Williams: Oncomine v2 and v3 done in 'real-time', could pull labs offline for validation, then migrate through. So… https://t.co/JGV5KmN6Bg
9:18am 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: In 2012 - sent an RFI, asked clinicians what was needed - core needle biopsy low input, accurate seq from… https://t.co/lndETe4Xrl
Williams: After Ion Torrent sequencing, BAM files to a matching algorithm called 'Matchbox'. Up-front - shipping ki… https://t.co/N6QLFraQqy
9:16am 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: Four centers, MDA (Stan Hamilton), MGH (John Iafrate), Yale (Jeff Sklar), NIH (Frederick) and recently Da… https://t.co/HrHys2t4qf
9:14am November 16th 2017 via Hootsuite
Williams: Also open to pts refractory to Rx. Shows decision tree; it's a 'signal finding trial'. May only be 31 pts… https://t.co/FJb5FPmOY7
9:13am 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
Williams: Will give an overview and focus on the assay. Precision medicine defined: tailring Rx for each individual… https://t.co/rJTm1APRDQ
9:10am November 16th 2017 via Hootsuite
Good morning #AMP2017 - Molecular Diagnostics for Biomarker-Driven Clinical Trials. First up: Mickey Williams (NCI)… https://t.co/ebRbbIyADc
9:09am 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 @biorxivpreprint: Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplifi… https://t.co/RRiYCfjy5I
9:55pm 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: Biggest challenges ahead: analyzing data. 'The biggest headache.' Storage and compute. Cloud important. 'I d… https://t.co/9ItpznNPIV
3:46pm 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: For tumor heterogeneity: "Should we take more than one sample, and run more than one library?" MET exon 14 s… https://t.co/bLxFUW4EJR
Rossi: Shows another sample with over 160 segmental copy changes up and down. Sometimes focal changes have selectio… https://t.co/nR1ZQnRfwV
3:39pm 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
Hampton: Talks about TruSight 170; 'on track to being an IVD with our Pharma partners'. All the way from extraction… https://t.co/xelYzTqnFK
3:14pm November 15th 2017 via Hootsuite
Illumina workshop: Perspectives on comprehensive clinical genomics: innovating for today and tomorrow. Garret Hampt… https://t.co/SUoqdOQf0W
3:13pm 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 with an on-site server for bioinformatics. Now showing input at 15ng, on-target of 72%, 86% mapped reads,… https://t.co/2r29YjzktM
2:31pm 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
Gunn: 40M reads/sample; showed 100% sens/spec for 1.5%, 0.5%, for both products. For 0.25%, 95-100% sens/spec. Also… https://t.co/nrRcls59mB
2:18pm November 15th 2017 via Hootsuite
Gunn: Product 1: targeted kit; Product 2: expanded kit. Both have 17 key genes in targeted kit; expanded an add'l 60 genes #AMP2017
2:14pm November 15th 2017 via Hootsuite
Gunn: Input is 4mL plasma; FRUO; CNV, SNV, indels and fusions; software and report with secondary analysis as an automated report #AMP2017
Gunn: In-house development, bioinformatics, purchase existing kit, all possible. With Roche: Early-access across 3… https://t.co/oPFhWWdJbh
2:13pm November 15th 2017 via Hootsuite
Gunn: ResearchDx is a CDX-development lab. A 'Contract Dx Organization' in Irvine CA: who was faced with the request in '16 #AMP2017
2:10pm November 15th 2017 via Hootsuite
Gunn: Hard to gauge demand, given phlebotomy oncology samples going straight to testing labs #AMP2017
2:09pm November 15th 2017 via Hootsuite
Gunn: LB promise less invasiveness, lower cost, longitundinal monitoring, better outcomes. Seeing sporadic adoption across the US. #AMP2017
2:08pm November 15th 2017 via Hootsuite
Gunn: FFPE was 'never intended for long-term storage of nucleic acids'. Tissue biopsy disadvantages: invasive, adve… https://t.co/kIH9s4KB9T
Gunn: From a pathologist's perspective: they are trying to adapt. Clear advantages: improved TAT, preservation of F… https://t.co/TztSuCKxPj
2:05pm November 15th 2017 via Hootsuite
Gunn:Introduction of this kit 'has enabled us to enter the liquid biopsy era'. Intorduction to the kit - multiple tumor types. #AMP2017
2:04pm November 15th 2017 via Hootsuite
Roche Workshop: Shelly Gunn (ResearchDx/PacificDx) A lab's perspective: evaluating the new AVENIO ctDNA analysis kits #AMP2017
2:02pm November 15th 2017 via Hootsuite
Longshore: Combine both tissue and plasma samples on the same plate. Commentary on NGS: cumbersome, seems overkill… https://t.co/zzUQGul6Jn
12:35pm November 15th 2017 via Hootsuite
Longshore: Points out how quick real-time cobas 480 results are compared to a 50-gene NGS one; also high sample fai… https://t.co/ol8cHxdFNX
12:25pm November 15th 2017 via Hootsuite
Longshore: but 50-gene NGS seems 'quite a waste' for KRAS, NRAS and BRAF. Utility of cobas z 480: many have them on… https://t.co/YXcQWu6g1r
12:23pm November 15th 2017 via Hootsuite
Longshore: KRAS 12, 13 and 61: 12%. Expanded RAS: 17% of add'l pts. 61, 117, 148. NRAS mutations, and BRAF another… https://t.co/EwBUKTLBnc
12:21pm November 15th 2017 via Hootsuite
Longshore: Many CDx collaborations. Shows a photo of a KRAS codon 12,13 and 61 giant stack of paperwork. "A robust amount of work." #AMP2017
John Longshore (Carolinas Pathology Group) start with their Healtcare system - very large for the Carolinas, base… https://t.co/HipNNI03eZ
12:19pm November 15th 2017 via Hootsuite
