Ioannis Ladas (Dana-Farber) Sensitive detection of MSI in tumors and liquid biopsies using nuclease-based enrichment #AACR18
5:37pm April 15th 2018 via Hootsuite
A2 Yu: Size of probes around 14-30bp #AACR18
5:34pm April 15th 2018 via Hootsuite
Q: How close do primers need to be for amplification? Yu: Enrichment depends on the probe that targets top/bottom overlap #AACR18
5:33pm April 15th 2018 via Hootsuite
Q: Any clinical samples tried? Yu: Serial dilutions to mimic for recurrence monitoring. #AACR18
5:31pm April 15th 2018 via Hootsuite
Yu: Shows downstream of multiplex PCR (ampliseq, or truseq),multiplex NaME-PrO, and multiplexed HRM, then NGS #AACR18
5:27pm April 15th 2018 via Hootsuite
Yu: Dev closed-tube amplification, show 0.1% - 1% original signal at 2-13% due to wtDNA suppression. #AACR18
5:25pm April 15th 2018 via Hootsuite
Yu: #AACR18 Method NaME-Pro uses unique method of digestion of wtDNA using DSN enzyme per '16 NAR https://t.co/qDb4L8eXy3
5:24pm April 15th 2018 via Hootsuite
Fangyan Yu (Broad / Dana Farber MA) Method for sensitive detection of tumor fingerprints in plasma #AACR18
5:23pm April 15th 2018 via Hootsuite
Q: Will you do HER2 analysis? Jacobs: Working on it but nothing far along at present #AACR18
5:21pm April 15th 2018 via Hootsuite
Q: Comment on costs? Jacobs: Cost and labor efficient. 1 min hands-on time, can be very competitive #AACR18
5:20pm April 15th 2018 via Hootsuite
Q: 1 mL of plasma? Sens? Jacobs: All depends on input material, can get very low. They apply a limit. #AACR18
5:18pm April 15th 2018 via Hootsuite
Jacobs: RAS testing on ctDNA predicts sens to first-line anti-EGFR Rx (CAPRI-GOM trial ongoing) #AACR18
5:17pm April 15th 2018 via Hootsuite
Jacobs: Ras agreement between NGS and Idylla: 97% overall, 2/5 discordant was low freq. #AACR18
5:14pm April 15th 2018 via Hootsuite
Jacobs: Clinical study RASANC recently publ here https://t.co/r7ICG6FAri #AACR18
5:10pm April 15th 2018 via Hootsuite
Jacobs: ctKRAS (21 muts), ctNRAS-BRAF (23 muts), RASANC prospective clin trial for mCRC for Ras testing cp to tissue #AACR18
5:09pm April 15th 2018 via Hootsuite
Jacobs: All centered around their single-sample, single cartridge Idylla system. 2h TAT, shows nice video animation of process #AACR18
5:08pm April 15th 2018 via Hootsuite
Bart Jacobs (BioCarta Belgium) Analytical and clinical validation of the Idylla ctKRAS and ctNRAS-BRAF liquid biopsy tests in mCRC #AACR18
5:06pm April 15th 2018 via Hootsuite
Q: Why Inivata? Woodhouse: Pan-cancer in his opinion, not the best approach. Very focused panel for spec clinical Q's #AACR18
5:04pm April 15th 2018 via Hootsuite
Q: What gene to normalize? Woodhouse: Std housekeeping gene, RPP30 #AACR18
Q: Yield of cfDNA from 10mL, normalize? Woodhouse: Copies input is by ddPCR, far more accurate. #AACR18
5:03pm April 15th 2018 via Hootsuite
Q: 0.0625 is 6/10K copies; how much plasma? Woodhouse: Reality: stg and type of cancer; they've seen a range. Need to quote AF #AACR18
5:02pm April 15th 2018 via Hootsuite
Q: TAT? Woodhouse: 7-14 days; can deliver faster #AACR18
5:00pm April 15th 2018 via Hootsuite
Q: How to get around NGS error rate? Woodhouse: Error corrections, no use of UMIs, highly tuned system. #AACR18
Q: Amt input? Woodhouse: Work with input copies; 10000 and 2000 copies. 10mL in Streck #AACR18
4:59pm April 15th 2018 via Hootsuite
Woodhouse: Study recent published PLOS https://t.co/E3H6erHfSp #AACR18
4:58pm April 15th 2018 via Hootsuite
Woodhouse: All published breakpoints generated as contrived, all picked up (but one). Orthogonally, ddPCR failed with only 2 copies #AACR18
4:57pm April 15th 2018 via Hootsuite
Woodhouse: Shows sens down to 0.125% for ROS1-SLC34A2, and ALK-EML4. Fusions can occur in exonic or intronic regions #AACR18
4:55pm April 15th 2018 via Hootsuite
Woodhouse: 109 healthy individuals, 99.997% for SNV. Operators, lots, days. Took 18 indels, 1-24bp. Also gene fusions by amplicons #AACR18
4:54pm April 15th 2018 via Hootsuite
Woodhouse: Shows ddPCR and NGS AF's, nice concordance across mutations shown. Shows SNV detection down to 0.06%. Have 69000x depth #AACR18
4:52pm April 15th 2018 via Hootsuite
Woodhouse: In that context even low AF T790M relevant. ctDNA ref std from Horizon 37 muts at range of AF's Shows very high concordnc #AACR18
4:50pm April 15th 2018 via Hootsuite
Woodhouse: #AACR18 Fusion, CNVs, SNVs, indels. 40% of ctDNA is below 1% AF in NSCLC. Remon et al looked at EGFR T790M+ pts to Osimertinib
4:49pm April 15th 2018 via Hootsuite
Woodhouse: #AACR18 hyb-based approaches - A-tailing 51%, ligation, other inefficiencies. Inivata has optimized a spec amplicon-based method
4:48pm April 15th 2018 via Hootsuite
Sam Woodhouse (Inivata UK) Analytical validation of InVisionFirst, high-sensitivity broad molecular profiling of ctDNA #AACR18
4:47pm April 15th 2018 via Hootsuite
Q: Price? Lou: China's policy isn't open to LDT; qPCR has passed CFDA; their assay isn't a lot more than what is currently offered #AACR18
4:46pm April 15th 2018 via Hootsuite
Lou: Shanghai Chest Hsop - 10K thoracic surgeries/y; affiliated with Jiao Tong Univ. Acknowledges Grace from Accuragen #AACR18
4:42pm April 15th 2018 via Hootsuite
Lou: de novo 19-del variants not picked up by ARMS, ddPCR. Claims 6 copy detection w/96% detection rate. No FPs in 50 normal smpls #AACR18
4:41pm April 15th 2018 via Hootsuite
Lou: Using ddPCR to compare, shows R^2 at 0.95; discrepency accounted for by sampling bias and composition differences. #AACR18
4:40pm April 15th 2018 via Hootsuite
Lou: 38 untreated pt samples - ctDNA mutation composition resembles previously reported distribution #AACR18
4:37pm April 15th 2018 via Hootsuite
Lou: 94% concordance between users, 20 ng exogenous DNA shows data consistency. n=134, NSCLC; 50 normal. #AACR18
4:36pm April 15th 2018 via Hootsuite
Lou: Shows data down to 0.05%, 'Wang et al submitted'. (Said it was reference material but not from who...) #AACR18
4:35pm April 15th 2018 via Hootsuite
Lou: Slide compares NGS error correction; points out errors introduced w/circular template ampl (PCR) vs RCA #AACR18
4:34pm April 15th 2018 via Hootsuite
Lou: Concatemer-based error correction: true mutations are repeated in the concatemer. Ligate circles, use RCA to amplify #AACR18
4:32pm April 15th 2018 via Hootsuite
Jiatao Lou (Shanghai Jiao Tong Univ CN) Detection of actionable muts in cfDNA NSCLC samples using a novel amplicon-based Firefly #AACR18
4:30pm April 15th 2018 via Hootsuite
Q: Do you need to broaden gene panel? Ortiz-Cuaran: For now, Emma (Green, Inivata), larger panel >cost >time limiting use #AACR18
4:28pm April 15th 2018 via Hootsuite
Q: Rec for clinical practice? Ortiz-Cuaran: Has to be prospective w/an interventional study. Longer PFS or not? #AACR18
4:27pm April 15th 2018 via Hootsuite
Q: Sample coll? Ortiz-Cuaran: Streck: reduced beyond 3-4d, also if nurses 'didn't really mix after collection' also reduced yield #AACR18
4:26pm April 15th 2018 via Hootsuite
Q: Clin prog, molecular prog timing? Ortiz-Cuaran: time to progression was 4-12 w #AACR18
4:25pm April 15th 2018 via Hootsuite
Ortiz-Cuaran: Found increaseed heterogeneity in 3rd vs 1st-gen EGFRinh. Showed distribution of resistance mutations #AACR18
4:23pm April 15th 2018 via Hootsuite
Ortiz-Cuaran: Liver and bone mets - more predictive. No assoc'n betwen initial ctDNA load, and response to Osomeritib #AACR18
4:22pm April 15th 2018 via Hootsuite
Ortiz-Cuaran: n=46 first pt cohort, 1st linke EGFR TKI, subsequent treatment described. Shows 9/13 sens (70%) relapse #AACR18
4:21pm April 15th 2018 via Hootsuite
