(ArcherDX): Starts with ccfDNA intro. Reviews error rate of NGS about 1%, as errors are removed, mutations of interest also lost #AMP2016
11:11am November 9th 2016 via Hootsuite
Thornes: FLT3 doesn't require knowledge of sequence; so NGS not req'd. Co-submit to FDA with TMO, including DHF and locked software #AMP2016
10:48am November 9th 2016 via Hootsuite
Thornes: View TMO as a partner for FDA submissions. FLT3 ITD MRD strategy: initial screen via CE-Sanger, follow-up MRD w/NGS-based #AMP2016
10:45am November 9th 2016 via Hootsuite
Thornes: Dev QC proc's; discussed with FDA; validated across all instruments (on a serial-number-specific basis) #AMP2016
10:44am November 9th 2016 via Hootsuite
Thornes: FLT3 is 30% of AML samples; multiple targeted Rx in dev. They use fragment analysis, with an RUO-labeled instrument #AMP2016
10:43am November 9th 2016 via Hootsuite
Thornes: CE vs NGS 'are complementary'. TAT, Sensitivity, Cost/sample, Level of detail. #AMP2016
10:42am November 9th 2016 via Hootsuite
Thornes: Look at gene rearr, chromosome transloc (inlcudeing BCR-ABL1, PML-RARA, IGH-CCDN1). LabPMM harmonized testing #AMP2016
10:39am November 9th 2016 via Hootsuite
Thornes: Has ISO and CLIA/CAP labs in San Diego, Munich, and Tokyo. Invivoscribe has PCR-based assays, leukemia and lymphoma assays #AMP2016
10:38am November 9th 2016 via Hootsuite
Jordan Tornes (Invivoscribe LabPMM) "IVD Dev with the Applied Biosystems Capillary Electrophoresis Platform' #AMP2016
10:37am November 9th 2016 via Hootsuite
Lopategui: Compares anatomic pathology to molecular effort with a Rembrandt painting (modified to show microarray instead of pt) #AMP2016
10:35am November 9th 2016 via Hootsuite
Lopategui: Tood pts from '14-15 and known survival w/multifocal lung ca; Ex of StgIV looking like StgI; 2/11 equivocal cases #AMP2016
10:32am November 9th 2016 via Hootsuite
Lopategui: Topic 2 - multifocal lung cancer characterization by NGS. Tumor 1 vs 2, synchronous or metachronous? #AMP2016
10:22am November 9th 2016 via Hootsuite
Lopategui: For synchronous mets, found PIK3CA in primary in one pt, another found at metastatic site. Points out dual-targeting #AMP2016
10:17am November 9th 2016 via Hootsuite
Lopategui: Looking at lung mets and distant lymph, for metachronous; ATM and TP53 found, but aren't actionable (yet) #AMP2016
10:13am November 9th 2016 via Hootsuite
Lopategui: Split 12 pts with CRC w/ metachronous and synchronous metastases. 40 samples in total. FFPE microdissected #AMP2016
10:09am November 9th 2016 via Hootsuite
Jean Lopategui (Cedars Sinai, CA): NGS ID's mutational distinction between primary and metastatic CRC #AMP2016
10:08am November 9th 2016 via Hootsuite
Vennemeyer: Mentions free software Minor Variant Finder for CE Sanger sequencing https://t.co/Z6g92cub8e #AMP2016
10:06am November 9th 2016 via Hootsuite
Eric Vennemeyer (Thermo Fisher Scientific): Introduces @thermofisher and @iontorrent presence at #AMP2016
10:05am November 9th 2016 via Hootsuite
Garlick: Mentions Cardiac Hypermyotrophy paper JMD '16 https://t.co/5dsLIJ8XCQ #AMP2016
9:48am November 9th 2016 via Hootsuite
Garlick: Closes with 20 new Seraseq products launched, including Oncology, NIPT, Inherited disease, and infectious disease #AMP2016
9:47am November 9th 2016 via Hootsuite
Garlick: Poster I18 (S. Lincoln) on technically challenging germline mutation detection #AMP2016
9:46am November 9th 2016 via Hootsuite
Garlick: Mentions BioReference Labs, Weill-Cornell, VCU, Jackson Labs participation in inter-laboratory study Poster TT06 #AMP2016
Garlick: Poster TT06 (Sat AM) from Dartmouth, a multi-laboratory study using biosynthetic controls for somatic tumor detection #AMP2016
9:45am November 9th 2016 via Hootsuite
Garlick: Poster S13 (Sat AM) DNA and RNA fusion FFPE reference materials in engineered GM24385; TruSight15 and FusionPlex assays #AMP2016
9:44am November 9th 2016 via Hootsuite
Garlick: Poster S47 (Sat AM) highly multiplexed controls at 40 variants, GMP mfg, dPCR-assayed, across 3 different lots #AMP2016
9:42am November 9th 2016 via Hootsuite
Garlick: Poster TT35 (Sat AM) - ccfDNA Trisomy 13 reference material, commutable, stable long-term for 275 days #AMP2016
9:41am November 9th 2016 via Hootsuite
Q: Cloud-based data storage? de Abreu: Still working with the hospital; for QC data believes it is okay with hosp admins #AMP2016
9:40am November 9th 2016 via Hootsuite
de Abreu: TAT suffered during that time, it took 2 weeks of time to ID the problem and solve it. #AMP2016
9:38am November 9th 2016 via Hootsuite
Q: How much time would you save w/this software? de Abreu: Last Dec, one reagent failed, tech support called. 'Some fail.' 2 weeks #AMP2016
de Abreu: (SeraCare offers no-charge evaluations - info on iQ NGS software here: https://t.co/LTLys53W01 ) #AMP2016
9:35am November 9th 2016 via Hootsuite
de Abreu: Cp manual tracking - Can't do lot #'s, visual correlation, multiple operators, time to add data, drilling down #AMP2016
9:34am November 9th 2016 via Hootsuite
de Abreu: Run-level QC - showing drill-downs to details, and ability to have multiple levels of user-access. #AMP2016
9:33am November 9th 2016 via Hootsuite
de Abreu: Shows multi-variable graph (7 var's at once) Tracking 'even things you didn't know' #AMP2016
9:32am November 9th 2016 via Hootsuite
de Abreu: Shows software interface, tracking over time. Lays out details: Run stats, variant stats, material used. #AMP2016
de Abreu: The software (info online https://t.co/7ahzI333CV ) allows to customize parameters; visualize perf data; export metrics #AMP2016
9:30am November 9th 2016 via Hootsuite
de Abreu: Want a unified QC tracker - across the 4 workflow steps. So automate the tracking; SeraCare iQ NGS software #AMP2016
9:28am November 9th 2016 via Hootsuite
de Abreu: A single lot #, for a number of previous runs, taking a lot of time. So TAT suffers, clinicians and pts are waiting. #AMP2016
de Abreu: When a problem occurs: call support, email files, look things up by lot #'s, tracked on a new spreadsheet, manual compare #AMP2016
9:27am November 9th 2016 via Hootsuite
de Abreu: Doing a correlation: lot numbers? Instrument issues? Operator problems? Can't see over time. #AMP2016
9:26am November 9th 2016 via Hootsuite
de Abreu: Shows Excel of 1y of data 'and it's not all there'. 50+ lines, 20+ columns: cannot be worked on at the same time #AMP2016
9:25am November 9th 2016 via Hootsuite
de Abreu: Reviews similar metrics for routine runs - run info, extraction, lib prep qPCR metrics, seq metrics, data analysis. #AMP2016
de Abreu: Shows 20+ line Excel sheet, x 25+ columns. Color-coded. Then for routine running - more spreadsheets. Every run... #AMP2016
9:24am November 9th 2016 via Hootsuite
de Abreu: Seq: clonality is important metric; Data: sample metrics, on-target, % amplicon drop-out, variant metrics, allele freq #AMP2016
9:23am November 9th 2016 via Hootsuite
de Abreu: Library: What's the LOD for input, for allelic freq? Library quant thresholds? Seq: Run metrics, inst-spec #AMP2016
9:22am November 9th 2016 via Hootsuite
de Abreu: Validation needs QC across the workflow. Extraction: # of slides, % tumor content, Nucl Acid quant/quality #AMP2016
9:21am November 9th 2016 via Hootsuite
de Abreu: 5 questions and no answers - shows typical 4-steps of NGS (extraction, library, seq, data analysis); all have variables #AMP2016
9:20am November 9th 2016 via Hootsuite
de Abreu: No guidelines for NGS clinical testing on QC metrics, and resources needed to track them. (!!) #AMP2016
9:19am November 9th 2016 via Hootsuite
de Abreu: Shows validation - sens, spec, robustness, reprod. (Note: see SeraCare blog post https://t.co/r6jESfe4Yo ) #AMP2016
de Abreu: Optimizing an entire test, and validation is the 'most impt part', shows figure ACMG 2013 ref https://t.co/tuUFHJ7oSA #AMP2016
9:18am November 9th 2016 via Hootsuite
de Abreu: For cancer they use TMO CHP v2, ArcherDX FusionPlex Solid Tumor, myeloid, others. #AMP2016
9:16am November 9th 2016 via Hootsuite
