Arcila: 70min hands-on time, scale-able to 96 samples; analysis is 'easy to read summary'. (NB: I've used it and this is true.) #AMP2015
12:34pm November 4th 2015 via Hootsuite
Arcila: 2 gene-specific primers incorporated. Lyophilized reagent eliminates master-mix, eliminate freeze/thaw cycles #AMP2015
12:33pm November 4th 2015 via Hootsuite
Arcila: Goes into the molecular barcoding: single-molecule counting, de-duplication, as well as error correction "important for us" #AMP2015
12:32pm November 4th 2015 via Hootsuite
Arcila: Developed two custom panels, one for solid tumor, another for heme tumors. Explains the biochemistry. #AMP2015
12:31pm November 4th 2015 via Hootsuite
Arcila: Workflow is 'tech friendly' - lyophilized reagents minimizes errors in pipetting. No bioinf. programming needed. #AMP2015
Arcila: Describes Archer's FusionPlex assay; 20ng input; single sequencing; compatible on both Ion PGM and MiSeq #AMP2015
12:30pm November 4th 2015 via Hootsuite
Dr Arcila of Memorial Sloan Kettering at @archerdxinc workshop #AMP2015 https://t.co/vy3sHj1N5N
12:29pm November 4th 2015 via Hootsuite
Arcila: Some genes are promiscuous; 302 known AML fusions - MLL for example. For the clinical lab, WGS, targeted capture; RNA-Seq #AMP2015
12:28pm November 4th 2015 via Hootsuite
Arcila: Gene fusion chart: skyrockets in 2011 from 200 to >8K in 2014. #AMP2015
12:26pm November 4th 2015 via Hootsuite
Arcila: Chr banding is laborious; FISH requires fluor. probes, generally 1-2 genes/assay. RT-PCR is for specific fusion product #AMP2015
12:25pm November 4th 2015 via Hootsuite
Arcila: Malignant drivers; shows timeline from Nat Rev Cancer from 1960 bcr-abl to 9,928 gene fusions today #AMP2015
12:24pm November 4th 2015 via Hootsuite
Arcila: Fusion genes can also occur via local deletions or inversions; can be highly complex, difficult to char & visualize #AMP2015
12:23pm November 4th 2015 via Hootsuite
Next: Maria Arcila (Memorial Sloan Kettering CC, NY) Addressing gene fusions in cancer and their emerging complexity #AMP2015 @archerdxinc
ArcherDx's Joshua Stahl (VP R&D) Shows correlation between CNV and mRNA over-expression of EGFR, MET, CCND1 #AMP2015
12:21pm November 4th 2015 via Hootsuite
Schreuer: Showed a case where 50 days earlier than progressive disease via scan, the signal showed up in V600E ctDNA #AMP2015
11:34am November 4th 2015 via Hootsuite
Schreuer: Shows progression slide - they were able to get 2 months of earlier progression based on ctDNA. #AMP2015
11:33am November 4th 2015 via Hootsuite
Schreuer: Showed KM plot - where it could be a prognostic marker after treatment. #AMP2015
11:31am November 4th 2015 via Hootsuite
Schreuer: Reiterates case for monitoring ctDNA. After BRAF/MEK inh treatment - 4d after treatment rapid drop of V600E in ctDNA #AMP2015
11:30am November 4th 2015 via Hootsuite
Schreuer: 36pts, 229 samples, stage IV melanoma. Baseline: 75% positive, aligns w/BEAMing data #AMP2015 '15 ref https://t.co/dP2ddRHIzu
11:29am November 4th 2015 via Hootsuite
Schreuer: V600E a useful marker. Immediate centrifuge, sep plasma; immed store at -80C, extract from 1mL plasma via Idylla method #AMP2015
11:27am November 4th 2015 via Hootsuite
Schreuer: But the therapy doesn't work long; followup with anti-PD1. Can help monitor during course of Rx #AMP2015
11:26am November 4th 2015 via Hootsuite
Schreuer: Reviews adv of liquid biopsy - (NB - here's my blog post https://t.co/nAn0ufHBbU) accessing BRAF V600 for targeted Rx #AMP2015
11:25am November 4th 2015 via Hootsuite
Max Schreuer (Univ Hosp Brussels) Quantitative measurement of BRAF V600 mutant cell-free DNA in pts w/BRAF mut. metastatic melanoma #AMP2015
11:24am November 4th 2015 via Hootsuite
RT @AMPath: Two of #AMP2015 Super Volunteers - check out those ribbon chains! https://t.co/V2Rw3cqzF7 https://t.co/OnNqg5WRRU
11:23am November 4th 2015 via Hootsuite
Jensen: 2h FFPE sample to data; no purification step needed. #AMP2015
11:22am November 4th 2015 via Hootsuite
Jensen: 'But Idylla errors were observed in 3/85' - but were genotyped correctly upon reanalysis (no explanation) #AMP2015
11:20am November 4th 2015 via Hootsuite
Jensen: Of 35 analyzed by NGS, 100% picked up by Idylla KRAS. 100% concordance of n=85. #AMP2015
Jensen: Cobas picked up 2 FPs - a problem, no anti-EGFR treatment offered. Got 100% overlap between Idylla and Therascreen, n=217 #AMP2015
11:18am November 4th 2015 via Hootsuite
.@RocheDiaUSA As I arrived late I didn't catch the presenters name - but it was a really well-done talk. Enjoyed it very much!
11:16am November 4th 2015 via Hootsuite in reply to RocheDiaUSA
Jensen: Did orthogonal verification with NGS, RGQ therascreen and Entrogen assays. 100% for wt and mutated samples #AMP2015
11:14am November 4th 2015 via Hootsuite
Jensen: Each sample was 10um FFPE tissue section. % tumor ranged from 10% to 100%; 35 wt, 50 mutated. Bar chart of mutation distr. #AMP2015
11:13am November 4th 2015 via Hootsuite
Jensen: 21 KRAS mutations in codon 12/13; also codons 59/61/117/146. Didn't see 59/117 due to low freq. 85 smpls #AMP2015
11:11am November 4th 2015 via Hootsuite
First: Steffen Grann Jensen (Herlev Hosp Copenhagen Denmark) Can Idylla testing be used as a tool for KRAS mutation analysis? #AMP2015
11:09am November 4th 2015 via Hootsuite
Idylla Existing: BRAF (melanoma), KRAS (colon), NRAS-BRAF-EGFR, ctBRAF. Also Ebola, influenza, RSV for 2015 #AMP2015
11:08am November 4th 2015 via Hootsuite
Idylla fully automated, closed system, and can be stacked up to 8 independently working. #AMP2015 https://t.co/corGaA8jHU
Idylla 'is the first sample-in, results-out instrument for oncology'. Shows instrument, console (display) and cartridge #AMP2015
11:05am November 4th 2015 via Hootsuite
BioCartis workshop #AMP2015 "A rapid, easy to use and fully automated system with broad applicability in oncology and infectious disease"
11:01am November 4th 2015 via Hootsuite
(Speaker was Dr. Longshore at Pathology Associates Services for the Roche workshop.) #AMP2015
10:50am November 4th 2015 via Hootsuite
RT @RocheDiaUSA: Dr. Longshore discussing Advances in Non-Small Lung Cancer Testing & Treatment. #AMP2015 https://t.co/ZjMKUPEYdo
10:48am November 4th 2015 via Hootsuite
Roche: Disclaim "Use of plasma samples in development'. Closes with a photo of a cigarette machine in NC at a lung cancer conf! #AMP2015
Roche: How to incorporate PCR, IHC, NGS as complementary techniques? NGS or qPCR from tissue; plasma via qPCR, NGS, then real-time #AMP2015
10:47am November 4th 2015 via Hootsuite
Roche: At least six IHC markers could be used; ability of PD-L1 for biomarker appears to differ dramatically between tumor types #AMP2015
10:45am November 4th 2015 via Hootsuite
Roche: Nivolumab is a 'complementary diagnostic'; both for melanoma have no biomarker marking. Need biopsy progression #AMP2015
10:44am November 4th 2015 via Hootsuite
Roche: PD-L1recently approved (Sept / Oct 2015). Pembrolizumab (anti-PD-L1) has a companion diagnostic (IHC) #AMP2015
Roche: 18 biomarkers from smallest sample. 2011 Pao review: https://t.co/DEaaP07xgE broad distribution of actionable mut #AMP2015
10:42am November 4th 2015 via Hootsuite
Roche: Pt-centered care; improved biomarker testing and Rx selection; #AMP2015 Molecular pathology '13 Nat Rev ref https://t.co/6WeaYqQHcE
10:40am November 4th 2015 via Hootsuite
Roche: 'Multidisciplinary tumor boards should be everyone's priority if you don't already have one' #AMP2015
10:38am November 4th 2015 via Hootsuite
Roche: Tissue awareness, tissue stewardship is a new concept for pathology. 'Plan ahead for biomarker testing' #AMP2015
Roche: Electromagnetic navigational bronchoscopy to help guide precise sampling; example of 6mm size tumor, T790M positive #AMP2015
10:37am November 4th 2015 via Hootsuite
Roche: And for companion Dx - a few hundred dollar test is favored to guide therapy, to insure effectiveness #AMP2015
10:35am November 4th 2015 via Hootsuite
