Patel: Showing E coli data, size distribution of reads looks comparable; mean RL 4.4kb vs 4.5kb manual. Alignment 85% vs 88% #Tricon
5:16pm February 22nd 2017 via Hootsuite
Patel: Has an automated library prep platform, showed data with 48kb library prep vs manual; DNA yield comparable #Tricon
5:14pm February 22nd 2017 via Hootsuite
Kamlesh Patel (Sandia NL): Portable sequencing: fundamentals in seq technology with nanopores, sample prep and data analysis #Tricon
5:13pm February 22nd 2017 via Hootsuite
Q: source of noise in ddPCR? Singh: some get mutant and WT both templates are there #Tricon
3:08pm February 22nd 2017 via Hootsuite
Singh: Points out the importance of using controls - (SeraCare has them.) https://t.co/jeMAm7uG3w #Tricon
3:07pm February 22nd 2017 via Hootsuite
Singh: They can use cell-culture DNA as a surrogate. #Tricon
3:05pm February 22nd 2017 via Hootsuite
Singh: Showed LoD studies, down to 0.3%; blow that was not consistent. 3 droplets was their cutoff #Tricon
Singh: RET M918T test is via ddPCR; showed validation cohort n=63. They use 10ng input; cp ccfDNA and FFPE. R^2=9.94 Pyro vs dPCR #Tricon
3:04pm February 22nd 2017 via Hootsuite
Singh: Test for melanoma, lung ca, medullary thryroid for ctDNA #Tricon
3:01pm February 22nd 2017 via Hootsuite
Singh: Shows scan of plasma ccfDNA and FFPE, with 140bp peak. Are not enthusiastic about synthetics. #Tricon
3:00pm February 22nd 2017 via Hootsuite
Singh: ccfDNA technology choices paper '15 PLoS https://t.co/HPAVJTlRwA #Tricon
2:58pm February 22nd 2017 via Hootsuite
Singh: Did cp of QIASymphony vs manual of 3mL plasma; showed comparable yield and Alu115/Alu247 also very similar #Tricon
2:57pm February 22nd 2017 via Hootsuite
Singh: Purple tops are oka, but only within 16h; shows Mehrotra JMD (under review) data #Tricon
2:56pm February 22nd 2017 via Hootsuite
Singh: For testing platforms - Allele-spec qPCR/ddPCR/NGS/BEAMing? DNA input? workflow, sensitivity? #Tricon
2:54pm February 22nd 2017 via Hootsuite
Singh: We are taking NGS tumor assays that were 5% or 2% and pushing the limit. Logistics - what to isolate? How? #Tricon
2:53pm February 22nd 2017 via Hootsuite
Rajesh Singh (MD Anderson TX) Mutation screening of liquid biopsies: technical challenges. #Tricon
2:51pm February 22nd 2017 via Hootsuite
Luthra: Challenges - lack of harmonization for pre-analytic steps such as peri blood collection, storage, ctDNA isolation #Tricon
2:50pm February 22nd 2017 via Hootsuite
Luthra: Feb 17 single-gene test by ddPCR, developed in-house. Has collaboration with Guardant Health, co-develop 73 cancer genes #Tricon
2:49pm February 22nd 2017 via Hootsuite
Luthra: Pt w/colon ca, adjuvant Rx, relapse 1y, plasma at 14mo 39% in plasma but 0% PIK3CA tissue, clonal divergence? #Tricon
2:47pm February 22nd 2017 via Hootsuite
Luthra:.MDACC case studies; Stg IV Colon ca; deep seq w/ Ampliseq; chemo. Found 1% plasma, not in tissue, later found 0.2% in tissue #Tricon
2:46pm February 22nd 2017 via Hootsuite
Luthra: Looking at RET M918T in medullary thyroid carcinoma: If >1%, poor survival. (Master's degree student project) #Tricon
2:44pm February 22nd 2017 via Hootsuite
Luthra:Correlation of BRAF with clinical outcome: BRAFi and MEKi '16 ref https://t.co/TlubGIRTth Looked at BRAF V600E #Tricon
2:43pm February 22nd 2017 via Hootsuite
Luthra: And concordance bet tissue and ctDNA is 32% (panc) to 97% (colorectal). #Tricon
2:39pm February 22nd 2017 via Hootsuite
Luthra: ccfDNA is from both normal and tumor cells; shows long list of 9 references with concordance across cancer types, genes, ct #Tricon
2:38pm February 22nd 2017 via Hootsuite
Luthra: ctDNA discovered in 1947; but decades to develop. Applications for monitoring, MRD, resistance det, tumor burden #Tricon
2:36pm February 22nd 2017 via Hootsuite
Raja Luthra (MD Anderson TX) Mutation screening of liquid biopsies: promise and clinical utility #Tricon
2:34pm February 22nd 2017 via Hootsuite
Q:How much DNA into assay? Scudder: 2mL plasma, not quantitated #Tricon
2:32pm February 22nd 2017 via Hootsuite
Scudder: #Tricon AstraZeneca published AURA3 in '16 NEJM https://t.co/NVtpAAxQCT Erlotinib approved in summer '16, other approved later
2:31pm February 22nd 2017 via Hootsuite
Scudder: Osimertinib, clin utility of PPA L858R also 75%. NPA also 98%. Tissue neg, plasma pos, 'considered wrong, affecting stats' #Tricon
2:29pm February 22nd 2017 via Hootsuite
Scudder: Clin response: improved PFS from both plasma and tissue. EGFR+ in tissue and plasma, similar benefit #Tricon
2:28pm February 22nd 2017 via Hootsuite
Scudder: Agreement between tissue and plasma, PPA 76%, NPA 98%. #Tricon
Scudder: In the meantime their sample prep kit was approved. Detected 0.3% in wt background. PPA 87% for ex90del/L858R #Tricon
2:27pm February 22nd 2017 via Hootsuite
Scudder: Found untreated Stg IV recurrent NSCLC, FDA allowed it. 'Now even more complex'. Two clinical trials: clin and analytic #Tricon
2:26pm February 22nd 2017 via Hootsuite
Scudder: Clinical validation - 217 enrolled, 180 w/2mL of plasma, not enough for analytical studies. #Tricon
2:25pm February 22nd 2017 via Hootsuite
Scudder: Used contrived samples, diluting cell line DNA in healthy donor plasma; showed commutability, equiv results at LOD conc #Tricon
2:24pm February 22nd 2017 via Hootsuite
Scudder: FDA requested cancer plasma, not normal plasma for NSCLC. Est 32L of plasma (!) FDA 'were ultimately receptive' #Tricon
2:23pm February 22nd 2017 via Hootsuite
Scudder:Used allele-spec PCR tech, multiplexed for tissue. Did IUO erlotinib Ex19del L858R, UD-IVD; osimertinib, T790M US-IVD #Tricon
2:22pm February 22nd 2017 via Hootsuite
Scudder: #Tricon Clinical drug resp is ultimate indicator of how good the drug will be. ddPCR hard to multiplex https://t.co/c9n9L47iqb
2:21pm February 22nd 2017 via Hootsuite
Scudder: v2 was similar to the first one; 3-well test (too much info too fast). AURA2: NCT02094261, EGFR T790M+, first-line prog #Tricon
2:20pm February 22nd 2017 via Hootsuite
Scudder: erlotinib and osimertinib, a whole other level of complexity. (US-IVD most challenging) #Tricon
2:18pm February 22nd 2017 via Hootsuite
Scudder: Drives need for constructing contrived (synthetic) samples to evaluate test performance. Pharma interest to co-dev #Tricon
Scudder: Most had EGFR of <200 copies/mL (!) Had to work with IRB, ICF, HIPAA rules, population is ill. 40mL blood max #Tricon
2:17pm February 22nd 2017 via Hootsuite
Scudder: Prospective collection and time to screen; 'spent $2M just buying samples from vendors'. 1000 specimens, to find 80 w/muts #Tricon
2:16pm February 22nd 2017 via Hootsuite
Scudder: In '13 - no validated methods, no int'l stds, EGFR Mut Test v2 det 42 mutations under dev. Had to validate LOD etc #Tricon
Scudder: #Tricon Reviewed results from '14 ref https://t.co/UW5k4AjEXi activating mutations persist in plasma
2:15pm February 22nd 2017 via Hootsuite
Scudder: #Tricon Clearing ct EGFR DNA, increased OS and PFS. Predictive for survival. Denmark study next https://t.co/65piOUdh8S
2:12pm February 22nd 2017 via Hootsuite
Scudder: FASTACT-2 PhIII study was Erlotinib and chemo, and EGFR +/- status comparing tumor to plasma #Tricon
2:11pm February 22nd 2017 via Hootsuite
Scudder: 166bp or 140bp, half-life of 1.5h. Naked DNA lasts only a few minutes. Shows long list of genes https://t.co/V6K3aYQIvQ #Tricon
2:10pm February 22nd 2017 via Hootsuite
Scudder: Platelets are 'basically a large exosome'; CTCs, ctDNA, small vesicles. Most ctDNA is histone-assoc'd. #Tricon
2:08pm February 22nd 2017 via Hootsuite
Scudder: Challenges 'could be significant' at times. Drawing from https://t.co/DZUMLgjoY5 cancer cells are constantly growing/dying #Tricon
2:07pm February 22nd 2017 via Hootsuite
