Martin: 1000's of events measured in minutes. Semi-quant assay. Can be done quantitatively if amplification-free #Tricon
3:49pm February 23rd 2017 via Hootsuite
Martin: Bulk is needed: for ease of detection from bkgnd. Shows electrical signal over time. #Tricon
3:48pm February 23rd 2017 via Hootsuite
Martin: Only a few cycles are needed (no endpt), 2PG probe-payload binds to spec target seq - inc specificity and to increase bulk #Tricon
3:47pm February 23rd 2017 via Hootsuite
Martin: Nasal swab, cheek swab, urine, serum plasma etc. Background does not need removal. Ampl. is via isothermal or conventional #Tricon
Martin: No optics, no chemistry since it is solid state. Showed the multiple interrogations over time #Tricon
3:45pm February 23rd 2017 via Hootsuite
Martin: Silicon chip, 30nm pore, voltage pulls molecules through it, impeding current. Single 'event' has depth, duration #Tricon
3:44pm February 23rd 2017 via Hootsuite
100's of amplicons are detected across the pore, shown on a screen. They used a Y-chr marker for their amplification #Tricon
3:42pm February 23rd 2017 via Hootsuite
Starts with a 2 minute video: with demo of saliva, lysis, application of sample, 7m amplification and detection. Manual push #Tircon
Trevor Marting, Dan Heller (Two Pore Guys CA) Handheld, single-molecule sensitive diagnostic platform #Tricon (Two guys from Two Pore Guys)
3:40pm February 23rd 2017 via Hootsuite
Chow: ID of different taxa w/PhyloChip compared to V4 with abundance shifts. (Although would you do only V4 for this measurement?) #Tricon
3:27pm February 23rd 2017 via Hootsuite
Chow: Shows control data from NIST (non-16S genes); shows sens down to pM conc across 44 samples. #Tricon
3:26pm February 23rd 2017 via Hootsuite
Chow: Sampling and pooling: 1ug stool typically has 1T 500bp fragments; to sequence 1M reads is only 1 millionth of the population #Tricon
3:24pm February 23rd 2017 via Hootsuite
Chow: Other probes are for discovery; 60K operational taxonomic units at once, regardless of community complexity #Tricon
3:23pm February 23rd 2017 via Hootsuite
Chow: StrainSelect their other database. PhyloChip is a hardware tool, hyb array in 4th iteration. All 16S rRNA regions; 1M probes #Tricon
3:22pm February 23rd 2017 via Hootsuite
Chow: Offer strain-level annotation: GreenGenes db, most referenced; comprehensive for clinically relevant microbiome data #Tricon
3:21pm February 23rd 2017 via Hootsuite
Chow: From sample collection through isolation and data processing, all validated. 16S Phylochip product #Tricon
Chow: 16S annotation incomplete, inconclusive; OTU-based observations depend on other co-sampled spp; sequencing data incomplete #Tricon
3:20pm February 23rd 2017 via Hootsuite
Chow: Focus on their research services, rather than their drug dev/therapy side. Lists challenges... #Tricon
3:19pm February 23rd 2017 via Hootsuite
Cheryl-Emiliane Chow (Second Genome) Improving the utility of microbiome research #Tricon
3:18pm February 23rd 2017 via Hootsuite
Janku: Data suggests increased amounts of mutant DNa in plasma (BEAMing) are assoc'd with shorter survival in metastatic ca #Tricon
3:13pm February 23rd 2017 via Hootsuite
Janku: Shows a great chart from Diehl on the input in ng and % allele frequency called 'the numbers game' #Tricon
3:10pm February 23rd 2017 via Hootsuite
Janku: Prospective work by '16 ref https://t.co/FZPxFlHOPe shows four months head-start on detection of resistance. #Tricon
3:09pm February 23rd 2017 via Hootsuite
#Tricon MT @TrevorWBrown: @daleyuzuki of @SeraCare giving a talk in the ccfDNA session on ctDNA controls. https://t.co/ucUiyDBtpf
3:07pm February 23rd 2017 via Hootsuite
Janku: Urine '17 ref https://t.co/pywnrYos34 Concordance betwen urine cfDNA and FFPE tissue 75-89%. Volume dependency #Tricon
3:06pm February 23rd 2017 via Hootsuite
Janku: Agreements from 93-95%, goes into discrepancies between FFPE and ddPCR #Tricon
3:03pm February 23rd 2017 via Hootsuite
Janku: Showing concordance between KRAS multiplex via ddPCR to FFPE '16 Ann Oncol https://t.co/Spvxhk1Nec #Tricon
3:02pm February 23rd 2017 via Hootsuite
Janku: Plasma positive DNA discrepant compared to BEAMing or ddPCR found 100% concordance, so the prior discrepency was biological #Tricon
2:59pm February 23rd 2017 via Hootsuite
Janku: Shows Idylla data for BRAF V600E, TAT of 1h 15m. Found 88% agreement between cfDNA by Idylla vs FFPE #Tricon
2:58pm February 23rd 2017 via Hootsuite
Janku: Reviewed use for early det, Rx guidance, and surveillance. BEAMing data chart from '15 ref https://t.co/sYIeo2KK9I #Tricon
2:57pm February 23rd 2017 via Hootsuite
Janku: Clinical review of ctDNA '15 https://t.co/faJdFvSAsM #Tricon
2:55pm February 23rd 2017 via Hootsuite
Filip Janku (MD Anderson CC TX) Liquid biopsies in precision oncology #Tricon
2:53pm February 23rd 2017 via Hootsuite
Patel: Needing both strand sequencing; method from Univ WA PNAS '12 https://t.co/jPqUaI1jWM presented at #Tricon
2:48pm February 23rd 2017 via Hootsuite
Patel: Pre-existing modes of damage - De-amination causing C->T; oxidation causes G->T via guanine to 8-oxo-guanine by storage #Trico
2:45pm February 23rd 2017 via Hootsuite
Patel: Early detection - you need broad coverage. Shows chart from '15 ref https://t.co/eUl5Cf0gOo #Tricon
2:44pm February 23rd 2017 via Hootsuite
Patel: Response is not immediate via CT scans; slow enough w/chemo, 'notoriously slow w/immunotherapy' #Tricon
2:41pm February 23rd 2017 via Hootsuite
Patel: Nonresponder shows PIK3CA E542K rising from day 0 trhough day 45, then slow decline. Data overlaid w/RECIST tumor burden data #Tricon
Patel: Immunotherapy is now in vogue; some remarkable, durable responses. Shows data of responder KRAS Q61R declineing 40d on trtmnt #Tricon
2:39pm February 23rd 2017 via Hootsuite
Patel: Showed pre- and post-Rx KRAS mutation in blood, at 50d undetectable going out 5 mos. #Tricon
2:37pm February 23rd 2017 via Hootsuite
Patel: Case study: 75y/o F w/Stg I lung adenocarcinoma; 2.9x2.5cm tumor; KRAS G13R; treated with stereotactic body RT #Tricon
2:36pm February 23rd 2017 via Hootsuite
Patel: Able to get <1b in 100K error rate; 70 amplicons in 35 genes; $20 cost/1mL plasma; can run 100 smpls/HiSeq lane; 1 tube assay #Tri
2:34pm February 23rd 2017 via Hootsuite
Patel: Ref shows spiked-in 0.2% mutant KRAS G12S; used overlapping paired-end sequencing to clean-up errors, along w/barcoding. #Tricon
2:30pm February 23rd 2017 via Hootsuite
Patel: Mainly focuses on PCR-based approaches; uses ultra-deep NGS amplicon approach; 10K to 50K seq depth https://t.co/e4bBCBvHjv #Tricon
2:29pm February 23rd 2017 via Hootsuite
Patel: Their lab mainly focuses on PCR-based approaches; uses ultra-deep NGS amplicon approach; 10K to 50K sequencing depth #Tricon
2:26pm February 23rd 2017 via Hootsuite
Patel: Reviews methods: PCR: mutant enrichment (COLD, LNA/PNA, ARMS) and compartmentalization (dPCR, BEAMing) NGS: Amplicon, hyb #Tricon
2:23pm February 23rd 2017 via Hootsuite
Patel: Cp to ctDNA where at 2w the response marker drops. ctDNA needs to be thought abt differently than protein markers #Tricon#Tricon
2:21pm February 23rd 2017 via Hootsuite
Patel: Shows slide of response markers to chemo cycle #'s, and weeks on Rx: imaging vs protein markers, response lowers slowly #Tricon
2:20pm February 23rd 2017 via Hootsuite
Patel: Protein markers are secreted from live cancer cells; ctDNA is released from dying cancer cells. #Tricon
2:19pm February 23rd 2017 via Hootsuite
Patel: Emphasis today will be on treatment response assesment, and early detection. #Tricon
2:17pm February 23rd 2017 via Hootsuite
Abhijit Patel (Yale CT) Technological challenges and clinical applications of ctDNA #Tricon
2:16pm February 23rd 2017 via Hootsuite
Krishnan: NanoVita instrument, 40min time, shows cfDNA capture and quant in lung, panc cancer pts. Exosomes and cfDNA #Tricon
1:17pm February 23rd 2017 via Hootsuite
