Tsui #NGDx18 Their central lab - per mL yield ranges from 1-3300 ng, mean 22ng. 10.5K samples as of '16.
9:49am August 22nd 2018 via Twitter Web Client
Tsui #NGDx18 Can see global copy number, by protocol. Risberg eet al J Mol Diag (in press)
9:48am August 22nd 2018 via Twitter Web Client
Tsui #NGDx18 Shows internal data ddPCR and bioAnalyzer traces - for sensitivity, characteristics of size. Also GC content x coverage
9:47am August 22nd 2018 via Twitter Web Client
Tsui #NGDx18 '18 ref https://t.co/x2vtpLucTi MagMAX was the most stable post-purification.
9:44am August 22nd 2018 via Twitter Web Client
Tsui #NGDx18 Effect of shipment '13 ref https://t.co/6NovWSPILk
Tsui #NGDx18 '16 CellSave data https://t.co/9rNrtzkL1w '17 PAXGene data https://t.co/lUN56nRU23
9:43am August 22nd 2018 via Twitter Web Client
Tsui #NGDx18 Effect of proprietary tubes - Streck BCT at RT, Parpart-Li '16 ref. Shows stable up to 168h. Very usef… https://t.co/XRRtQPe4B9
9:41am August 22nd 2018 via Twitter Web Client
Tsui #NGDx18 EDTA shown to be better for PCR too. '04 ref https://t.co/cAwCgZzEZq
9:40am August 22nd 2018 via Twitter Web Client
Tsui #NGDx18 Effect of double-spins - '02 ref https://t.co/2PDaJQESTt
9:38am August 22nd 2018 via Twitter Web Client
Tsui #NGDx18 Stable in K-EDTA. Plasma vs Serum '16 ref https://t.co/NiA6YLJDdz
Tsui #NGDx18 '03 Clin Chem figure of plasma vs serum of beta-globin GEq/mL https://t.co/TIHGONc2Ie
9:37am August 22nd 2018 via Twitter Web Client
Tsui #NGDx18 (If 1% of 3000 GEq, only 30 copies of mutant alleles present in 1mL plasma.)
9:35am August 22nd 2018 via Twitter Web Client
Tsui #NGDx18 Healthy: <1 - 12.5 ng/mL plasma. Cancer: 10 ng/mL or about 3000 Genome Eq (GEq). If 5% in metastatic, ave 8-10%; early stg &
Tsui #NGDx18 Uses a nice figure from '14 ref https://t.co/jZhhSkt3kn many types of analytes, including CTCs and cfDNA
9:34am August 22nd 2018 via Twitter Web Client
Tsui #NGDx18 Illust. the challenges of cancer mgmt; an oppy to noninvasively sample the cancer genome.
9:33am August 22nd 2018 via Twitter Web Client
Tsui #NGDx18 Blood easy to access; NIPT wide adoption; much can be learned from that field.
9:31am August 22nd 2018 via Twitter Web Client
Dana Tsui (MSKCC) #NGDx18 Pre-analytical and analytical considerations for cell-free DNA profiling
9:29am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 Future - viruses, microbiome, 2ndary germline testing.
9:13am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 Can pick up clonal hematopoeisis even in tumor-only sequencing (!) JAMA Onc https://t.co/U8XoVhZv7t
9:10am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 Clonal hematopoiesis - a new area, not fully worked out. Started a clinic for this '17 ref https://t.co/rreaWCavkm
9:08am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 And HLA class I influences I-O Rx response '18 Science https://t.co/pxayc7EgMo
9:06am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 TMB cutoffs associated with different tumor types - it varies. Points to this NEJM https://t.co/dhqMA0ts8n
9:05am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 Never smokers - more targetable drivers, targeted Rx; smokers - more TMB, go with I-O Rx.
9:02am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 Can ID 1500 Microsats, looking at MSI, across 12K retrospective samples. Also TMB.
9:01am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 Shows cancer type-agnostic examples - ERBB2, NTRK fusions. '18 NEJM https://t.co/Qlowi7g5IF
8:58am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 Points to this '18 review as 'this is hitting the mainstream' https://t.co/6vdb83mI6Z
8:56am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 If no actionable Rx, more likely to receive I-O Rx. Shows nice benefits for lung ca in the Jordan paper.
8:55am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 Their rationale for selection; of n=860, about 50% had an alteration that could be targeted w/drug… https://t.co/36ePYmH7kb
8:54am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 MSKCC ad: 'There will never be one cure for cancer. There will be millions.'
8:52am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 NYS approval in '14; TM in '15; FDA clearance as Cl II in Nov '17. 200 cases/week, 5x HiSeq 2500. 30K samples to-date
8:51am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 So will need targeted RNAseq, they use ArcherDx. Min input is 250ng. (Note: @Pillar_Bio 's poster h… https://t.co/5vHyw6IbE5
8:50am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 Primary Nature Med '17 ref on MSK-IMPACT https://t.co/lnJd1f2xNq ALK/RET/ROS are tiled, and EWSR1 a… https://t.co/hkY7QExqSN
8:49am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 Clinical trial matching; All data goes out to cBioPortal and portion goes to AACR Project Genie
8:47am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 OncoKB '17 ref https://t.co/zSRcxr4k8A freely available, continually updated.
Ladanyi #NGDx18 Several iterations, now 468 genes, 6,614 exons. 70 introns, 20 rearranged genes. TERT prom, 1.52MB target
8:45am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 Guidelines from 2018 for lung cancer and TKI's https://t.co/mXdhr0DrYo
8:44am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 Old: Histology 'what kind of cancer is it?' Pathology: how far has it spread? New: NGS: what alterations?
8:42am August 22nd 2018 via Twitter Web Client
Ladanyi #NGDx18 Alt title: Leveraging scalable clinical cancer genomics to disrupt the cancer care ecosystem and empower stakeholders!
8:41am August 22nd 2018 via Twitter Web Client
Mark Ladanyi (MSKCC) #NGDx18 Clinical genomic profiling using the MSK-IMPACT large panel NGS assay to guide pt sele… https://t.co/GGV4fCBo6t
8:40am August 22nd 2018 via Twitter Web Client
Mohapatra #NGDx18 Showed CNV validation and dPCR at 100%
3:39pm August 21st 2018 via Twitter Web Client
Mohapatra #NGDx18 Need 500x min coverage, for a min AF of 5%. Shows nice PPA/PPV analytical performance.
3:37pm August 21st 2018 via Twitter Web Client
Mohapatra #NGDx18 Their TAT is <10d. Have had 31 ref standards;;; including Acrometrix, Horizon, long list, PGP tri… https://t.co/3370yGL
3:33pm August 21st 2018 via Twitter Web Client
Mohapatra #NGDx18 Validation confirms suitability for intended use. Accuracy, precision, analytical sensitivity, an… https://t.co/HSX5U4QfpM
3:25pm August 21st 2018 via Twitter Web Client
Mohapatra #NGDx18 Clinical actionability - NCCN clinical trials, My Cancer Genome. Goes through @iontorrent workflo… https://t.co/sniAQyhXeF
3:21pm August 21st 2018 via Twitter Web Client
Mohapatra #NGDx18 Lays out the development of Oncomine Comprehensive, described here https://t.co/Rv73N33gVv
3:17pm August 21st 2018 via Twitter Web Client
Mohapatra #NGDx18 Imptc of ref stds for assay dev; broad investigation of the genome, but complexity in interpreting.
3:15pm August 21st 2018 via Twitter Web Client
Garlick #NGDx18 Only 4 of 17 'hard' variants were detected by all 10 workflows; only 3 workflows detected all 17.
3:10pm August 21st 2018 via Twitter Web Client
Garlick #NGDx18 A 'hard variants' reference material with 23 variants. Shows summary chart of pre-print https://t.co/1OHRkXNWW2
3:09pm August 21st 2018 via Twitter Web Client
Garlick #NGDx18 '17 S Lincoln presented results from 30K samples at ESHG 2017 abstract: https://t.co/SVkapLMQBA
3:07pm August 21st 2018 via Twitter Web Client
Garlick #NGDx18 Use samples 'that support intended use'. Webinar May 24 transcript: https://t.co/LuqHJAk4ss
3:06pm August 21st 2018 via Twitter Web Client
