RT @Julia_Karow: @QIAGEN launches GeneReader at #AMP2015 today https://t.co/sX37EMzgUB
9:01pm November 4th 2015 via Hootsuite
MinION Sequencing Untangles RNA Transcripts in a Difficult Gene - Bio-IT World https://t.co/IM3NZ6pd4W
8:55pm November 4th 2015 via Hootsuite
Peer Schatz, CEO of @QIAGEN addressing guests at #AMP2016 reception on the GeneReader launch https://t.co/q8DocjIL7V
8:48pm November 4th 2015 via Hootsuite
ArcherDx, GenomOncology Ink Co-Marketing Agreement, Collaborate on NGS Workflow | GenomeWeb https://t.co/nOpocxGbqq
6:05pm November 4th 2015 via Hootsuite
.@BradyCooper_NGS Great to see you here at #amp2015 - great @archerdxinc workshops, very enjoyable!
5:07pm November 4th 2015 via Hootsuite in reply to BradyCooper_NGS
Q&A: Regulatory Expert Karen Becker Provides Context for Theranos, FDA Interactions | GenomeWeb https://t.co/iHRcSRKfq1
5:05pm November 4th 2015 via Hootsuite
Steelman: Q:Differentiator? A: Ease of use, and how easy it was for informatic analysis. #AMP2015
4:51pm November 4th 2015 via Hootsuite
Steelman: Q:10-40 samples? A: 4-10 samples / cell. #AMP2015
4:47pm November 4th 2015 via Hootsuite
Steelman: Q: Did you try using FFPE repair upfront of MiSeq? A:No, b/c all reagents are all part of GeneReader workflow #AMP2015
4:46pm November 4th 2015 via Hootsuite
Lazarus: Reiterates the need for actionable content, and an easier-to-use system. #AMP2015
4:44pm November 4th 2015 via Hootsuite
Lazarus: "Today marks the worldwide launch and availability of the (GeneRead) system" #AMP2015
4:42pm November 4th 2015 via Hootsuite
Steelman: (It looks like their pipeline can call at 1%.) Not reportable on MiSeq. #AMP2015
4:40pm November 4th 2015 via Hootsuite
Steelman: Showed nice data where their FFPE sample prep reduces FP's (at 2.5%, from 25 var to 14). ">90% of FPs are C->T change" #AMP2
4:39pm November 4th 2015 via Hootsuite
Steelman: AF's from same samples were differentMiSeq, due to different analysis pipelines, processes, enrichment assays #AMP2015
4:38pm November 4th 2015 via Hootsuite
Steelman: #AMP2015 Shows excellent KRAS concordance with two orthogonal technologies, also w/MiSeq https://t.co/5zmoGH2TVn
4:36pm November 4th 2015 via Hootsuite
Steelman: Details 43 FFPE samples, 3-20y old, 700-800bp DNAs, across 3 systems, 92.0% of amplicon at >500x; 98.6% of var's at >500x #A
4:34pm November 4th 2015 via Hootsuite
Steelman: GeneReadLink can then communicate back out to a LIMS system of choice via APIs #AMP2015
4:32pm November 4th 2015 via Hootsuite
Steelman: GeneRead Link is a middleware app: to provide a web-based interface to print out work instructions, work-lists, reports #AMP2015
Steelman: Flexible and scalable with the flowcells; all at once or staggered. QCI has functions designed for the content #AMP2015
4:30pm November 4th 2015 via Hootsuite
Steelman:As well as automated processes. 10-40 samples simultaneously or staggered. Panel design, bifx pipeline integrated #AMP2015
4:28pm November 4th 2015 via Hootsuite
Steelman: All optimized to work together. They are including optimized for FFPE reagents - opt yield, C->T artifact repair #AMP2015
4:27pm November 4th 2015 via Hootsuite
Steelman: #AMP2015 shows the new GeneReader from @QIAGEN https://t.co/sKNngJpkLL
4:25pm November 4th 2015 via Hootsuite
Steelman: Also skilled bioinformatics, and robust audit trail for the process. #AMP2015
4:24pm November 4th 2015 via Hootsuite
Steelman: NGS still has a barrier to entry; a need for staff experienced in practice and protocols (extraction, library, seq) #AMP2015
4:23pm November 4th 2015 via Hootsuite
Scott Steelman (The Broad Inst) "Actionable insights delivered through fully integrated workflow" #AMP2015
4:21pm November 4th 2015 via Hootsuite
Akkari:Shows streamlined report with actionability; links out to NCCN clinical trials. Approach can scale to 'other applications' #AMP2015
4:20pm November 4th 2015 via Hootsuite
Akkari: Ex. ERBB2 c.839C>T, c.884.C>T heavily published. GOF missense mutation for Her2, signif. freq in lung, br, ov and bladder #AMP
4:17pm November 4th 2015 via Hootsuite
Akkari: Venn diagram of genes that overlap: KRAS NRAS KIT BRAF PDGFRA ERBB2 ALK KIT PI3KCA Shows table of missing var's #AMP2015
4:16pm November 4th 2015 via Hootsuite
Akkari: The var coverage >500x, 99.8% side-by-side: better coverage as AmpliSeq >500x, 93.5% coverage cp to 96.4% #AMP2015
4:15pm November 4th 2015 via Hootsuite
Akkari: Br, Ov, CRC, Lung, Mel; 12 genes KRAS NRAS KIT BRAF etc. 330 amplicons, 16.7kb; 10ng x 4 input; 5% VAF. >500x 96.4% #AMP2015
4:14pm November 4th 2015 via Hootsuite
Akkari: So they queried top 5 tumor types, and variants tied to medical actionability. 'Necessary and sufficient list' of var's #AMP2015
4:13pm November 4th 2015 via Hootsuite
Akkari: As well as ACMG, CAP, AMP for content. Q's knowledgebase: tying together db's, guidelines, literature, clin trials, labels #AMP2015
4:12pm November 4th 2015 via Hootsuite
Akkari: Wanted high prevalence cancer, health impact, intervention, and established markers. Used prof guidelines NCCN, ESMO, ASCO #AMP2015
4:11pm November 4th 2015 via Hootsuite
Akkari: Challenges include content of panels, interpretation, uncertainty of reimbursement. #AMP2015
4:10pm November 4th 2015 via Hootsuite
First: Yassmine Akkari (Legacy Health) "Actionable insights delivered thru medical data-guided NGS panel design" #AMP2015
4:08pm November 4th 2015 via Hootsuite
Here at @qiagen #AMP2015 workshop, introduction by Ted Lazarus CMO. "The Main Event" (NB: The long-awaited GeneReader!)
4:02pm November 4th 2015 via Hootsuite
Sanders: And strong correlation to likelihood of infection susceptibility, not just CD3+ counts (unrelated) #AMP2015
3:40pm November 4th 2015 via Hootsuite
Sanders: Lowest at day 56 post; slow reconstitution even 1y later. A fraction of healthy controls, n=32 to n=17. #AMP2015
Sanders: Last - immune reconstitution with cord blood transplant. Showed mean of complexity across 1y #AMP2015
3:38pm November 4th 2015 via Hootsuite
Sanders: Showed CTLA4 blockage broadens peripheral TCR repertoire '14 ref https://t.co/dcms1Qqkob with tremelimumab #AMP2015
3:37pm November 4th 2015 via Hootsuite
Sanders: Looking at BRAF inhibitors, showed data that TIL clonality increased. #AMP2015 '13 ref https://t.co/gZt8jYHjOb
3:36pm November 4th 2015 via Hootsuite
.@3DiMMUNE But it's a fun challenge - to see how much I can absorb, and Twitter databasing my tweets at https://t.co/jOXMtXH7Rb
3:34pm November 4th 2015 via Hootsuite in reply to 3DiMMUNE
.@3DiMMUNE Ha ha - I'd spend all my time talking into a microphone! (Not!) Yes I'm writing on a laptop, and using PubMed like crazy.
3:33pm November 4th 2015 via Hootsuite in reply to 3DiMMUNE
Sanders: Showed melanoma figures, pre- and post- anti-PD1 treatment from this 2014 Nature ref https://t.co/rgy2IKiNBo #AMP2015
3:32pm November 4th 2015 via Hootsuite
Sanders: (NB: tilSeq is a research application) Looking at anti-PD-1 pre-treatment TIL #AMP2015
3:30pm November 4th 2015 via Hootsuite
Sanders: Showed figure from '13 review - oncology meets immunology https://t.co/DgCCPWo7jY TIL repertoire in melanoma #AMP2015
Sanders: For CTCL, looking at clonality of t-cells in the skin, can distinguish from other inflammatory skin diseases #AMP2015
3:27pm November 4th 2015 via Hootsuite
Sanders: Showed flow cytometry MRD sensitivity failure for MRD; and ability post-transplant sensitivity better than flow #AMP2015
3:26pm November 4th 2015 via Hootsuite
Sanders: Similar work 2014 Clin Cancer Res on B-ALL https://t.co/kpKX3tvqYK #AMP2015
3:25pm November 4th 2015 via Hootsuite
Sanders: Showed 44 samples with T-ALL, Wood 2012 Sci Trans Med ref https://t.co/ubRCQCydf9 #AMP2015
3:23pm November 4th 2015 via Hootsuite
