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
Gutekunst: Puts up figure from Garraway JCO 2013 and the wide heterogeneity. Lists out 9 flavors of @illumina instruments #NGDx15
12:42pm August 18th 2015 via Hootsuite
Gutekunst: Predisposition to cancer - can it be screened for earlier? Prognosis? Treatment response? Monitorinig? #NGDx15
12:40pm August 18th 2015 via Hootsuite
Chair of Companion Dx session points out this resource: http://t.co/bSDhUotrZC #NGDx15
12:39pm August 18th 2015 via Hootsuite
Karen Gutekunst (Illumina CA) "Universal testing for actionable genomic variants in cancer: a paradigm shift in precision oncology" #NGDx15
12:38pm August 18th 2015 via Hootsuite
Powers: Reviews changes to clinical recommendations based upon number of patients with clinical actionable above family history #NGDx15
12:22pm August 18th 2015 via Hootsuite
Powers: ~9% BRCA1/2 pos, about 4% carry non-BRCA pathogentic var's. A 40% increase in yield #NGDx15
12:19pm August 18th 2015 via Hootsuite
Powers: Showed 100% sens and 100% spec against >50 samples with known del/dups #NGDx15
12:18pm August 18th 2015 via Hootsuite
Powers: Listed genes with '100% no-call rate': DNAF2, INPP5E, MBL2, NF1, NRAS, PMS2 Need other methods Validated against 869 smpls #NGDx15
12:17pm August 18th 2015 via Hootsuite
Powers: Test algorithm for PMP22 dupe, CFTR Del exons 2-3. Larger CNV events but examine target-by-target. #NGDx15
12:15pm August 18th 2015 via Hootsuite
Powers:Going into validation - use a 29-gene hereditary panel (now up to 64 genes) Very hard to find samples NIBSC for Lynch #NGDx15
12:14pm August 18th 2015 via Hootsuite
Powers: 3-exon deletion in BRCA illustrated against normal samples. Split-read detection (method 2) - detecting breakpoints #NGDx15
12:13pm August 18th 2015 via Hootsuite
