Diehn: Assay affected by number of molecules recovered; mutations covered; and error rate of sequencing #Tricon
11:49am February 23rd 2017 via Hootsuite
Diehn: Stg I-IV: shows ROC curve from '14 Nature Med ref https://t.co/Z1E17xGury as little as 1.9pg/mL #Tricon
Diehn: Before did tissue first then ctDNA; now they can skip the tissue. Later draws, look for new mutations (resistance) that arise #Tricon
11:47am February 23rd 2017 via Hootsuite
Diehn: Look at population-level analysis; look for recurrent mutations; drill down to panel. Tumor/normal, monitor over time #Tricon
11:46am February 23rd 2017 via Hootsuite
Diehn: Assumptions for the above: 30ng cfDNA; 50% efficiency; 90% probability of detection. #Tricon
11:45am February 23rd 2017 via Hootsuite
Diehn: WES down to 5%; WGS down to 1%; amplicons down to 0.3%; barcoded amplicon (SafeSeqS) to about 0.05%, CAPP-Seq 0.002% #Tricon
11:44am February 23rd 2017 via Hootsuite
Diehn: Cp to how low you can go: Sanger, Pyro is sens to 10%; Allele-spec PCR is 0.1-0.05%; dPCR down to 0.05% or less #Tricon
11:43am February 23rd 2017 via Hootsuite
Diehn: Limited input (a few thousand copies per mL of blood). Then from the cancer, only a few molecules. #Tricon
11:42am February 23rd 2017 via Hootsuite
Diehn: Then if recurring, re-test for additional therapy, and then monitor again. #Tricon
11:41am February 23rd 2017 via Hootsuite
Diehn: Illustrates screening, non-invasive genotyping, local treatment response, detect minimal residual disease, surveillance... #Tricon
Diehn: Mutations are involved in pathogenesis, part of the biology of the disease. And some muts are actionable #Tricon
11:40am February 23rd 2017 via Hootsuite
Diehn: Shows diagram from Crowley et al, shed into bloodstream; ctDNA attractive due to specificity (cp to protein markers). #Tricon
11:39am February 23rd 2017 via Hootsuite
Diehn: Will describe CAPP-Seq, then clin appl to adv lung ca, and clin appl to early stage lung ca #Tricon
11:38am February 23rd 2017 via Hootsuite
Max Diehn (Stanford CA) Deep sequencing of circulating tumor DNA for personalized cancer detection and monitoring. #Tricon
11:37am February 23rd 2017 via Hootsuite
Patel: Lots of effort both academically and commercially (i.e. Grail) where we'll learn much more in the years to come. #Tricon
11:36am February 23rd 2017 via Hootsuite
Patel: Finding occult metastatic disease may not have same impact as early-detection. Known mutations w/aging: clonal hematopoeisis #Tricon
11:35am February 23rd 2017 via Hootsuite
Patel: Second biological challenge: are the same mutations found in healthy individuals? #Tricon
Patel: Technical challenges - broad coverage is needed, bckgrnd errors need to be suppressed. Biological ones: enough DNA? and... #Tricon
11:34am February 23rd 2017 via Hootsuite
Patel: Promise of ctDNA: very little physiologic background; in principle, all the signal is tumor-derived #Tricon
11:33am February 23rd 2017 via Hootsuite
Patel: For protein biomarkers - there's non-zero background. Ex: PSA: tumor-derived PSA hard to detect early (little cp to bckgnd) #Tricon
11:32am February 23rd 2017 via Hootsuite
Abhijit Patel (Yale CT) Opening remarks for Circulating Cell-Free DNA symposia at #Tricon
11:31am February 23rd 2017 via Hootsuite
FYI @SeraCare @DaleYuzuki presents at #Tricon 10:15am "Improved material for developing, validating, and monitoring liquid biopsy assays"
10:20am February 23rd 2017 via Hootsuite
MT @TwoPoreGuys: Very excited to share our tech! Two Pore Guys to Present at #TRICON @BusinessWire https://t.co/g9IlTsTktA
10:17am February 23rd 2017 via Hootsuite
RT @JamesDHayden: Great article on the use of #machinelearning in #clinicaltrials and #drugdev @IBMWatsonHealth https://t.co/yNW4TWdFWp
10:00pm February 22nd 2017 via Hootsuite
RT @atulbutte: Flying cars… finally coming soon? https://t.co/sES3gnEciJ
9:40pm February 22nd 2017 via Hootsuite
(Staudt: Here's a Scientific American piece about this project https://t.co/1OSo7N8EHW #Tricon )
8:13pm February 22nd 2017 via Hootsuite
(I found Lou Staudt's slides online https://t.co/LgdK4kzmmX #Tricon)
8:12pm February 22nd 2017 via Hootsuite
Staudt: Do culture conditions need optimization? For different organs and tumor types? Sensitivity to post-surgery handling? #Tricon
8:11pm February 22nd 2017 via Hootsuite
Staudt: How easy to perform in different labs? Proprietary reagents w/batch variability? #Tricon
8:10pm February 22nd 2017 via Hootsuite
Staudt: Do various culture methods favor different geneitc/epigenetic subpopulations w/in primary tumor? #Tricon
8:09pm February 22nd 2017 via Hootsuite
Staudt: Called a pilot: will genetic and epigenetic nature of primary tumor affect ability to be estab. in-vitro? #Tricon
8:08pm February 22nd 2017 via Hootsuite
Staudt: Primary biopsies sent to centers; link from site to center will be maintained to have some level of response to Rx #Tricon
8:06pm February 22nd 2017 via Hootsuite
Staudt: Models may also suggest novel Rx '14 Science https://t.co/JbK6MOfxdD #Tricon
8:05pm February 22nd 2017 via Hootsuite
Staudt: Keratin14 marker: cells invade mam gland, minority of popul'n, but invasion were all K14+ '13 Cell https://t.co/KcprYIyRhR #Tricon
8:02pm February 22nd 2017 via Hootsuite
Staudt: Models w/known drivers, recapitulate cell subtypes. Shows data of organoids '14 Cell in prostate ca https://t.co/t5zf6gGyu2 #Tricon
8:00pm February 22nd 2017 via Hootsuite
Staudt: Conditional reprogramming making it simpler, Wnt signalling '12 ref https://t.co/PonWxMwJan
7:58pm February 22nd 2017 via Hootsuite
Staudt: New tech - organoids from Clevers '11 ref https://t.co/XQ7TaQPWXU #Tricon
7:57pm February 22nd 2017 via Hootsuite
Staudt: Models for combinations of lesions do not exist; rare subtypes underrep or nonexistent; models don't recapitulate subpops #Tricon
7:56pm February 22nd 2017 via Hootsuite
Staudt: Cell lines do not have annotations that relate to primary tumor. Today know 'are suspect' genetically (i.e. prostate ca) #Tricon
7:55pm February 22nd 2017 via Hootsuite
Staudt: Combining structural with functional genomics. Unmet need: genetic analysis down to 0.5% (NTRK fusions), and most no models #Tricon
7:54pm February 22nd 2017 via Hootsuite
Staudt: Contracted with ATCC. Today we have correlative science; now want models. Putative driver genes, model, fn genomics #Tricon
7:53pm February 22nd 2017 via Hootsuite
Staudt: Working with Leidos, created a competition, w/Broad (Jesse Boehm), CSHL (Dave Tuveson), Univ Verona (Scarpa), Hubrect. #Tricon
7:51pm February 22nd 2017 via Hootsuite
Staudt: 3y from now is the end; Mike Stratton at Wellcome Trust/CRUK had the same idea; Hubrecht Inst ("HUB") Hans Clevers #Tricon
7:50pm February 22nd 2017 via Hootsuite
Staudt: Full genomic characterization; clinical annotation, including resp to last Rx. A scaleable effort #Tricon
7:49pm February 22nd 2017 via Hootsuite
Staudt: Goal - create 1000 new cancer cell lines; a 'project so good people wouldn't complain that there is less R01 money' #Tricon
7:48pm February 22nd 2017 via Hootsuite
Lou Staudt (NCI MD) The human cancer model initiative #Tricon
Dow: Shows time-lapse of 3d growth, with and without Rsponding w/ and post-Dox. #Tricon
7:26pm February 22nd 2017 via Hootsuite
Dow: Can be taken out, regrown in 3D Matrigel. No serum req'd but requires EGF, Noggin, Rspondin1 factors. #Tricon
7:25pm February 22nd 2017 via Hootsuite
Dow: Also MB size Ptprk-Rspo3 inversion, showed 3 color FISH. Inducible mice, made organoids, can harvest intestinal crypts #Tricon
Dow: Fusion partner up-regulated, likely the driving event. EIF3E-RSPO2 (R-spondin) fusion engineered, shows data #Tricon
7:24pm February 22nd 2017 via Hootsuite
