Roy: Data visualization tools is a growing need; also historical and kb lookup. #AMP2015
5:54pm November 5th 2015 via Hootsuite
Roy: DNA vars, RNA fusions, CNV manually assembled - so had to develop split variant annotation, integrate after, kb after that #AMP2015
5:52pm November 5th 2015 via Hootsuite
Roy: Their reporting solution SeqReporter - '14 J Mol Dx https://t.co/NWDmKWTbsU #AMP2015
5:48pm November 5th 2015 via Hootsuite
Roy: Report design: how does it look in LIMS? EMR? Page width? Font? Special chars? Minor things can cause problems - IDH1 mislabel #AMP2015
5:45pm November 5th 2015 via Hootsuite
Roy: Started in '12 with one @iontorrent PGM, now onto 6 incl; now CNA, fusions, 700-1k cases/mo; 5TB/mo. From 1-5 cases/mo in '12 #AMP2015
5:42pm November 5th 2015 via Hootsuite
Roy: There is no standardized reporting for oncology test reports. One ref '14 https://t.co/vagYhynVO4 #AMP2015
5:39pm November 5th 2015 via Hootsuite
Roy: There is complexity around interpretation, and varying levels of annotation. #AMP2015
5:30pm November 5th 2015 via Hootsuite
Roy: A report is iterative - plays a role in data interpretation (DNA QC, var calls, annotation...) Data on var + metadata #AMP2015
5:29pm November 5th 2015 via Hootsuite
Roy: Context of Sanger: challenge of clinical NGS reporting 'proportional to the increasing complexity of molecular testing' #AMP2015
5:24pm November 5th 2015 via Hootsuite
Somak Roy (U Pittsburgh) "Implementation of Clinical Reporting System for NGS-based Assays for Oncology: An Evolving Landscape" #AMP2015
5:22pm November 5th 2015 via Hootsuite
Berger: Listed out kinase fusion - finding RET/ROS across other tumor types (NTRK1/3) open for clinical trials #AMP2015
11:40am November 5th 2015 via Hootsuite
Berger: List of mutation frequencies - after TP53, TERT is #2. CNAs top is CCND1 #AMP2015
11:39am November 5th 2015 via Hootsuite
Berger: Distribution of mutations, ave 7 somatic mut's. Some have zero (only CNA), others without any observable mutations #AMP2015
11:38am November 5th 2015 via Hootsuite
Berger: 250ng is their std input, so by tissue type success rates vary. 6.8K successful, dense pie chart (NSCLC, Br, CRC majority) #AMP2015
11:37am November 5th 2015 via Hootsuite
Berger Stats, allele counts, accept/reject calls. For 8K smpls: 84% results. 8% not enough H&E tumor; 3.2% not enough DNA #AMP2015
11:36am November 5th 2015 via Hootsuite
Berger: Able to store sequencing results, use web services for downstream info analysis. CVR = Clinical Var Results system #AMP2015
11:35am November 5th 2015 via Hootsuite
Berger: Now at 500/mo; expect to double. Need automated processes, from accession to sign-out. LIMS from Sapio (custom) #AMP2015
11:33am November 5th 2015 via Hootsuite
Berger: Non-billable tumors - CMO and philantropy; consent to IRB. Blood for ctDNA, biopsies. Bar chart of samples since 2014 #AMP2015
Berger: NY State DOH validation approval. Adv Dx and prognostic data, eligable for clin trials #AMP2015
11:31am November 5th 2015 via Hootsuite
Berger: Both a research and clinical tool. #AMP2015 cBioPortal online tool https://t.co/o3bcnGOR7R Mark Ladanyi mentioned.
11:30am November 5th 2015 via Hootsuite
Berger: 1000x coverage, very good >98% at 50X of target. Shows IGV of somatic mutation, also CNA of amplification of ERBB2, FGFR2 #AMP201
11:28am November 5th 2015 via Hootsuite
Berger: Also cancer suscept. genes, rearranged genes (to gain breakpoint info), and TERT promoter. Optimization of probes #AMP2015
11:27am November 5th 2015 via Hootsuite
Berger: 410 genes, goes beyond what the core actionable genes, uses HiSeq rapid run. Target is 1.3MB #AMP2015
11:26am November 5th 2015 via Hootsuite
Berger: Describes MSK-IMPACT, recently published here https://t.co/pLCrchjVX9 #AMP2015
11:25am November 5th 2015 via Hootsuite
Berger: And FFPE DNA quality a problem; heterogeneity; aneuploidy... NGS can help. Sample prep (enrichment methods), systems... #AMP2015
11:23am November 5th 2015 via Hootsuite
Berger: Increasing #'s of CNAs, fusions. Little tissue, many tests - lung adenocarcinomas and parallel analyses via Sequenom, FISH #AMP2015
11:21am November 5th 2015 via Hootsuite
Berger: BRAF in 1-2% in lung ca, can use drugs approved for melanoma. Requires molecular Dx application. Shows CNV, dels, fusions #AMP2015
11:20am November 5th 2015 via Hootsuite
Michael Berger (MSKCC) "Enterprise-wide Clinical Sequencing to Match Patients to Personalized Cancer Treatments" #AMP2015
11:19am November 5th 2015 via Hootsuite
.@nj_tee Seeing and hearing the patient stories from him brought his message home, for sure.
10:44am November 5th 2015 via Hootsuite in reply to nj_tee
Druker: Firmly believes that double or triple combination drug therapies is the future, and drug co's need to cooperate #AMP2015
10:24am November 5th 2015 via Hootsuite
Druker: Concludes with photos of many cancer survivors and their stories, patients from all over the world 'still alive and well' #AMP2015
10:19am November 5th 2015 via Hootsuite
Druker: A local storage model, did from Portland, Austin TX and Boston MA. 'Scalable, federated system' computing locally #AMP2015
10:17am November 5th 2015 via Hootsuite
Druker: WGS, WES, RNA-Seq, metabolomics, proteomics: now it is how we make sense of all this data. Working with Intel on it #AMP2015
10:15am November 5th 2015 via Hootsuite
Druker: Oncogene pie chart of NSCLC - KRAS, EGFR, ALK, BRAF, PIK3CA... Shows dramatic example of BRAF V600E with BRAF and MEKi #AMP2015
10:14am November 5th 2015 via Hootsuite
Druker: We are still treating empirically; but moving toward molecular abnormalities, basing treatment on this information. #AMP2015
10:13am November 5th 2015 via Hootsuite
Druker: To other malignancies - need to do better molecular detection, to treat early, and match patient to the drug. #AMP2015
10:12am November 5th 2015 via Hootsuite
Druker: Imatinib has not worked in most common tumors - the target is expressed, but not critically dependent on mechanism #AMP2015
10:10am November 5th 2015 via Hootsuite
Druker: GIST KIT+ - >80% response. But flipped - it was the mutated target. 'We have to sequence to understand responders' #AMP2015
Druker: GIST was a surprise to Novartis, for a new clinical trial. They need a $500M/y threshold #AMP2015 '02 ref https://t.co/8rLc1jSDDN
10:08am November 5th 2015 via Hootsuite
Druker: Imatinib also works with melanoma KIT mutations, others with PGDF. GIST KIT+: 5K/y, <5% resp to chemo #AMP2015
10:07am November 5th 2015 via Hootsuite
Druker: Ponatinib for this last mutation, also approved. Relapses are mostly due to kinase domain mutations; CML a managable cond. #AMP2015
10:05am November 5th 2015 via Hootsuite
Druker:Nilotinib, dasatinib, both approved; based upon mutational profile. T315I is the one remaining imatinib resistance mut #AMP2015
10:04am November 5th 2015 via Hootsuite
Druker: Shows 3D protein representation and small molecule drug as it fits into the flipped 'off' conformation, and new TKI's #AMP2015
10:03am November 5th 2015 via Hootsuite
Druker: Judy patient number 7 - many getting the 'same remarkable results'. She is the longest, 17y on the medication (still) #AMP2015
9:57am November 5th 2015 via Hootsuite
Druker: 60% of pts, durable response. News clip from NBC. Instead of a 'last family vacation', 3-5y, then STI571 'sensational' #AMP2015
9:55am November 5th 2015 via Hootsuite
Druker: Imatinib, $4B in sales last year. STI571 (CGP 57148B) (imatinib) aka Gleevec #AMP2015 '96 ref https://t.co/UdED0yPq9T
9:53am November 5th 2015 via Hootsuite
Druker: Also believed toxicity would be lethal (KO models). And: only 5K patients/y, no money to be made #AMP2015
9:51am November 5th 2015 via Hootsuite
Druker: Common thought: the 500 kinases in the kinome not a target due to lack of specificity. Also: ATP conc is too high #AMP2015
Druker: In '85, bcr-abl and its tyrosine kinase activity 'required for fn'. Binds ATP, where the inhibitor can block that binding #AMP2015
9:50am November 5th 2015 via Hootsuite
Drukers: His vest covered w/burrs; he asked 'why', and looked at it under a microscope. He asked the 'critical question' #AMP2015
9:47am November 5th 2015 via Hootsuite
