Wood-Bouwens: Shows 182 d Rx course; and wt ccfDNA molecules/mL from 6K downt to 2K and day 154 spike. ctDNA/mL from 0 to 50. #AMP2017
9:28am November 18th 2017 via Hootsuite
Wood-Bouwens: Gemcitabine and cisplatin, monitoring TP53 E285K, and RPP30 (general ccfDNA quant to det tumor burden) #AMP2017
9:27am November 18th 2017 via Hootsuite
Wood-Bouwens: Better sens is from more DNA input. Now they have their first longitudinal pt - Pt has bile-duct ca TP53 p.E285K #AMP2017
9:26am November 18th 2017 via Hootsuite
Wood-Bouwens: Shows 1ng, 300 haploid equiv, only 3 KRAS G12D mutant molecules called. Shows expected and meas at 0.1% 10ng input #AMP2017
9:25am November 18th 2017 via Hootsuite
Wood-Bouwens: Basically a training set with a confidence interval. '17 ref called 'data gridding' https://t.co/c4yF1iP2QH #AMP2017
9:24am November 18th 2017 via Hootsuite
Wood-Bouwens: High density droplets - clustering is clear. Low conc, hard to cluster. Uses a mixed ca cell line, with 50% mutants. #AMP2017
9:23am November 18th 2017 via Hootsuite
Wood-Bouwens: The longer amplicon can then be differentiated between empty, wild type, and mutant products. #AMP2017
9:22am November 18th 2017 via Hootsuite
Wood-Bouwens: Looking for dual allele - with reverse primers. Each droplet has all 3 primers; mutant allele primer has AAAT repeats #AMP2017
9:21am November 18th 2017 via Hootsuite
Wood-Bouwens: Single-color: forward primer is matches; genotyping reverse is perfect match or mutant. +/- amplicons #AMP2017
Wood-Bouwens: ctDNA's low abundance, fragmented, different between time points and pts. Need high sens and short TAT #AMP2017
9:19am November 18th 2017 via Hootsuite
Wood-Bouwens: Imaging is used but promise of liquid biospies to longitudinally monitor genetic features over time #AMP2017
9:18am November 18th 2017 via Hootsuite
Wood-Bouwens: Overall goal to 'reach every pt at every visit'. Illustrates time from original tissue biopsy to relapse, metastasis #AMP2017
9:17am November 18th 2017 via Hootsuite
Christina Wood-Bouwens (Stanford CA) TT82 High performance detection of cancer mutations from circ DNA using single-color dPCR #AMP2017
9:15am November 18th 2017 via Hootsuite
Restrepo: Cp to FISH and karyotype, 24/24 TP; 2/24 were neg on FISH and kayrotype, pos on NGS. 16/16 both neg #AMP2017
9:10am November 18th 2017 via Hootsuite
Restrepo: Yield correlated with age; used 50-200ng; used ArcherDx FusionPlex HemeV2. 42/43 Ct<30 (threshold for quality) #AMP2017
9:09am November 18th 2017 via Hootsuite
Restrepo: Also Promega Blood DNA kit, w/o RNAse step for total NA. Succeeded in every case - 0.1 to 11.3ug; av 4.9ug #AMP2017
9:07am November 18th 2017 via Hootsuite
Restrepo: 43 cases w/smears: from 1mo to 2y of RT storage. Hydrated w/lysis buffer, scrapted, heated 56C; Maxwell RSC #AMP2017
9:05am November 18th 2017 via Hootsuite
Restrepo: Imptc of fusion RNA; they use it for heme malignancies; retrospective and prospective tissue is scarce. #AMP2017
9:04am November 18th 2017 via Hootsuite
Tamara Restrepo (Boston Childrens MA) TT92 Extraction of RNA from archived bone marrow aspirate smears for targeted RNA seq #AMP2017
9:02am November 18th 2017 via Hootsuite
RT @gizbab: @gtsonga Greg Tsongalis receives the Jeffrey A Kant Leadership Award #AMP2017 #AMPlifier @AMPath https://t.co/IV0TVTWcLt
5:57am November 18th 2017 via Hootsuite
Hi #AMP2017 - take a look at Dr. Greg Tsongalis’ Poster ST131 “Evaluation of the Pillar NGS SLIMamp Cancer Hotspot Panel” at the break.
3:45pm November 17th 2017 via Hootsuite
Iafrate: Pathogenesis of Fusion+ tumors: bad luck, env exposure to radiation (other sources of DSBs) #AMP2017
3:44pm November 17th 2017 via Hootsuite
Iafrate: Eng cell lines or spiked artificial templates 'are a good start'. #AMP2017
3:43pm November 17th 2017 via Hootsuite
Iafrate: Normal tissues have 2 copies of DNA, and wide variation in RNA. Dilute into 'normal RNA' can be problem #AMP2017
Iafrate: Orthogonal approaches can be time consuming; need for new FISH probes for ex. LOD is also challenge #AMP2017
3:42pm November 17th 2017 via Hootsuite
Iafrate: Validation challenges: fusions are rare, RNA not routinely extracted (archives don't exist) #AMP2017
Iafrate: 39yo F left foot melanoma, MLPH-ALK, no other muts, expressed in melanocytes, coil-coil domain #AMP2017
3:41pm November 17th 2017 via Hootsuite
Iafrate: 73yo m Lung ACA, LPCAT1-TERT, surfactant metab promoter driving TERT, 'promoter hijacking' #AMP2017
3:40pm November 17th 2017 via Hootsuite
Iafrate: 3 cool cases: 63yo M Sigmoid Colon ACA, TCF7L2 = TCF4 binding domain, activates Wnt pathway EWSR1-TCF7L2 #AMP2017
Iafrate: Shows criteria they use: in-frame, canonical breakpoint, prevalent, supporting reads >100, known anchor #AMP2017
3:38pm November 17th 2017 via Hootsuite
Iafrate: True drivers have higher levels RNA; also splice site muts in gene. Criteria for calling novel fusions: ha… https://t.co/CCKvzhDRGZ
3:37pm November 17th 2017 via Hootsuite
Iafrate: May be seen as normal alt splicing. Learned: 2K pts, 20% have >0 Met ex14 skip reads #AMP2017
3:36pm November 17th 2017 via Hootsuite
Iafrate: #AMP2017 MET ex14-skipping '15 ref https://t.co/YqMG5onMy2 more common than ALK, intronic splice-site muts
3:35pm November 17th 2017 via Hootsuite
Iafrate: Potent, and hard to find. FGFR fusions, import. to cholangiocarcinomas. '13 https://t.co/OcNNpoimBI #AMP2017
3:34pm November 17th 2017 via Hootsuite
Iafrate: RET+ pts are older, non or light smokers, see resp to Vandetanib. NTRK: rare, about 0.5%, but impt #AMP2017
3:32pm November 17th 2017 via Hootsuite
Iafrate: #AMP2017 '13 ref https://t.co/jiJ5v588vy on RET: 2-3% in NSCLC, 5' end has hi-exp, auto-dimerization domain
3:29pm November 17th 2017 via Hootsuite
Iafrate: #AMP2017 Clin char of ROS1-rearr NSCLC 1% prevalence - amazing crizotinib resp. PFS 20 mos vs 10 mos https://t.co/30J7mCokU1
3:28pm November 17th 2017 via Hootsuite
Iafrate: #AMP2017 '17 NEJM ref for Criz vs Alec https://t.co/yiJeIL3syb
3:26pm November 17th 2017 via Hootsuite
Iafrate: PFS of Alectinib shown better than crizotinib. Criz may not penetrate CNS, while Alectinib may. Recent 1st line approval #AMP2017
3:25pm November 17th 2017 via Hootsuite
Iafrate: 2nd gen inhibitors - Alectinib for those who fail crizotinib, resp rate as good as criz first-line. #AMP2017
3:24pm November 17th 2017 via Hootsuite
Iafrate: Pts that don't respond - minority - 'were they false positives?' #AMP2017
3:23pm November 17th 2017 via Hootsuite
Iafrate: ALK-FISH 'became std of care after the first case'. #AMP2017
Iafrate: Shows data from 1K cases - many singletons. Onto Crizotinib, '07 discovery ref https://t.co/hWlDMtv0ya AMP2017
3:22pm November 17th 2017 via Hootsuite
Iafrate: 50 genes currently. RNA rearr are drivers in ~10% of assay samples. Of these: 15% are novel #AMP2017
3:20pm November 17th 2017 via Hootsuite
Iafrate: Has to be in-frame for fusion det, other criteria. Several hundred to thousands of targets. #AMP2017
3:19pm November 17th 2017 via Hootsuite
Iafrate: #AMP2017 Reviews anchored multiplex tech '14 Nature Med ref https://t.co/d1rJEuTiFh
Iafrate: Shows ALK fig from '10 https://t.co/jqP2SFbR8m with a small but real risk of FN via FISH #AMP2017
3:18pm November 17th 2017 via Hootsuite
Iafrate: Now totally different, about 20 fusions that are actionable. Prevalence listed: many <1%, others 3-5%. #AMP2017
3:15pm November 17th 2017 via Hootsuite
Iafrate: Bluprint Med '14 https://t.co/JcIqO0vgWl chart mining TCGA data. 5y ago were only 3 gene fusions #AMP2017
3:14pm November 17th 2017 via Hootsuite
Iafrate: Showed figure from '11 STM paper https://t.co/Kazpx2UVR9 and relapse. And shows mut freq in common cancers #AMP2017
3:12pm November 17th 2017 via Hootsuite
