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
Santani: Missed by first lab - b/c OMIM didn't have a disease name. First report of SOX5 point mutation same as large deletion #NGDx15
9:58am August 19th 2015 via Hootsuite
Santani:Now covers these two cases; classic dx odyssey. SOX5 - no disease associated with SOX5 del. 18 cases in lit #NGDx15
Santani: Of the rest - needed more phenotype data from physician. 2 prior were negative, now ID'd two new molecular diagnosis #NGDx15
9:57am August 19th 2015 via Hootsuite
Santani: But the clinical validation piece - variant filtration and interpretation process. 20 samples - 16/20 concordant #NGDx15
9:56am August 19th 2015 via Hootsuite
Santani:Their validation; used GIAB 'gold standard' NA12878, terrific way to test sens and spec of WES. #NGDx15
9:55am August 19th 2015 via Hootsuite
Santani: Their LIMS will generate reports as well.Rules for compliance. #NGDx15
9:53am August 19th 2015 via Hootsuite
Santani: The KB part of LIMS - not only tracking samples, but also genomic-savvy. 2y of effort: phenotype collection, images, test #NGDx15
Santani: "We will not use Excel" - 100's of thousands of vars, over 10 people needing to access data. Wanted a knowledge base #NGDx15
9:52am August 19th 2015 via Hootsuite
Santani:The final few - from 3 to 40 variants evaluated for pathogenicity. ACMG classifications 'outstanding' http://t.co/9LFZGOqHpJ #NGDx15
9:51am August 19th 2015 via Hootsuite
Santani: Each step - multiple databases, an intensive process. 100's of exome cases/mo. Trio WES - many families from Middle East #NGDx15
9:49am August 19th 2015 via Hootsuite
Santani:1,141 by mutation type; of that 512 disease genes; then 40 clinician board review select. Then 3 de novo selected #NGDx15
9:48am August 19th 2015 via Hootsuite
