Febbo: The cost assoc'd with the test is such a small proportion: high expectations of pts unmet, toxicity #Tricon
12:31pm February 24th 2017 via Hootsuite
Febbo: 17 genes in OncotypeSEQ Liquid Select; but population data needs to be imported back to inform decisions. #Tricon
12:30pm February 24th 2017 via Hootsuite
(NB: Dr. Febbo is an excellent, top-rate presenter. Excellent illustrations, very clear, high-density content. Kudos!) #Tricon
12:29pm February 24th 2017 via Hootsuite
Febbo: And the FDA is open to this; points to this FDA PDF https://t.co/erz38zvnEL as the model for oncology #Tricon
12:28pm February 24th 2017 via Hootsuite
Febbo: No single institution will develop enough. They have tested 600K pts with OncotypeDx. They have access to SEER, 38K pts' data #Tricon
12:26pm February 24th 2017 via Hootsuite
Febbo: Data sharing will be required; many 10's of thousands of tests administered by academia and companies #Tricon
Febbo: And the result? 250 pts total for the trial (!) Add background genetic context, AF, mut burden, disease context #Tricon
12:25pm February 24th 2017 via Hootsuite
Febbo: 132K pts, 20% of these mCRC, 80% adequate tissue, 8% w/PIC3CA, 30% eligable, 50% consent (all optimistic #'s) #Tricon
12:24pm February 24th 2017 via Hootsuite
Febbo: Need appropriate disease CONTEXT - hypothetical Ph II study of PIK3CA+ in mCRC, goes thru numbers. #Tricon
12:23pm February 24th 2017 via Hootsuite
Febbo: Blood profiling atlas in cancer (Blood PAC) as part of Cancer Moonshot '17 ref https://t.co/wYQePouh3U #Tricon
12:21pm February 24th 2017 via Hootsuite
Febbo: Indep guidelines play a critical role in helping ensure quality. NCCN, ESMO, country-spec ones #Tricon
12:20pm February 24th 2017 via Hootsuite
Febbo: Limitations: quality ("Bob's genome", "ccfDNA R Us") - and influential paper https://t.co/sH5uZdLwYq and FDA LDT response #Tricon
12:19pm February 24th 2017 via Hootsuite
Febbo: BELLE-2 Trial, PIK3CA mutations outperformed in ccfDNA Baselga SABCS abstract, manuscript publ. soon #Tricon
12:15pm February 24th 2017 via Hootsuite
Febbo: Refers to FASTACT2 w/cobas EGFR test; overall hazard ratio almost identical. Wu '13 https://t.co/vA3oEdHlKW #Tricon
Febbo: Overlap between FFPE and ccfDNA in EGFR: 17% to 94%. Bai '09; Kimura '07; Goto '2012; Douillard '14; Kim '13; Couraud '14 #Tricon
12:13pm February 24th 2017 via Hootsuite
Febbo: If base specificity is 99.9%, in 100kb smpl is 100 FP calls; specificity of sample is 0%. At six 9's, 1/100kb <1 FP call #Tricon
12:11pm February 24th 2017 via Hootsuite
Febbo: Specificity impt as well, reported on a per-sample basis (>99%); per variant, much higher: six 9's. #Tricon
12:09pm February 24th 2017 via Hootsuite
Febbo: Analytical spec's: across SNVs, indels, fusions, CNV gains. (2.7 copies at 95% detection rate) #Tricon
Febbo: Are pt outcomes improved, and physician behaviors changed as a result of clinical trials? OncotypeSEQ Liquid Select #Tricon
12:08pm February 24th 2017 via Hootsuite
Febbo: Analytical validity; then clinical validity (concord w/tissue or assoc of ctDNA var to drug benefit; then clinical utility #Tricon
12:07pm February 24th 2017 via Hootsuite
Febbo: 'We have to do a job for them' (Physicians, patients and payers); how liquid biopsy shines. #Tricon
12:06pm February 24th 2017 via Hootsuite
Febbo: Reviews the variety of oncology tests Genomic Health offers (Breast Recurrance, Breast DCIS, AR-V7 etc) and now ccfDNA #Tricon
12:05pm February 24th 2017 via Hootsuite
Febbo: Starts with CML and Gleevec and its importance in cancer treatment and molecular medicine #Tricon
12:04pm February 24th 2017 via Hootsuite
Phillip Febbo (Genomic Health CA) Building evidence of utility for cfDNA in cancer management #Tricon
12:03pm February 24th 2017 via Hootsuite
Kashyap: Showed taxon-taxon correlation stronger in responders; suggests higher colonization resistance #Tricon
12:00pm February 24th 2017 via Hootsuite
Kashyap: Used V4 and QIIME with assignment to OTU; '16 ref https://t.co/hvn5wYhF6n Showed ROC at AUC 0.85 for trtmt response #Tricon
11:59am February 24th 2017 via Hootsuite
Kashyap: Predicing gut microbiota signatures to preduct response to treatment after FMT #Tricon
11:57am February 24th 2017 via Hootsuite
Kashyap:Personalized nutrition, treatment, shows fig from '16 rev https://t.co/10sVTNELVR #Tricon
11:53am February 24th 2017 via Hootsuite
Kashyap: Short-chain fatty acids dictates 5-HT production, in a localized way. Tested subtracting carbohydrates, 5HIAA reduced #Tricon
11:49am February 24th 2017 via Hootsuite
Kashyap: Germfree (GF) mice, microbial colonization increases serotonin biosynthesis https://t.co/Xqz4lbqzjl #Tricon
11:46am February 24th 2017 via Hootsuite
Kashyap: Human gut microbiota alters levels of identifiable etabolites - host serotonergic 5-HIAAA. Serotonin (5-HT) enterochromaffin#Tricon
11:44am February 24th 2017 via Hootsuite
Kashyap: Intro w/traditional focus on the host organism's genome. 16S sequencing reviewed; pre-clinical model is into germfree mice #Tricon
11:42am February 24th 2017 via Hootsuite
Purna Kashyap (Mayo Clinic MI) Micorbiome-based precision medicine tools for personalized treatment approaches #Tricon
11:41am February 24th 2017 via Hootsuite
.@markgenome So nice to hear of the awesome work with cancer variant curation being done at @jacksonlab here at #tricon
8:33pm February 23rd 2017 via Hootsuite in reply to markgenome
Ortmann: Will need at least a 2-year leadtime for global launches. Pharma starts 4y before. #tricon
8:29pm February 23rd 2017 via Hootsuite
Ortmann: Country-wide implementation: Q’s Marketing and Sales presence worldwide, and need for personnel in Japan, China #tricon
8:28pm February 23rd 2017 via Hootsuite
Ortmann: The scope of CDx launch activities driven by pharma from a shopping list. Medical communication, KOL plan etc #tricon
8:26pm February 23rd 2017 via Hootsuite
#TriCon @QIAGEN Reinhard Ortmann directs CDx, points out launching a CDx is more than std IVD launch.
8:24pm February 23rd 2017 via Hootsuite
Well #tricon no power plugs in Moscone South=I’ll be off of Twitter, as I hate typing on glass slabs. But @qiagen on CDx is a nice talk!
8:21pm February 23rd 2017 via Hootsuite
Daber: Shows TP53 error rate on a per-base position along the gene - varies from 1% to no error at all. Plot of smple vs smple: no! #Tricon
8:02pm February 23rd 2017 via Hootsuite
Daber: People are now running parallel assays, but not getting reimbursed, to get the lower AFs. Are all regions sequenced equally? #Tricon
8:01pm February 23rd 2017 via Hootsuite
Daber: Pushing the LoD, '12 AFs were about 20%; in '17, 5% achievable. "Only w/custom algorithms can lower AF's be obtained" #Tricon
8:00pm February 23rd 2017 via Hootsuite
Daber: Showed deletion specificity by AF and length, ioptimizing from 1, 2-5, 6-10, 11-25, 25-50, 51-100bp bins #Tricon
7:59pm February 23rd 2017 via Hootsuite
Daber: Raw FASTQ's, run through pipeline to optimize and validate pipelines '13 ref https://t.co/0JZf7SQaQj #Tricon
7:58pm February 23rd 2017 via Hootsuite
Daber: FISH, IHC, NGS; also NGS technical challenges. Single gene assays <1%; challenging indels. Try to push a pipeline via sandbox #Tri
7:57pm February 23rd 2017 via Hootsuite
Daber: ImmunoRx - has different technologies dep on the drug; some NGS methods that may evolve for this #Tricon
7:56pm February 23rd 2017 via Hootsuite
Daber: On solid tumor, not a whole lot of change from '14 to '16. Mainly PD-1 that has changed for melanoma #Tricon
7:55pm February 23rd 2017 via Hootsuite
Daber: And now in '16: many more; drills into MPN prognostic significance from NCCN V2.2017 #Tricon
7:54pm February 23rd 2017 via Hootsuite
Daber: Precision diagnostics enables personalized medicine; test for ALK pos for example. 2014: Myeloid malignancie for MDS MPN AML #Tricon
7:53pm February 23rd 2017 via Hootsuite
Daber: Wet-lab and Dry-lab affect each other; will talk about personalizing var detection first #Tricon
7:52pm February 23rd 2017 via Hootsuite
