Hindson: For immune profiling: gene exp and paired TCR/BCR from the same cell. #AGBT18
4:24pm February 13th 2018 via Hootsuite
Hindson: Shows a 3d plot of single-cell RNA-seq data; est 10M cells in '16 analyzed; 100's of M in '19. Human Cell Atlas an example #AGBT18
4:23pm February 13th 2018 via Hootsuite
Hindson: Has a software called 'Supernova 2.0' for low-cost plant and animal de-novo genome assembly (i.e. donkey) #AGBT18
4:21pm February 13th 2018 via Hootsuite
Ben Hindson (10X Genomics workshop): Gave a brief 3y history, they are hiring https://t.co/hWgcZV2dFK and have over 500 installs #AGBT18
4:18pm February 13th 2018 via Hootsuite
Mason: Illumina read data - couldn't find pathogen samples in the swamped human DNA reads #AGBT18
1:06pm February 13th 2018 via Hootsuite
Mason: 65/66 agreement. 1/66: low-confidence path lab potential FP. #AGBT18
1:05pm February 13th 2018 via Hootsuite
Mason: From clinical samples: bead beat, total 50 hands-on, 90 min. Six samples, call from path, from qPCR, and H&S #AGBT18
Mason: What about human reads? 'no cross-reaction with human DNA' 5M GM19240 cells, showed replicate comparison R2=0.91 #AGBT18
1:03pm February 13th 2018 via Hootsuite
Mason: Showed box plots, able to get 10 cell detection as a conservative boundary. #AGBT18
Mason: Shows input cell number, simultaneous detection of 10 microorganisms at <1000 cells/mL from 1 sample, same tube #AGBT18
1:02pm February 13th 2018 via Hootsuite
Mason: 18 captures probe pairs per spp; for RNA, collab at Broad for ZymoBIOMICs stds and virus #AGBT18
1:01pm February 13th 2018 via Hootsuite
Mason: No library prep, <30m hands-on, 4 h sample to answer. took a panel of 11 organisms and HCV-1a virus (RNA) #AGBT18
1:00pm February 13th 2018 via Hootsuite
Chris Mason: Infections are 'rarely simple' Samonella, HIV+mycobacteria, TB and HCV etc. Ideally - universal, fast, cheap, accurate #AGBT18
12:59pm February 13th 2018 via Hootsuite
Chris Mason: Lots of tools have a hard time. 1 FASTQ in 12 tools: https://t.co/ZeuH28bppc Yikes. #AGBT18
12:58pm February 13th 2018 via Hootsuite
Chris Mason: Something like 70 tools; NIST effort https://t.co/EQqict3IOF #AGBT18
12:57pm February 13th 2018 via Hootsuite
Mason: Amount of antibiotic resistance - not if but when. Video https://t.co/Gvx7tSvZOc #AGBT18
12:55pm February 13th 2018 via Hootsuite
Mason: 'You don't pick 16S' for closely related spp'. Could we get very fast metagenomic answer? <6h is possible. But div time 20min #AGB
12:54pm February 13th 2018 via Hootsuite
Mason: Pathogens in space, published in late '17 https://t.co/QQztmQR11f #AGBT18
12:52pm February 13th 2018 via Hootsuite
Mason: With metagenomics "people love sampling everywhere". Mayor of Baltimore getting in on it. #AGBT18
12:51pm February 13th 2018 via Hootsuite
Chris Mason (Weill-Cornell Univ NY) Rapid and accurate cross-linking... (missed the title, oops) #AGBT18
12:50pm February 13th 2018 via Hootsuite
Beechem: med to large panels 22h. 20M to 80M reads, no library prep, 31h for 80M. Has 3 posters and talk tonight #AGBT18
12:49pm February 13th 2018 via Hootsuite
Beechem: Showing sped-up video of repeated cycles in an ordered array. TAT: 2.5h for infectious disease; small-med cancer panel 9h #AGBT18
12:47pm February 13th 2018 via Hootsuite
Beechem: Lam collaboration - semiconductor research. 9,800 employees, 34B market cap#AGBT18
12:46pm February 13th 2018 via Hootsuite
Beechem: TP53 mutation was c.422G>A. Error rate lower than Swift/MiSeq (0.11% vs 0.86%, 0.59% vs 0.97%) #AGBT18
12:45pm February 13th 2018 via Hootsuite
Beechem: Shows at #AGBT18 the sequencing build up of signal around a single base mutation. https://t.co/EZqhu9Fn3E
12:44pm February 13th 2018 via Hootsuite
Beechem: Hyb & Seq workflow concept - six bases at a time, interrogate the ID via exchange reaction w/colored dyes 1min color #AGBT18
12:42pm February 13th 2018 via Hootsuite
Beechem: Designed to be the simplest workflow, clinical grade sequencer. Tonight - Gene exp, mutation and CNV simultaneously #AGBT18
12:40pm February 13th 2018 via Hootsuite
Beechem: Shows key development in 2017: collaboration with @mason_lab and others; Lam Research co-development; liquid biopsy #AGBT18
Beechem: Hyb & Seq update: "Cancer Panels and Ordered Arrays". Shows photos from last year's live demo with @coregenomics last year#AG
12:39pm February 13th 2018 via Hootsuite
Davies: Across 12 ROs, 32 signalling pathways in-situ using DSP, showed up-regulation of PI3K-AKT at protein level. Next: 1000 RNAs #AGBT18
12:36pm February 13th 2018 via Hootsuite
Davies: Likes DSP due to quant nature (DAPI staining and counting nuclei). Shows ROI selection, CD45 staining, shows unpubl data #AGBT18
12:35pm February 13th 2018 via Hootsuite
Davies: Pt-matched melanoma FFPE brain and extracranial mets - will elaborate on this work at AACR. Single pt data shown #AGBT18
12:34pm February 13th 2018 via Hootsuite
Davies: Historical OS ~4mos. Improving with targeted / immune Rx, less effective than in non-CNS disease. #AGBT18
12:32pm February 13th 2018 via Hootsuite
Davies: Primary risk for melanoma pts - brain metastasis. Up to 40% pts at time of presentation, 70% at death. Common Rx failure #AGBT18
Davies: Validated regions loss of immune cells via DSP, including 'markers we hadn't thought of using before' #AGBT18
12:31pm February 13th 2018 via Hootsuite
Davies: Showed DSP data for P-PTEN, P-AKT, P-4EBP1; still hetergeneity across PTEN+/- areas. #AGBT18
12:30pm February 13th 2018 via Hootsuite
Davies: Presented data at SITC '17, via microdissection of DNA, RNA, protein. Applying DSP: shows PTEN + area, null area. #AGBT18
12:28pm February 13th 2018 via Hootsuite
Davies: PTEN on IHC shown. Sometimes one tumor had drastic hetergeneity. Thus - DSP can look at differences in PTEN #AGBT18
12:27pm February 13th 2018 via Hootsuite
Davies: Loss of PTEN causes resistance to checkpoint inh. '16 ref https://t.co/WTLc0cizP0 now a clin trial #AGBT18
12:26pm February 13th 2018 via Hootsuite
Davies: #AGBT18 '10 ref on BRAFi https://t.co/lPcJkiw3SI
12:25pm February 13th 2018 via Hootsuite
Davies: BRAF actively suppress immune response. BRAFi up-regs antigen exp, loweres immunosupp cytokines, ups TILs #AGBT18
12:24pm February 13th 2018 via Hootsuite
Davies: Also in pre-cancerous; necessary but not sufficient. PI3K/AKT. PTEN supp loss in 10-30%. He's been studying roles in resist#AGBT18
Davies: For melanoma: BRAF/NRAS explain activation in about 80% of ptx. Every cutaneous melanoma goes through this pathway. #AGBT18
12:22pm February 13th 2018 via Hootsuite
Davies: For biomarkers to personalize Rx: molecular and immune markers; better handle on hetergeneity. Maximize analysis of FFPE #AGBT18
Davies: Approvals from 0 pre-'98; 2011-2016 10 approvals. Targeted Tx BRAF DCR >90%, resp 1y. ImmunoRx: ORR10%-60% resp 2y #AGBT18
12:20pm February 13th 2018 via Hootsuite
Davies: In melanoma, no effective therapies until an improved understanding of the biology. TCGA confirmed: higher mut burden #AGBT18
12:18pm February 13th 2018 via Hootsuite
Michael Davies (MD Anderson) Intergrated interrogation of oncogenic signaling pathways, immunology, and heterogeneity in cancer #AGBT18
12:17pm February 13th 2018 via Hootsuite
Beechem: Shows almost 30 tech access participants. Remote control of the DSP from MDAnderson. DSP launches Q4 '18 for early access #AGBT18
Beechem: Shows impressive pathway information as a cell-type specific datasets. 'Pathways in space'. 'And just the beginning.' #AGBT18
12:15pm February 13th 2018 via Hootsuite
Beechem: Resolves 1028 mRNAs in a lymphoid tissue. Shows difference in expression data in epithelium, germinal cetner, CD3 area #AGBT18
12:13pm February 13th 2018 via Hootsuite
