Zimmerman: Peformed over 300K tests last year; CLIA-lab in San Carlos CA; launched their first test in '11 (paternity), '13 for NIPT #Tricon
6:11pm February 23rd 2017 via Hootsuite
Bernard Zimmerman (Natera CA) Personalized custom panels for the detection of circulatory tumor DNA mutations #Tricon
6:10pm February 23rd 2017 via Hootsuite
Mason: Federated query structure: single db shared across the UK #Tricon
5:55pm February 23rd 2017 via Hootsuite
Mason: For interpretation, lists WuxiNextCODE, Illumina, a few others. Has a BCIP (Bioinf. Clin Interpret. Partnership) #Tricon
5:54pm February 23rd 2017 via Hootsuite
Mason: Genes: 186 gene panels, 3709 genes, and browse-able here: https://t.co/5Adyl5N1Aw #Tricon
5:53pm February 23rd 2017 via Hootsuite
Mason: 'Databases are not very good when the knowledge is in people's heads' Thus they crowdsource expertise #Tricon
5:51pm February 23rd 2017 via Hootsuite
Mason: 200 disorders are nominated as std of care; eligibility criteria established; data model std'ized for clinicians #Tricon
5:50pm February 23rd 2017 via Hootsuite
Mason: FF designated as an official 'diagnostic source' as a consensus 'Human Tissue Authority' statement (!) #Tricon
5:47pm February 23rd 2017 via Hootsuite
Mason: Sequencing cancer genomes: decided that FF tissue instead of FFPE; embedded the processing of FF by the pathologists #Tricon
5:46pm February 23rd 2017 via Hootsuite
Mason: 'delivery partners' include Seq Centr in Hinxton and MRC to handle biorepository; GE Clinical Interpret. Partnership (GeCIP) #Tricon
5:39pm February 23rd 2017 via Hootsuite
Mason: Driving toward a coordinated response with a unified healthcare system. 13 GMCs (Genomic Medicine Ctrs) w/3-5M people #Tricon
5:37pm February 23rd 2017 via Hootsuite
Mason: To leave a legacy of a database that is useful to the NHS. 50% cancer, tumor/germline. 21PB of data (2K years of mp3's) #Tricon
5:35pm February 23rd 2017 via Hootsuite
Mason:Also ethically transparent programme based on consent; kick-start the dev of a UK genomics industry, trials, new Dx #Tricon
5:33pm February 23rd 2017 via Hootsuite
Mason:Objectives are: rare inh disease, cancer, pathogens; referring new diagnoses to NHS (new medical insight) #Tricon
Mason: David Cameron in Dec '13. Setup July '13, working group Prof Sally Davies est a strategic priorities working gp #Tricon
5:32pm February 23rd 2017 via Hootsuite
Joanne Mason (Genomics UK) The 100,00 Genomes Project: transforming the UK's National Health Service #Tricon
5:30pm February 23rd 2017 via Hootsuite
Lek: Re-assessment of previous reports of pathogenicity: abnormal liver fn. But var >1% in latino population, used to reassess #Tricon
5:15pm February 23rd 2017 via Hootsuite
Lek: Graphed diversity of their dataset; able to go from 11.9k down to 132 rare missense or truncating. Found likely causative gene #Tricon
5:11pm February 23rd 2017 via Hootsuite
Lek: Graphing haploinsufficiency, figure from '16 Nature https://t.co/HpxPCXKvpt #Tricon
5:09pm February 23rd 2017 via Hootsuite
Lek: ID genes with significant depletion of varation: observed vs expected; loss of function dpressed observations #Tricon
5:08pm February 23rd 2017 via Hootsuite
Lek: https://t.co/xWEhLl7xGq now at 70K views/wk #Tricon
5:06pm February 23rd 2017 via Hootsuite
Lek: Scalable pipeline for joint discovery: from 925TB of BAMs to 3.3TB of final VCFs. CPU days: 15.6K days, 950K, then 13.6 at VCF #Tricon
5:05pm February 23rd 2017 via Hootsuite
Lek: ExAC aggregated and called 92K exomes; with a subset of 60,706 'reference' samples (high-quality, unrelated, consented) #Tricon
5:03pm February 23rd 2017 via Hootsuite
Lek: When he arrived a few years ago: 500K exomes have been sequenced; silo'ed by project, inconsistently processed. #Tricon
5:02pm February 23rd 2017 via Hootsuite
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
