November 2017

Harris: Starts with ACS Siegel 2017 chart of '17 new cancer cases. Ref: https://t.co/BIF3wAVxEw Points out rarity of pediatric ca #AMP2017

9:36am November 16th 2017 via Hootsuite

Marian Harris (Boston Childrens Hosp) Molecular Diagnostics in Multi-Institutional Trials: A Pathologist's Perspective #AMP2017

9:35am November 16th 2017 via Hootsuite

Williams: Acknowledges pts, physicians, NCI clinical trials network, a core group of about 150 and 18 working groups. #AMP2017

9:33am November 16th 2017 via Hootsuite

Williams: Not a screen specifically for MATCH, but if they have one of the rare var's, will then enroll. #AMP2017

9:30am November 16th 2017 via Hootsuite

Williams: 6K pts enrolled in less than 2y; but a few arms are still open. FMI, MSKCC, Caris are up and running, screening routinely #AMP2017

9:30am November 16th 2017 via Hootsuite

Williams: Problem cases no pathology report, or no tumor in sample. One arm - no variant found yet to put on a protocol #AMP2017

9:28am November 16th 2017 via Hootsuite

Williams: 60% of samples were considered rare tumor types. Goal of TAT was 14d; currently 16d. 20% of cases 'were problem ones'. #AMP2017

9:27am November 16th 2017 via Hootsuite

Williams: Details of this validation published JMD Mar '17 https://t.co/DkM2Rr6rK4 #AMP2017

9:26am November 16th 2017 via Hootsuite

Williams: Looked at cross user, instrument, lab, and day: 'well above 95%'. Able to get 5560 of 5962 samples. 93% vs 80% common. #AMP2017

9:25am November 16th 2017 via Hootsuite

Williams:Showed one lab (MGH) with CNV at only 80% sens. Turned out sample was 3.7 copies, when threshold was 5 #AMP2017

9:23am November 16th 2017 via Hootsuite

Williams: For perf testing: as many different types as they could. 186 samples, 15 tissue types for sensitivity study #AMP2017

9:21am November 16th 2017 via Hootsuite

Williams: Feasibility 'turned out phenomenal'; assay performed 'extremely well in this blinded test'. Harmonized, locked SOPs #AMP2017

9:20am November 16th 2017 via Hootsuite

Williams: Run under FDA's 'Abbreviated IDE' - non-significant risk, updated clinical trial binders/docs, version SOP, site audits #AMP2017

9:19am November 16th 2017 via Hootsuite

Williams: Used Oncomine v1, 143 genes, 4066 annotated var's, RFP selected the four initial labs. #AMP2017

9:17am November 16th 2017 via Hootsuite

Williams: Biopsy sent to MDACC, archived and PTEN IHC and NA extracted. Sent to 4 lab network (20ng FFPE DNA/10ng FFPE RNA). #AMP2017

9:15am November 16th 2017 via Hootsuite

Williams: Example BRAF V600E melanoma response to BRAFi or BRAFi + MEKi. Open to solid tumors, lymphomas, melanoma, rare tumors #AMP2017

9:11am November 16th 2017 via Hootsuite

RT @ForbesTech: A plan to reduce antibiotic (ab)use by the global meat industry: https://t.co/n0PVDsIYWv https://t.co/M36uOW63JA

10:55pm November 15th 2017 via Hootsuite

RT @drob: New blog post: "Advice to aspiring data scientists: start a blog" https://t.co/Qe50E1dpE0 #rstats https://t.co/9KUBEiT392

8:45pm November 15th 2017 via Hootsuite

Rossi: But the MET exon skipping fusion was picked up via RNA. 'A critical component' #AMP2017

3:43pm November 15th 2017 via Hootsuite

Rossi: Integrating copy number and fusion data in one report important. MDM2 amplification, and MET exon skipping #AMP2017

3:38pm November 15th 2017 via Hootsuite

Rossi: 421 overlapping var's between TST26 and TST170. Shows high concordance for lung adenocarcinoma for copy number changes #AMP2017

3:37pm November 15th 2017 via Hootsuite

Rossi: Points to FASTQ file exchange program as a way to test for quality of informatic analyses '15 JMD https://t.co/HoL7TFXocq #AMP2017

3:32pm November 15th 2017 via Hootsuite

Rossi: Shows busy table: genes and chromosomes, and comparison to Oncoscan microarray. '16 JMD https://t.co/JeZMlJIOTT #AMP2017

3:30pm November 15th 2017 via Hootsuite

Hampton: 1 day of separate workflow, combined for sequencing; SNVs, indels, fusions, copy number. #AMP2017

3:23pm November 15th 2017 via Hootsuite

Hampton: Then look at commercial targets; shows list from TST170 of three 'that don't work all that well' ESCC, pRCC, Liver. #AMP2017

3:22pm November 15th 2017 via Hootsuite

Rossi: Stresses value of analyzing both DNA and RNA; presenting poster ST84. Oncologists when asked 'what do you want' is too much #AMP2017

3:21pm November 15th 2017 via Hootsuite

Michael Rossi (Sema4): Transition from TST26 to TST170 in an academic laboratory. Work today was done at Emory before his move. #AMP2017

3:18pm November 15th 2017 via Hootsuite

Hampton: NextSeq 550Dx 'highest capacity FDA-regulated system'. Earlier this year extended RAS, around MiSeq Dx. #AMP2017

3:16pm November 15th 2017 via Hootsuite

Hampton: TruSight Oncology - their hyb capture as a platfrom. 3rd-party analysis partners. #AMP2017

3:15pm November 15th 2017 via Hootsuite

Gunn: Conclude - meet their needs, able to detect fusions at 100% sens/spec. (Research Dx actually will exhibit at #AMP2017 this year.)

2:34pm November 15th 2017 via Hootsuite

Gunn: Showed exmaple of filtered var report with annotation. COSMIC, TCGA. #AMP2017

2:33pm November 15th 2017 via Hootsuite

Gunn: Now doing post-test evaluation on their own. Wanted to detect their LoD, used total of 60 samples, normal, contrived samples. #AMP2017

2:24pm November 15th 2017 via Hootsuite