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
de Abreu: CGAT Lab at Dartmouth - offers both clinical and research groups. 'Clinical Genomics and Adv Tech', under Greg Tsongalis #AMP2016
9:15am November 9th 2016 via Hootsuite
de Abreu: Will be showing 3 applications - prenatal, genetic disease, and oncology. Oncology - for their lab, largest area #AMP2016
9:13am November 9th 2016 via Hootsuite
Francine de Abreu (Dartmouth-Hitchcock CT) NGS-based assay validaiton and QC: a complete solution for the clinical sequencing lab #AMP2016
9:12am November 9th 2016 via Hootsuite
Garlick: Also cell lines have limited number and type of variants. Single background GM24385 also viewed as important by Palmetto #AMP2016
9:11am November 9th 2016 via Hootsuite
Garlick: Mentions Palmetto GBA MolDx guidelines; has shown concern about mixing cell lines as they are 'inherently difficult' #AMP2016
9:10am November 9th 2016 via Hootsuite
Garlick: Common GM24385 background is used with SeraCare's materials. VariantFlex is custom solution for IVD manufacturers #AMP2016
Garlick: Other highlights - NY State DOH recommending 3 well char reference samples; confirmation can be ceased after 20 variants #AMP2016
9:09am November 9th 2016 via Hootsuite
Full house at #amp2016 @seracare workshop in 217D https://t.co/T7m6tNy7JI
Garlick: Joint response con't: use in-kit or external control metrics alongside run seq metrics. #AMP2016
9:07am November 9th 2016 via Hootsuite
Garlick: Also rec'd 'do not accept TGP data as not appropriate surrogates for pathogenic variants'; use well-char ref materials #AMP2016
9:06am November 9th 2016 via Hootsuite
Garlick: FDA guidance - @SeraCare has given a joint response with @thermofisher with +/- controls for each batch... #AMP2016
Garlick: Outline - QC highlights since AMP '15; Francine de Abreu (Dartmouth-Hitchcock) NGS-based assay validation and QC; posters #AMP2016
9:04am November 9th 2016 via Hootsuite
Russell Garlick (CSO SeraCare Life Sciences): NGS-based Assay Validation and QC - a complete solution #AMP2016
9:03am November 9th 2016 via Hootsuite
Headed over now to @SeraCare workshop in 217 at #AMP2016 https://t.co/9NlxhoRgwH
8:46am November 9th 2016 via Hootsuite
Q: Ct values between autom and manual? Fleischhacker: Volumes slightly different (3mL vs 2.4mL) so values differed; yield similar #AMP2016
8:45am November 9th 2016 via Hootsuite
