Tsongalis: We keep pushing as what's not actionable today may be so next month or year. Remining is impt, accurate all over. #PMWC17
5:21pm January 24th 2017 via Twitter Web Client
Not aligned reads? Aisner: They BLAST all reads, and often soft-clipping was too aggressive. Indels of particular interest #PMWC17
5:20pm January 24th 2017 via Twitter Web Client
(Jim): Cancer moonshot - feels there has made some progress. Asiner: In CO, instrumentation works differently at altitude. #PMWC17
5:18pm January 24th 2017 via Twitter Web Client
Aisner: CAP attempted to do this, but due to scarcity of materials, didn't get going due to lack of participation #PMWC17
5:15pm January 24th 2017 via Twitter Web Client
Q: Datasharing to give? Why for free? Tsongalis: We do this now, on an individual basis. #PMWC17
5:14pm January 24th 2017 via Twitter Web Client
Tsongalis: The big thing is clinical usefulness. <100 genes w/clinically actionable variants. But he's cautious. #PMWC17
5:13pm January 24th 2017 via Twitter Web Client
Aisner: Data is forthcoming, but guidance would be invaluable for handling for ctDNA. #PMWC17
5:12pm January 24th 2017 via Twitter Web Client
Aisner: Pre-analytic variables more complex for ctDNA. Not a lot of understanding how to handle. Time? Temp? Tube? Spins? #PMWC17
5:11pm January 24th 2017 via Twitter Web Client
Garlick: Development of ctDNA; $340M invested; advice on taking new technology into your labs and to patients? #PMWC17
5:10pm January 24th 2017 via Twitter Web Client
Tsongalis: The complexity of the question (regarding panels, tests) not answerable by a repository #PMWC17
5:09pm January 24th 2017 via Twitter Web Client
Tsongalis: Feels inspection needs to be tightened, can be improved. Need to publish validation as often as they can #PMWC17
5:07pm January 24th 2017 via Twitter Web Client
Garlick: Outgoing FDA commissioner and transparency? Aisner: You get samples via CAP, or other sources. Then PT to show it. #PMWC17
5:06pm January 24th 2017 via Twitter Web Client
Tsongalis: Very difficult to find people with NGS experience - 'the biggest challenge of my career'. Some techs - can't get trained. #PMWC17
5:03pm January 24th 2017 via Twitter Web Client
Tsongalis: Need LOD for various types of mutations; different opinions, can't skimp on. Impacts life-extending Rx #PMWC17
5:02pm January 24th 2017 via Twitter Web Client
Tsongalis: How about validating a whole exome? How many samples would you need for every mutation? #PMWC17
5:01pm January 24th 2017 via Twitter Web Client
Tsongalis: A lucky catch, by sharing samples. Specimens for eval, validation, proficiency needed but hard to get. #PMWC17
Tsongalis: Weekly basis 'we look at metrics that we never thought we'd have to look at before' #PMWC17
5:00pm January 24th 2017 via Twitter Web Client
Tsongalis: Went back, looked at their whole process. 15% EGFR del in '13 missed. Updated, revalidation, now confirming for 3 mos #PMWC17
4:59pm January 24th 2017 via Twitter Web Client
Tsongalis: Shared samples with other lab that was also validating. Got the unwanted call "sample #7 had an exon 19 del" #PMWC17
4:58pm January 24th 2017 via Twitter Web Client
Tsongalis: For their validation - what caught them was their data analysis. #PMWC17
4:57pm January 24th 2017 via Twitter Web Client
Tsongalis: If you can't afford to validate a test properly, perhaps you shouldn't be running it. #PMWC17
4:56pm January 24th 2017 via Twitter Web Client
Tsongalis: Their method called CGAT - a close look at data analytics. Just b/c you have an instrument and kit, you still need QC #PMWC17
4:55pm January 24th 2017 via Twitter Web Client
Greg Tsongalis (Dartmouth Hitchcock) QC: Where the rubber meets the road #PMWC17
4:53pm January 24th 2017 via Twitter Web Client
Aisner: Showed poor quality FFPE QC, many pages of artifacts, still picked up EGFR exon 19 del #PMWC17
4:52pm January 24th 2017 via Twitter Web Client
Aisner: NGS metrics: % mapped. What happened to non-mapped? Amt of soft clipping? On-board QC (PhiX) #PMWC17
4:49pm January 24th 2017 via Twitter Web Client
Aisner: Flexibility important; what the quality is of the input - fluorometric, microgel, real-time PCR. 'None is foolproof' #PMWC17
4:48pm January 24th 2017 via Twitter Web Client
Aisner: Need to look at matrix effects - components of human tisue. Fixatives, processing. Metrics to establish: extracted nucl acid #PMWC17
4:46pm January 24th 2017 via Twitter Web Client
Aisner: Sharing a subset of slides presented at the FDA - webcast here https://t.co/LcTeIL5Q6c #PMWC17
4:45pm January 24th 2017 via Twitter Web Client
Dana Aisner (Univ CO SOM): Confronting and mitigating pre-analytic variability #PMWC17
4:43pm January 24th 2017 via Twitter Web Client
Garlick: Working with NIST and EDRN for ctDNA with reference materials #PMWC17
4:39pm January 24th 2017 via Hootsuite
Garlick: SeraCare is bringing products to FDA; de-novo application of 37 ver's at 10% VAF #PMWC17
4:37pm January 24th 2017 via Hootsuite
Garlick: Millions of NIPT samples/year yet no PT program in place. Tapestry network - 'Oncologists concerned CDx about lab results' #PMWC17
4:35pm January 24th 2017 via Hootsuite
Garlick: 2/6 labs report incorrect cardiomyopathy results (Vrijenhoek in EJHG) #PMWC17
4:34pm January 24th 2017 via Hootsuite
Russell Garlick (CSO SeraCare) Achieving Accurate NGS Test Results #PMWC17 NIPS error rate is 3.8%
4:33pm January 24th 2017 via Hootsuite
Q: Scene in China? Beresford: Feel that it'll become std of care sooner in China than here. #PMWC17
3:18pm January 24th 2017 via Hootsuite
Beresford: Shortening time from Dx to Rx '16 ref https://t.co/Pge68IaxIf #PMWC17
3:15pm January 24th 2017 via Hootsuite
Beresford: "actionable results in 72h for pts with NSCLC" - shortening time from Dx to Rx for NSCLC. Usually 3-6w for tissue testing #PMWC17
3:13pm January 24th 2017 via Hootsuite
Beresford: genestrat test now has actionable muts (EGFR, ALK, ROS, RET), also T790M result; reflex to verstrat for Pt-Rx or TKI #PMWC17
3:12pm January 24th 2017 via Hootsuite
Beresford: Prognostic, based upon 8 parameters. Describes advanced-NSCLC for their VeriStat, covered by Medicare, 220M pt coverage #PMWC17
3:11pm January 24th 2017 via Hootsuite
Beresford: Estimated 150K publications for biomarkers. They have a MALDI-ToF MS test called VeriStrat, with spectra #PMWC17
3:07pm January 24th 2017 via Hootsuite
Paul Beresford (Biodesix) Discovering, developing, validating and commercializing liquid biopsy tests in oncology #PMWC17
3:06pm January 24th 2017 via Hootsuite
Otto: Critical to look beyond ctDNA - CTCs, tissues, proteins, RNA. #PMWC17
3:03pm January 24th 2017 via Hootsuite
Otto: Need to demonstrate contam. control, detection. Precision for intra- and inter-run. Also concordance w/orthogonal validation #PMWC17
3:02pm January 24th 2017 via Hootsuite
Otto: Claim 50% conversion efficiency for >5000x sequencing. Analytic validation - use mix of cell lines, synthetic spike-ins #PMWC17
3:01pm January 24th 2017 via Hootsuite
Otto: They've built kits to maximize stability. Also: how to interpret negative results? 2w stability in their kits. #PMWC17
3:00pm January 24th 2017 via Hootsuite
Otto: Clinical challenge: no path review, thus need for low AF measurement. Need SNV, indel, CNA, fusions. Limited smpl stablity #PMWC17
2:57pm January 24th 2017 via Hootsuite
Otto: Yield, dynamic range is highly variable. ctDNA is indirect interrogation. Potential insight into 'systemic' disease (resist) #PMWC17
2:55pm January 24th 2017 via Hootsuite
Geoff Otto (Foundation Medicine) Development and analytic validation of a ctDNA genomic profiling assay #PMWC17
2:53pm January 24th 2017 via Hootsuite
Pralahad: Developed 200 documents for CAP, down to single-cell level. Collab w/Genomic Health, also participating in Moonshot #PMWC17
2:52pm January 24th 2017 via Hootsuite
Pralahad: Looking at AR-V7, published JAMA '16 https://t.co/uaMeBs5vf2 want to optimize process from phlebotomy to result #PMWC17
2:50pm January 24th 2017 via Hootsuite
