Saddar: #ampeu2018 Homology-directed repair if a repair template available, where precise point mutations, indels or tags inserted.
9:46am May 1st 2018 via Twitter Web Client
Saddar: #ampeu2018 As cell lines, relevant, reprod and reliable source. Cas9-mediated DSB, using gRNA directing Cas9 to site.
9:45am May 1st 2018 via Twitter Web Client
Saddar: #ampeu2018 Need for FNA: most common for lung ca pts, lack of validation and standardization of specimens cross labs
9:44am May 1st 2018 via Twitter Web Client
Saddar: #ampeu2018 CRISPR and role in gene editing, they use it to create reference materials. Accuref is a div of Applied Stem Cell
Sonika Saddar (Accuref CA US) #ampeurope2018 Development and Characterization of Multigene Molecular Cytopathology… https://t.co/7T0Q7SceNV
9:42am May 1st 2018 via Twitter Web Client
Q: 5% and 1% in plasma is high; did the variant exist? Van Casteren: #ampeu2018 Some labs wanted to retest, but not… https://t.co/mf2Gqmsnu6
9:41am May 1st 2018 via Twitter Web Client
Q: Other metrics to compare labs? Yield, coverage? Van Casteren: #ampeu2018 They do collect it but haven't analyzed it, will expand it.
9:39am May 1st 2018 via Twitter Web Client
Q: Commentary on tech used? Van Casteren: #ampeu2018 asked each lab to treat as pt samples. Everything they current… https://t.co/K5UjzhQMtS
9:38am May 1st 2018 via Twitter Web Client
Van Casteren: #ampeu2018 Conclude - need further improvement needed for optimal pt treatment. Much higher FN rates relative to tissue.
Van Casteren: #ampeu2018 For different mut EGFR T790M by error type; main error is FNs in plasma.
9:35am May 1st 2018 via Twitter Web Client
Van Casteren: #ampeu2018 Looked at 5%, 1% VAF w/1 sample across 21; also tissue. 70% / 40% correct. 'Generally worse in plasma smpls'
9:33am May 1st 2018 via Twitter Web Client
Kaat Van Casteren (Leuven, Belgium) #ampeurope2018 External Quality Assessment Schemes for Gene Mutation Testing in… https://t.co/kYEpJAn3Q8
9:32am May 1st 2018 via Twitter Web Client
Hinerfeld: #ampeurope2018 Shows reprod data. 44-plex on FFPE lymphoid tissue, spatial structure and function.
8:55am May 1st 2018 via Twitter Web Client
Hinerfeld: #ampeurope2018 Internal to the DSP scope, a digital micromirror device (DMD) to select specific location… https://t.co/lLohU17QWf
8:51am May 1st 2018 via Twitter Web Client
Hinerfeld: #ampeurope2018 Able to do single-molecule counting; 40+ validated antibodies.
8:49am May 1st 2018 via Twitter Web Client
Hinerfeld: #ampeurope2018 and then the tags can be collected. They have a mock-up of the instrument in their exhibit.
Hinerfeld: #ampeurope2018 Protein reaents, RNA probes: a 4-channel microscope, stain and imaged. Can determine exac… https://t.co/gMVJGBHMfq
8:48am May 1st 2018 via Twitter Web Client
Hinerfeld: #ampeurope2018 Limited samples for IHC; Digital Spatial Profiling was then developed. More: https://t.co/tf5nE7XsjJ
8:46am May 1st 2018 via Twitter Web Client
Hinerfeld: #ampeurope2018 https://t.co/aUGnUQX0Xi '17 ref where it's not only about exp, but co-colocation of CD8, PD-L1
Doug Hinerfeld: #ampeurope2018 Powering precision oncology research: High plex multi-analyte profiling on FFPE w/Spatial Resolution
8:44am May 1st 2018 via Twitter Web Client
Q: Could it be possible to det the partner? van Kempen: #ampeurope2018 May be sufficient to know the driver for Rx
Q: 100 ng total RNA? What if less? van Kempen: #ampeurope2018 Counts may be too low, however felt it was feasible nonetheless.
8:43am May 1st 2018 via Twitter Web Client
Q: How does it work with a number of sample types?? van Kempen: #ampeurope2018 Manuscript under review; IHC concord 96% FISH 64%.
8:42am May 1st 2018 via Twitter Web Client
van Kempen: #ampeurope2018 Able to get down to 10% tumor cell % w/100ng total RNA input for ALK/RET/ROS1. 20% NRG1, 5%METx14
8:34am May 1st 2018 via Twitter Web Client
van Kempen: #ampeurope2018 100 ng total RNA from cell lines, get 20% LOD. Onto MET ex 14 skip, probe design, data.
8:33am May 1st 2018 via Twitter Web Client
van Kempen: #ampeurope2018 Due to high ROS1 endogenous expression, ROS1 meas noisy. NRG1 fusion design reviewed. Us… https://t.co/gqd1fwA1UW
8:29am May 1st 2018 via Twitter Web Client
van Kempen: #ampeurope2018 Example: EML4_6:ALK_20 fusion. Shows data from 65 pt samples, ROS1 signals via this method noisy
8:26am May 1st 2018 via Twitter Web Client
van Kempen: #ampeurope2018 NanoString Sprint: very easy, automated to use. Analysis - lots of numbers, use Excel to setup over-exp 3' end
8:24am May 1st 2018 via Twitter Web Client
van Kempen: #ampeurope2018 Shows even bigger list: "driven by expression, not mutation" (Bernards, earlier today) "Must have said it 20x"
8:20am May 1st 2018 via Twitter Web Client
van Kempen: #ampeurope2018 An imbalance probe design: 1:1 of WT; ratio >>1 of kinase to 5' partner.
8:19am May 1st 2018 via Twitter Web Client
van Kempen: #ampeurope2018 Designed panel for ALK/ROS1/RET/NTR1/NRG1/METex14skipping. Listed all the exons - many for each driver
8:18am May 1st 2018 via Twitter Web Client
van Kempen: #ampeurope2018 FISH for more DNA fusions means more slides. Diagram of NanoString approach '18 JMD https://t.co/rTtqzsi5H1
8:17am May 1st 2018 via Twitter Web Client
van Kempen: #ampeurope2018 Expects 2020-2025: list of molecular guidelines '18 JTO https://t.co/VOJRyb6h40
8:16am May 1st 2018 via Twitter Web Client
van Kempen: #ampeurope2018 '80's 3 types; 2002-2013 'big bang': BRAF in melanoma, then in NSCLC. Fig from https://t.co/LcWhOYVf5G
8:13am May 1st 2018 via Twitter Web Client
van Kempen: #ampeurope2018 1914 lung ca started to increase as smoking became more prevalent. 1970's: HSCLC, SCLC; w/chemoRx
8:11am May 1st 2018 via Twitter Web Client
Leon van Kempen (Groningen NE) #ampeurope2018 RNA profiling of gene fusion events in lung cancer using NanoString nCounter Platform
Gerlach: #ampeurope2018 'We have a great booth'; FYI take a look at their virtual reality demo! FWIW https://t.co/dIfeOVO0jR from #AACR18
8:10am May 1st 2018 via Twitter Web Client
Gerlach: #ampeurope2018mRNA, lncRNA, gene fusions, miRNA, SNV, CNV, protein: 3D biology. Now: morphology-driven digital spatial profiling
8:09am May 1st 2018 via Twitter Web Client
Gerlach: Up to 800 reporter probes, two probes of 50bp apiece #ampeurope2018 biotinylated probe captured on slide, no ampl
8:08am May 1st 2018 via Twitter Web Client
Gerlach: #ampeurope2018 "Simple enough for Dx." (Yet disclaimed right underneath 'For Research use only, not for us… https://t.co/xCOJIWEsmQ
8:07am May 1st 2018 via Twitter Web Client
Gerlach: #ampeurope2018 Software (nSolver analysis), even data analysis as a service, and contract mfg.
8:06am May 1st 2018 via Twitter Web Client
Gerlach: #ampeurope2018 'enabling the fastest path to signature developmnt; panels for RNA, DNA, Protein. FDA-marked ProSigna assay
8:05am May 1st 2018 via Twitter Web Client
Nanostring workshop: Jay Gerlach, Dir Product Mgmt #ampeurope2018
8:04am May 1st 2018 via Twitter Web Client
VanderWalde: #ampeurope2018 In CRC: 95% of MSI-H also TMB-H; 82% of TMB-H also MSI-H.
6:19am May 1st 2018 via Twitter Web Client
VanderWalde: #ampeurope2018 70% of MSI-H also TMB-H; 27% of TMB-H also MSI-H
6:18am May 1st 2018 via Twitter Web Client
VanderWalde: #ampeurope2018 Shows overall (busy) Venn: MSI-H, SMB-H, both, total PD-L1+, and none. Small overlap, MSI/TMB higher
VanderWalde: #ampeurope2018 Shows dot plot from ref, MSI status by NGS cp to Fragment Analysis (FA).
6:17am May 1st 2018 via Twitter Web Client
VanderWalde: #ampeurope2018 His recent publ https://t.co/ZnFSpKibwa MSI on a large number of pts. 2189 pts comparsi… https://t.co/ugWNPbH6iF
6:14am May 1st 2018 via Twitter Web Client
VanderWalde: #ampeurope2018 As a surgical oncologist: just wants to 'know what to do'. Freq of MSI-H: shows same Le '17 fig
6:07am May 1st 2018 via Twitter Web Client
VanderWalde: #ampeurope2018 Need a large panel (>1.5MB); at 500x can detect VAF at 5%. But is it relevant to TMB? F… https://t.co/BOBLeHD
6:00am May 1st 2018 via Twitter Web Client
