Rosenfeld: Activating and resistance mutations both monitored by ctDNA. Shows relative mutation levels in TKI/chemo course #NGDx15
2:42pm August 19th 2015 via Hootsuite
.@crushaFTW this whole afternoon there's a session called 'Clinical Application of Cell-free DNA'. Inivata and Mt. Sinai so far.
2:39pm August 19th 2015 via Hootsuite
Rosenfeld: Solid tumor <50% enough material to determine mutation. ctDNA concordance >95%. #NGDx15
2:38pm August 19th 2015 via Hootsuite
Rosenfeld: Will over 100's of amplicons, focus on lung ca related genes. Reported pilot study at EACR, cp solid tumor to ctDNA #NGDx15
2:36pm August 19th 2015 via Hootsuite
Rosenfeld: Inivata formed to improve TAm-Seq platform, showed improvement to background. Range of sensitivity 'will vary dep on mut' #NGDx15
2:34pm August 19th 2015 via Hootsuite
Rosenfeld: Exome sequencing http://t.co/ymOgUgo0CD Was able to sample metastatic tumors after, and drew phylogenetic analysis #NGDx15
2:25pm August 19th 2015 via Hootsuite
Rosenfeld: 50% from tumor can use other tools - WES. Used at TGEN to look at novel resistance mechanism #NGDx15
2:21pm August 19th 2015 via Hootsuite
Rosenfeld: Can use multiple mutations to track overall tumor burden. Levels of tumor burdan can be surprisingly high (90%!) #NGDx15
2:20pm August 19th 2015 via Hootsuite
Rosenfeld: Different mutations can show diverging patterns. 1y follow-up, TP53 and PIK3CA over time shown #NGDx15
2:19pm August 19th 2015 via Hootsuite
Rosenfeld: "Having multiple mutations to track is like having two watches but not being sure what the time is" #NGDx15
2:18pm August 19th 2015 via Hootsuite
Rosenfeld: Expanding the target 48 amplicons 2012 ref in his group http://t.co/VYWYsxxU6o Now expanded to 175 amplicons #NGDx15
Rosenfeld: Shows several data slides from 2014 Bettegowda et al http://t.co/Xm6UTPzHi2 Levels increase w/inc stage #NGDx15
2:15pm August 19th 2015 via Hootsuite
Rosenfeld: Presents data from Dawson et al 2013 metastatic breast cancer http://t.co/9fCsejw9sJ #NGDx15
2:14pm August 19th 2015 via Hootsuite
Rosenfeld: Talks about CA125 for OvCa Recent Martignetti paper http://t.co/LaSfa9uClJ Other data from Diehl et al #NGDx15
2:13pm August 19th 2015 via Hootsuite
Rosenfeld: 2008 paper: http://t.co/2h9XCLiiLW But goes way back: '91 ref: http://t.co/gcw66ggujb #NGDx15
2:08pm August 19th 2015 via Hootsuite
Rosenfeld: Introduces ctDNA - non-invasive stratification, monitoring response, monitor resistance to treatment #NGDx15
2:04pm August 19th 2015 via Hootsuite
Nitzan Rosenfeld (Inviata Ltd) "Monitoring the cancer genome in plasma using circulating tumor DNA" #NGDx15
2:02pm August 19th 2015 via Hootsuite
Martignetti: A2:Feels he can go down to 0.001% #NGDx15
1:25pm August 19th 2015 via Hootsuite
Martignetti: Q:Their sensitivity? A:Have done some mixing expts, .01% based upon mixing. Qubit was variable. #NGDx15
1:24pm August 19th 2015 via Hootsuite
Martignetti: 'ctDNA can impact critical clinical inflection points in patient care' - Est of clinical utility. #NGDx15
1:20pm August 19th 2015 via Hootsuite
Martignetti: Another case where ctDNA and CA125 plotted over course of treatment. Had evidence to guide using ctDNA #NGDx15
1:19pm August 19th 2015 via Hootsuite
Martignetti: But data comparing ctDNA to surgery showed much better numbers. #NGDx15
1:15pm August 19th 2015 via Hootsuite
Martignetti: What is ground truth? comparing CA-125 results to CAT scans. Sens around 91% spec ~80% #NGDx15
1:14pm August 19th 2015 via Hootsuite
Martignetti: Showed data of ctDNA levels over course of therapy. One case - PFS with ctDNA 'going down to zero' #NGDx15
1:13pm August 19th 2015 via Hootsuite
Martignetti: Uses a variety of tools for personalized biomarker detection - from RNA-Seq and WES down to focused panels #NGDx15
1:12pm August 19th 2015 via Hootsuite
Martignetti: Showed example of OvCa pt with 4y of samples. CA-125 only showed on a few occasions, illustrating need for better mkrs #NGDx15
1:11pm August 19th 2015 via Hootsuite
John Martignetti (Icahn School Med Mt Sinai NY) "Precision-based circulating tumor DNA det in gynocologic cancer pts" #NGDx15
1:10pm August 19th 2015 via Hootsuite
,@owlmonkey It was Stephen Turner's 2008 AGBT talk - not the 2015 one. I don't believe it was recorded. Memories are long though!
11:44am August 19th 2015 via Hootsuite in reply to owlmonkey
Garlick: Q:Can you create amplification controls? A:In the works. Q:Flexible content? A:Yes #NGDx15
10:29am August 19th 2015 via Hootsuite
Garlick: Improving QC does reduce laboratory risk. All about co-development. #NGDx15
Garlick: List of advisers incl Errol Norwitz (Tufts), Greg Tsongalis (Dartmouth), Diana Bianco (Stanford), Helen Fernandex (Cornell) #NGDx15
10:28am August 19th 2015 via Hootsuite
Garlick: Plan to develop 1%, 0.1%, and below. Can be used for co-development of ctDNA assays, SeraCare has history with collab's #NGDx15
10:27am August 19th 2015 via Hootsuite
Garlick: Digital PCR can confirm trisomic content, across T13, T18 and T21. Same core tech for ctDNA - target KRAS, NRAS, EGFR, BRAF #NGDx15
10:25am August 19th 2015 via Hootsuite
Garlick: Nucleosome-type body - used for NIPT, data by LabCorp, normalized values seens at 21% for T13, 18% for T18 and 13% for T21. #NGDx15
10:24am August 19th 2015 via Hootsuite
Garlick: Take fragmented DNAs (12% fetal, 88% maternal), packaged to stabilize and mixed into a matrix (manufactured) w/low DNA #NGDx15
10:23am August 19th 2015 via Hootsuite
Garlick: Onto NIPT - applicable to ctDNA. Have technology to take normal female cells, and UCSF-licensed trisomic trophoblasts #NGDx15
10:22am August 19th 2015 via Hootsuite
Garlick: Within 6 mos - a sensitivity panel, from 10% down to 1%. Looking at CVs, much wider below 5%. Can supply in 3mo with custom #NGDx15
10:21am August 19th 2015 via Hootsuite
Garlick: Doing run control charts across 4 mutations over 8 months, 28 runs: 95% confidence w/only 6 measurements #NGDx15
10:19am August 19th 2015 via Hootsuite
Garlick: Example on different iteration of Torrent Suite software versions (4.4, 4.0 and 3.2) and difference in call sensitivity NGDx15
10:18am August 19th 2015 via Hootsuite
Garlick: Data shows two different Ion AmpliSeq panels; reprod; and also assay differences (1 lower from one panel, 1 lower on other) #NGDx15
10:17am August 19th 2015 via Hootsuite
Garlick: Listed 26 mutations and genes, 15 actionable ones, small and large indels, and SNVs. Product 1, these will be added to #NGDx15
10:16am August 19th 2015 via Hootsuite
Garlick: The AF20 means allelic frequency at 20%; 26 constructs quantitated via dPCR, pooled and spiked into GM24385 #NGDx15
10:15am August 19th 2015 via Hootsuite
Garlick: Has a library of 70 mutated targets. Shows three examples of mutations at a 20% VAF in an 80% wild-type background. #NGDx15
10:14am August 19th 2015 via Hootsuite
Garlick: For oncology - custom, RUO and IVD. Have been collaborating with Mickey Williams at NCI-Frederick, CRADA agreement #NGDx15
10:12am August 19th 2015 via Hootsuite
Garlick: Now doing a study where 54 metrics are being measured. The clinical lab director has many pressures: cost, TAT, regulation #NGDx15
10:10am August 19th 2015 via Hootsuite
Garlick: Many issues, from detecting allelic frequency, what about changes in the assay? There hasn't been much inter-lab cp data #NGDx15
10:09am August 19th 2015 via Hootsuite
Garlick: SeraCare started with seroconversion panels for HIV in the '80s. Accurun controls the familiar name. #NGDx15
10:07am August 19th 2015 via Hootsuite
Russell Garlick (SeraCare MA) "Qualitative and quantitative tools for performance monitoring in NGS tumor profiling assay" #NGDx15 @seracare
10:05am August 19th 2015 via Hootsuite
Santani: Got in touch with a physician in Sweden - published in AJHG Mar 2015 #NGDx15 http://t.co/VdRs6NAaER
10:03am August 19th 2015 via Hootsuite
Santani: Second case, de novo mut in KAT6A, unknown association. Searched via Google (!) 3 pages later, a Facebook page #NGDx15
10:00am August 19th 2015 via Hootsuite
