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
Bob Daber (Gnosity Consults) Pushing the limits - challenges of somatic variant detection #Tricon
7:51pm February 23rd 2017 via Hootsuite
Mockus: Future, Maine Cancer Genomics will sequence 1800 pts over 3yrs, mech for clinical review https://t.co/0WSgAU4Be5 #Tricon
7:44pm February 23rd 2017 via Hootsuite
Mockus: Drug classes controlled vocabulary for target spec, hyperlinked to PubMed sources Glossary: https://t.co/22HIgszZTZ #Tricon
7:42pm February 23rd 2017 via Hootsuite
Mockus: Setup Cron jobs for automated updates. Long table of decision matrix posted here: https://t.co/Zn67kemymE #Tricon
7:39pm February 23rd 2017 via Hootsuite
Mockus: Even PDX and other functionalities (unmet needs, expression etc.) Easy to build, but hard to keep updated. #Tricon
7:37pm February 23rd 2017 via Hootsuite
Mockus: Genes, variants, clinical trials; Rx approach, disease oncology; CNVs, SNVs, Fusion, expression data is all there. #Tricon
7:36pm February 23rd 2017 via Hootsuite
Mockus: @jacksonlab has made their CKB open to the public, for not-for-profit use https://t.co/5ZZxofquU6 (Amazing. Kudos!) #Tricon
7:35pm February 23rd 2017 via Hootsuite
Mockus: JAX has a CKB (clinical KB, literature-based), also patient curated kb (tumor type and alteration data) #Tricon
7:34pm February 23rd 2017 via Hootsuite
Mockus: Guidelines also from AMP/CAP, '17 JMD https://t.co/XnDcN5zbfc #Tricon
7:31pm February 23rd 2017 via Hootsuite
Mockus: Guidelines came out recently: WashU's CiVIC '17 Nature Gen https://t.co/BfmWr1nZKY MSKCC too #Tricon
7:30pm February 23rd 2017 via Hootsuite
Mockus: 2nd need is guidelines ofr interpretation (actionability) - but what does that include? #Tricon
7:28pm February 23rd 2017 via Hootsuite
Mockus: First need: nomenclature - SNV, SNP, Ins, Del, indel, dup. It can be an accounting problem (+/- strands etc) #Tricon
7:27pm February 23rd 2017 via Hootsuite
Mockus: How to find which somatic var's important? 400 gene panel may have 2000 var's, 300 protein, 25 db mapped, 3-5 'actionable' #Tricon
7:26pm February 23rd 2017 via Hootsuite
Mockus:and Names of vendors with connections: QIAGEN, N-of-One, ArcherDx, PierianDx etc. about 20-25. #Tricon
7:24pm February 23rd 2017 via Hootsuite
Mockus: Showed seven major nodes as a network, not very well connected. Vendors: bioinf, content, dx, integrator, platforms #Tricon
7:23pm February 23rd 2017 via Hootsuite
Mockus: Did a data map of data silos, color coded by type (pharma, cancer, non-profit, dx lab etc) and size - interesting! #Tricon
Susan Mockus (Jackson Laboratories CT) Creating standards and transparency for interpretation of somatic variants #Tricon
7:22pm February 23rd 2017 via Hootsuite
Zimmerman: Next: RUO, optimize process, costs; std protocol to remove re-pooling for each bespoke panel. H2 '17 launch internal #Tricon
6:30pm February 23rd 2017 via Hootsuite
Zimmerman: May be able to ID adjuvant chemotherapy-sensitive disease. cfDNA branch rise may predict metastatic recurr #Tricon
6:28pm February 23rd 2017 via Hootsuite
Zimmerman: Showed SCC StgI pts, 15/16 able to pick up trunk mutations; 50% detected on the trees. Levels clearly lower. #Tricon
6:25pm February 23rd 2017 via Hootsuite
Zimmerman: Showed large sens/spec chart. Onto TRACERx CRUK to monitor lung-cancer evolution, building trees https://t.co/bjYzKFKmVN #Tricon
6:24pm February 23rd 2017 via Hootsuite
Zimmerman: Per-sample cost is on the order of $100; showed assay sensitivity by spike titrations; 99% sens at 0.1% AF #Tricon
6:20pm February 23rd 2017 via Hootsuite
Zimmerman: Targeted 20-30 SNVsper pt (>100 possible) for max sens. 40K read depth; use synth mutant spikes, 33ng input #Tricon
6:17pm February 23rd 2017 via Hootsuite
Zimmerman: SNV sens claimed single-cell down to 20% AF #Tricon
6:15pm February 23rd 2017 via Hootsuite
Zimmerman: Shows T21 data from gDNA and single-cell; 28k-plex mmPCR; shows Br ca bulk and single-cell very similar #Tricon
Zimmerman: Natera's Panorama 'fastest growing molecular test in history' Detect CNV to 2.5% https://t.co/kH6igjQKfD #Tricon
6:13pm February 23rd 2017 via Hootsuite
