 4h; RT at days 1 thru 5 #AMP2016
1:23pm November 9th 2016 via Hootsuite
(Personal GenomeDx): Size of ctDNA is 120-200bp; half-life of about 2h. Shares workflow, construct 'families' of common muts #AMP2016
1:22pm November 9th 2016 via Hootsuite
(Personal GenomeDx): Shows gel image of 150bp and 320bp; serum has decrease at 150bp and much 'more noise' (gDNA) #AMP2016
1:20pm November 9th 2016 via Hootsuite
(Personal GenomeDx): Studied serum vs plasma: from panc ca pts, about 100x less GEC in plasma. % AF 10x higher from same pt #AMP2016
1:19pm November 9th 2016 via Hootsuite
(Personal GenomeDx): For ctDNA: 10-25% of NSCLC pts have insufficient tissue. One challenge - whether from primary or metastasis #AMP2016
1:17pm November 9th 2016 via Hootsuite
(Personal GenomeDx): FFPE and low quality RNA, shows bioanalyzer traces; shows r^2 of 0.97 between RNA alone and RNA/DNA #AMP2016
1:15pm November 9th 2016 via Hootsuite
(Personal GenomeDx): Use hyb capture, shows they can regularly go below 5% MAF. Onto co-extraction of DNA/RNA, have workflow #AMP2016
1:14pm November 9th 2016 via Hootsuite
(Asuragen) Challenge - if there's enough leukocyte material in the assay to ensure LOD; i.e. is pt sample above MR4.7 level. #AMP2016
12:11pm November 9th 2016 via Hootsuite
(Asuragen) Starts with the 6K pt samples they used for validation of their test, and their Armored RNA tech for calibrators/ctls #AMP2016
12:09pm November 9th 2016 via Hootsuite
Asuragen workshop "FDA-cleared, clinically proven CML monitoring at the MR4.7 level" #AMP2016
12:08pm November 9th 2016 via Hootsuite
Q: FP rate? Kudlow: Have quiet bases with 1 or 2 bases, 'can get down to sub 0.1%'. Aggregate can get 0.1% w/100ng #AMP2016
11:55am November 9th 2016 via Hootsuite
Kudlow: Mentions John Iafrede at MGH. Q: Ligation efficiency? A: About 90%; lib conversion est. 25%-40% #AMP2016
11:54am November 9th 2016 via Hootsuite
Kudlow: Shows nice stacked read screenshot titled 'error correction in practice'. Second fig, raw reads -> error corrected cleanup #AMP20
11:47am November 9th 2016 via Hootsuite
Kudlow: E.g. 0.3% vs. 3.2% PCR vs Reveal-based, reported AF is much lower on PCR due to lost mutations #AMP2016
11:45am November 9th 2016 via Hootsuite
Kudlow: With variable length amplification, better capture. Showed 1500-2000 GECs cp amplicon to Reveal. Amplicon under-reports AF #AMP2016
11:44am November 9th 2016 via Hootsuite
Kudlow: Ability to come in from either direction (+ and - strands). With fixed amplicon size, shows graph of prob of missing mut #AMP2016
11:41am November 9th 2016 via Hootsuite
Kudlow: Reveal product has 28 genes; has ability to customize assay at https://t.co/l888DyLEPa #AMP2016
11:39am November 9th 2016 via Hootsuite
Kudlow: Region targeted can be from both sides. Shows AF down to 0.1%. Lyophilized reagents; from 50uL purified cfDNA #AMP2016
11:37am November 9th 2016 via Hootsuite
Kudlow: Can get independent observations of a given variant, giving confidence in low AF calls. Heavily nested primers then used. #AMP2016
11:35am November 9th 2016 via Hootsuite
Kudlow: Method: Tag and monitor; end-repair and dA-tail w/random 8-mer w/random DNA end. Then adapter ligate #AMP2016
Kudlow: Also the sampling bottleneck; samples are diluted, showing LMW fx lots of other gDNA (as blood collected) #AMP2016
11:34am November 9th 2016 via Hootsuite
Brian Kudlow (VP of R&D, ArcherDX): Aim was to get something easy, informatics to get at the origin of some of these fragments #AMP2016
11:32am November 9th 2016 via Hootsuite
Q: Sens and FP rate at 0.1%? (ArcherDX): Next talk with Brian Kudlow #AMP2016
11:30am November 9th 2016 via Hootsuite
Q: ssDNA followed by nested; contamination? (ArcherDX): Selectivity of the chemistry, also software helps w/sample switching #AMP2016
(ArcherDX): Points out TT15 poster (Sat AM) to dive into details of Reveal product. #AMP2016
11:28am November 9th 2016 via Hootsuite
(ArcherDX): At 0.1% - if not handled properly, w/contaminating gDNA, not an issue with Archer's method. PCR - will affect freq's #AMP2016
11:25am November 9th 2016 via Hootsuite
(ArcherDX): Showing 11% vs 100% capture between PCR approach and AMP approach. A sampling bottleneck issue. #AMP2016
11:23am November 9th 2016 via Hootsuite
RT @QIAGEN: Excited to bring back the #GeneReader #NGS System with new & improved chemistry to US customers https://t.co/PrzXEYTAZ0 #AMP
11:22am November 9th 2016 via Hootsuite
(ArcherDX): Even if seq data is perfect, still need enough amount of starting material. Need to ensure capture of 'every molecule' #AMP2016
11:20am November 9th 2016 via Hootsuite
(ArcherDX): Need a 'ton of material' to get to 0.001%; 300K GEC (genome equiv copies) for 3 variants detected #AMP2016
11:19am November 9th 2016 via Hootsuite
(ArcherDX): Illustrates Q30 becoming >Q60 due to error correction / barcoding technology. 0.1% in 300 GEC is 0.3 var's #AMP2016
11:18am November 9th 2016 via Hootsuite
(ArcherDX): They look at read provenance, how they enrich ctDNA. Use of molecular barcodes enables. Increase of depth reduces error #AMP2016
11:15am November 9th 2016 via Hootsuite
(ArcherDX): Q60 accuracy isn't available from NGS to be able to get to 0.1% detection; reviews many sources of error in NGS #AMP2016
11:13am November 9th 2016 via Hootsuite
(ArcherDX): (Here's a list of Archer's #AMP2016 presence https://t.co/eRWMCCMK0Q )
11:12am November 9th 2016 via Hootsuite
