Lek: Shows photos of two small kids of a rare disease, unaffected parents. Number of missense or protein-truncating is 11,928. #Tricon
5:01pm February 23rd 2017 via Hootsuite
Lek: Focus on improving Dx on rare muscle disease patients. 'Which of the 3M variants cause disease?' #Tricon
Monkol Lek (Mass Gen Hosp MA) Using exome aggregation (ExAC) dataset for the interpretation of rare variants in Mendelian diseases #Tricon
4:59pm February 23rd 2017 via Hootsuite
Unbound probes? Martin (Morin): They don't show up, or at bottom, because they are so short. Payloads are neutrally charged too. #Tricon
4:20pm February 23rd 2017 via Hootsuite
(FYI, Two Pore Guys is hiring a lot of commercial people, if you are in the Bay Area. https://t.co/ufLVYw75ci #Tricon )
4:19pm February 23rd 2017 via Hootsuite
How does this compare to ONT? Martin (Morin) Not sequencing DNA; this is amplicon detection, via solid state pores #Tricon
4:18pm February 23rd 2017 via Hootsuite
Martin (Morin) Probe payloads are very different than the target. #Tricon
4:17pm February 23rd 2017 via Hootsuite
dsDNA through pore:LAMP for ds is hard, probes? Martin (Morin):HDA, SDA, TwistDx, PNA, others can be quickly melted #Tricon
4:16pm February 23rd 2017 via Hootsuite
Partner FDA discussions? Heller:Not market-ready device yet, early customers is agriculture w/very high volumes. FDA is marketing #Tricon
4:15pm February 23rd 2017 via Hootsuite
Heller: end-user price for reader targeted about $500. #Tricon
4:14pm February 23rd 2017 via Hootsuite
Costs? Heller: COGs $3-5/strip. Multiplex is 25-50 chips/strip, COGs much higher ($30-40, but much more tests) Reader: tens of $ #Tricon
4:13pm February 23rd 2017 via Hootsuite
Q:How to quant? Martin (oops, should read Morin) is using basically a known calibrant, only semi-quantitative #Tricon
4:11pm February 23rd 2017 via Hootsuite
Heller: Regulatory is partner-borne. Master files for approvals provided. New biomarkers approval handled by the partner. #Tricon
4:09pm February 23rd 2017 via Hootsuite
Heller: The exclusivity is based on the target, not the assay; that can be changed; various dimensions of exclusivity #Tricon
4:08pm February 23rd 2017 via Hootsuite
Heller: Everyone gets exclusivity, in exch for 5%. Are in clinical study with UCSF now. A test-at-home assay for cfDNA from urine #Tricon
4:07pm February 23rd 2017 via Hootsuite
Heller: Partner may negotiate anywhere from 20% to 80% per test; depending on the price sens of the market (i.e. Ag) #Tricon
4:05pm February 23rd 2017 via Hootsuite
Heller: The business is the platform, and existing assays easily ported over; mfg of reader and strips. Shows example terms #Tricon
4:04pm February 23rd 2017 via Hootsuite
Dan Heller (Two Pore Guys con't) Non-optical removes barriers to adoption: inexpensive, battery operated, large menu of assays #Tricon
4:02pm February 23rd 2017 via Hootsuite
Martin: Complex passing through pore is detected with/without bound ligand. 3log dyn range, low pM LOD, can do kinetic on/off rates #Tricon
4:00pm February 23rd 2017 via Hootsuite
Martin: Complex passing through pore is then detected with/without bound ligand. #Tricon
3:58pm February 23rd 2017 via Hootsuite
Martin: Can use for binding: DNA w/linker on the probe, with a binding domain molecule (aptimer, peptide, whatever), target analyte #Tricon
3:57pm February 23rd 2017 via Hootsuite
Martin: Shows list of potential analytes, from environmental samples to small molecule drugs. Reagents are dried, stablized on strip #Tricon
3:56pm February 23rd 2017 via Hootsuite
Martin: Alternatively, can place multiple chips per strip to increase sample throughput. #Tricon
3:54pm February 23rd 2017 via Hootsuite
Martin: Few cycles of amp, not many errors; multiplexing can vary the payload, 5 molecules per pore can be detected #Tricon
Martin: Math model in real-time, 5-10 min time to result; LOD <50 targets; 1% sens; accuracy 2%, can multiplex to 50/chip #Tricon
3:52pm February 23rd 2017 via Hootsuite
Martin: KRAS in whole blood; spiked G12D, 89bp target. Used 'unbiased ampl' (not explained), add diff probe payloads #Tricon
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
