Velculescu: Somatic rearr associated with MET amplification detected in PGDx assays. #NGDx15
3:00pm August 18th 2015 via Hootsuite
Velculescu:Detection of genetic resistance or sensitivity after targeted therapy. 2013 ref: http://t.co/B8Z7l8wgML #NGDx15
2:58pm August 18th 2015 via Hootsuite
Velculescu: Can detect six months earlier for pancreatic cancer Sausen 2015 Nature Comm http://t.co/6LDiBeItbL #NGDx15
2:57pm August 18th 2015 via Hootsuite
Velculescu: Fig. from Diehl et al Nature Med 2008 http://t.co/eLKwBRKSji No plasma detection - disease-free. In plasma - poor prog #NGDx15
2:55pm August 18th 2015 via Hootsuite
Velculescu: Dev a panel of 60 genes, and about 12 rearr's. About 10% detection in blood. NSCLC can be ID'd in sputum too. #NGDx15
2:54pm August 18th 2015 via Hootsuite
Velculescu: (Data in same Leary 2012 paper.) ERBB2 ampl. observed in a Colorectal cancer pt. Observed rearr in tumor and plasma #NGDx15
2:53pm August 18th 2015 via Hootsuite
Velculescu: Actionable mutations via cell-free DNA (where 1/4 of lung ca fall - not enough tissue). ERBB2 amplification via plasma #NGDx15
2:52pm August 18th 2015 via Hootsuite
Velculescu: Monitoring tumor progression over time - can be done with CNV, point mutations, or rearr's #NGDx15
2:51pm August 18th 2015 via Hootsuite
Velculescu: Found large-scale rearrangements via PARE.Detectable across tumor types, and variety of structural alterations #NGDx15
2:49pm August 18th 2015 via Hootsuite
Velculescu: Looked at 10 pts directly in blood, Science Trans Med 2012 looking at chromosome arms http://t.co/X0bS72w951 #NGDx15
2:46pm August 18th 2015 via Hootsuite
Velculescu: The challenge is finding the rare mutation in blood, including digital karyotyping and PARE; tumor-spec alterations #NGDx15
2:45pm August 18th 2015 via Hootsuite
Velculescu: 2004 Samuels et al Science on PIK3CA http://t.co/ayw44wgneY In addition to therapeutic target - diagnosis via blood #NGDx15
2:44pm August 18th 2015 via Hootsuite
Velculescu: First Sanger-based exomes in colorectal and breast, then GBM and Medullo, then NGS-based. One gene: PIK3CA #NGDx15
2:43pm August 18th 2015 via Hootsuite
Victor Velculescu (Johns Hopkins MD) "Liquid biopsies for cancer detection and characterization" #NGDx15
2:41pm August 18th 2015 via Hootsuite
Ladanyi:A2:Only can take MSK patients, no outside. (No clear answer here; would say a minority of ca pts have NGS tests avail) #NGDx15
2:39pm August 18th 2015 via Hootsuite
Ladanyi:Q:How many pts get profiled vs. not? A:# of centers with large panels like theirs (410 genes) is only ~10. #NGDx15
2:37pm August 18th 2015 via Hootsuite
Ladanyi:Q:Data after generation? A:Sometimes will bounce to tumor board for problematic cases. #NGDx15
2:36pm August 18th 2015 via Hootsuite
Ladanyi:Q:Is it 85% actionable? A:No, 85% get a result. Later will they determine therapeutic effectiveness. #NGDx15
2:35pm August 18th 2015 via Hootsuite
Ladanyi:Q:Is database setup for sharing w/other centers? A:Effort is underway. #NGDx15
2:34pm August 18th 2015 via Hootsuite
Ladanyi:Shows Time magazine cover story - V600, went on the basket trial. Another with standard therapy didn't fare so well. #NGDx15
2:32pm August 18th 2015 via Hootsuite
Ladanyi:/Vemurafenib basked-study concept in BRAF V600-mutated tumors - waterfall shows some 'tremendous responses' #NGDx15
2:31pm August 18th 2015 via Hootsuite
Ladanyi: Basket trial concepts - only just now becoming possible. Multi-histology, biomarker-selected #NGDx15
2:29pm August 18th 2015 via Hootsuite
Ladanyi: Showed @nanostring data for MET exon 14 skipping. These pts are responsive to MET inhibition. (4/4; 3-4% of LuCa) #NGDx15
2:27pm August 18th 2015 via Hootsuite
Ladanyi: Shows Met exon 14 skipping mutations in LuCa - RNA-Seq, TCGA data. IMPACT regularly picks this up. #NGDx15
2:26pm August 18th 2015 via Hootsuite
Ladanyi: Their data flows into cBioportal database http://t.co/kQjK5II0ZB #NGDx15
2:23pm August 18th 2015 via Hootsuite
Ladanyi:Specific inclusion of introns to test fusoins - shows CD74/ROS1, ALK/EML4 fusions from DNA.600-650x coverage #NGDx15
2:22pm August 18th 2015 via Hootsuite
Ladanyi: Shows CNV with ERBB2, FGFR2 data. Chart of most common amplifications, deletions. Amplifications may be underappreciated. #NGDx15
2:20pm August 18th 2015 via Hootsuite
Ladanyi:For insufficient DNA, may use RainDance or AmpliSeq as complementary. Pie chart of many different tumor types shown #NGDx15
2:18pm August 18th 2015 via Hootsuite
Ladanyi:Their sensitivity goes down to 2% for hotspot mutations. NY State compliant. 85% success rate. 7.3% insufficient DNA. #NGDx15
2:17pm August 18th 2015 via Hootsuite
Ladanyi: 19 chosen for clinical validation; +'ve controls available from their prior work. 410 genes now. Sensitivity 5% non-hotspot #NGDx15
2:16pm August 18th 2015 via Hootsuite
Ladanyi: Their input is 100ng. Content selected by committee; 341 genes, 5,166 exons. Introns of 14 rearranged genes. #NGDx15
2:15pm August 18th 2015 via Hootsuite
Ladanyi: MSK-IMPACT: patients with advanced solid cancers, to get them into targeted therapy clinical trials. #NGDx15
2:14pm August 18th 2015 via Hootsuite
Ladanyi: MSKCC 'Impact' - launched Details published May 2015 http://t.co/lMquTVCCBq #NGDx15
2:13pm August 18th 2015 via Hootsuite
Ladanyi:Hybrid requires typically more material, better for CNV and rearrangements, also on higher TP NGS instruments #NGDx15
2:12pm August 18th 2015 via Hootsuite
Ladanyi: Capture of most actionable genes - PCR or hybrid; detection of CNV. Amplicon - smaller targets, not so good for CNV, rearr #NGDx15
2:11pm August 18th 2015 via Hootsuite
Ladanyi: Pts may only have 10-20 unstained sections. NGS is efficient and cost-effective; sens typically higher #NGDx15
2:10pm August 18th 2015 via Hootsuite
Ladanyi: 'We need clinical NGS to navigate the cancer storm'. Advanced disease pts - small biopsies, easily exhausted #NGDx15
2:09pm August 18th 2015 via Hootsuite
Ladanyi: EGFR and ALK testing part of NCCN testing. Why? Of 100K LuCa: 29K KRAS, 20K EGFR, BRAF 1500, ALK 4000, ROS1: 1000 etc #NGDx15
2:08pm August 18th 2015 via Hootsuite
Ladanyi: Points to this Pao et al 2010 review http://t.co/WSfLD37ob0 And reviews critizotinib response by ALK+ lung adenocarcinoma #NGDx15
2:07pm August 18th 2015 via Hootsuite
Ladanyi: Using Lung cancer as the illustration - reviews #TCGA 2014 July Nature paper http://t.co/DrWw6POryN and EGFR TKI #NGDx15
2:06pm August 18th 2015 via Hootsuite
Marc Ladanyi (Memorial Sloan Kettering NY) "Testing for cancer heterogeneity" #NGDx15
2:04pm August 18th 2015 via Hootsuite
Gutekunst:Rel1 can run 8 samples on MiSeqDx, 27h runtime. >500x coverage. #NGDx15
12:56pm August 18th 2015 via Hootsuite
Gutekunst:Report will deliver 'filtered actionable calls' - reported by category. Rel1:44kb target, 250 amplicons, 7h assay prep #NGDx15
Gutekunst: 5% VAF, 20ng input for Rel1 and DNA-only; 5% VAF 40ng input for Rel2 (both DNA and RNA) #NGDx15
12:54pm August 18th 2015 via Hootsuite
Gutekunst:Library QC, on the MiSeqDx, full reporting. Release 2 panel: for the NextSeqDx. >150 genes. 'FISH consolidation' #NGDx15
12:53pm August 18th 2015 via Hootsuite
Gutekunst: Dev a 'Oncogene Panel Release 1'. Guidelines for sample prep and QC metrics; library prep for 15 genes. FFPE-optimized #NGDx15
12:52pm August 18th 2015 via Hootsuite
Gutekunst: Standards, quality metrics: sample processing, content, sequencing, data analysis and reporting. 'Published, made avail.' #NGDx15
12:50pm August 18th 2015 via Hootsuite
Gutekunst: Oncology stakeholders - leading cancer centers, research centers, pharma, biotech, CROs - Actionable Genome Consortium #NGDx15
12:47pm August 18th 2015 via Hootsuite
Gutekunst: Lists 12 CDx. Illustrates multi-target test, a 'universal oncology test system' GEN piece http://t.co/sjOhCDYDSU #NGDx15
12:46pm August 18th 2015 via Hootsuite
Gutekunst: Mention NextSeq500 going through FDA. Have 2 business units for clinical applications, one is cancer. One drug, one test #NGDx15
12:45pm August 18th 2015 via Hootsuite
