Patterson: Cp to IHC - amount of expertise required is much reduced; 12 markers instead of 2. Stable for weeks to years, time 3h #NGDx15
5:33pm August 18th 2015 via Hootsuite
Patterson: Their IncellPrep Tissue Suspension: take fresh tissue, make cell suspension directly or from FFPE. #NGDx15
5:32pm August 18th 2015 via Hootsuite
Patterson: For CDx - they can lay out cancer pathways looking at RNA, DNA and protein. Breast, Lung, Head & Neck. #NGDx15
5:31pm August 18th 2015 via Hootsuite
Patterson:Looking at oncogene overexpression, and morphology measurements. on 2 dimensions #NGDx15
5:30pm August 18th 2015 via Hootsuite
Patterson:Shows ''OncoTect 3Dx-M" - "The slide-less Pap" with low-grade cp to high-grade lesion, incorporating ploidy, morphology #NGDx15
5:29pm August 18th 2015 via Hootsuite
Patterson: RNA on Y-axis, DNA in cell-cycle on X; Oncogene overexpression on G0 in low-grade; high-grade shift to right #NGDx15
5:28pm August 18th 2015 via Hootsuite
Patterson: For HPV OncoTect CE-IVD - comparing performance with HPV DNA, similar negative predictive value. #NGDx15
5:27pm August 18th 2015 via Hootsuite
Patterson: Simultaneous ID of DNA, RNA, protein from single-cells. Already out on the market. They make kits with existing flow tech #NGDx15
5:26pm August 18th 2015 via Hootsuite
Patterson:Platform agnostic, assay-times of 3h, without need to sort cells or purify nucleic acids. #NGDx15
5:25pm August 18th 2015 via Hootsuite
Patterson: Shows movie - Ab binding, can permeabilize, mRNA and intercalating dye for DNA cell-cycle, proliferation. #NGDx15
Patterson: Have HPV, HIV, HCV, Cervical and Anal cancers. Stains for protein, RNA and cell morphology #NGDx15
5:24pm August 18th 2015 via Hootsuite
Patterson: Taking 'single cell diagnostics to the next level'. Creating a 'universal sample' - CTC, FNA, FFPE enabled. #NGDx15
5:23pm August 18th 2015 via Hootsuite
Bruce Patterson (InCellDx CA) "Liquid-biopsy technology generates a cell suspension sample out of fresh or FFPE tissue" #NGDx15
.@crushaFoz Do a search under "#NGDx15 Velculescu" for notes on his liquid biopsy talk...
5:12pm August 18th 2015 via Hootsuite in reply to crushaFoz
Smith: 'NGS within 2y will be technique of choice in cancer care' #NGDx15
3:34pm August 18th 2015 via Hootsuite
Smith:Digital PCR - looking at rare events (RainDance). #NGDx1
3:33pm August 18th 2015 via Hootsuite
Smith:WES: seeing routine clinical practice. RNA-Seq, methylation - but we don't understand the role of methylation #NGDx15
3:32pm August 18th 2015 via Hootsuite
Smith:WGS - what about storage of the data? They do 5kb mate-pairs and 2GB may be sufficient. They look for HPV integration #NGDx15
3:30pm August 18th 2015 via Hootsuite
Smith: QIAGEN integrated end-to-end solution. But the middle box - 'not a platform at all'. #NGDx15
3:28pm August 18th 2015 via Hootsuite
Smith: Helicos bankrupt; Oxford has improved 'a lot'; in time 'it could mature'. GNUBio, purchased by BioRad; NabSys optical mapping #NGDx15
Smith: Briefly describes Complete Genomics (CGI), now BGI, Revolocity and benchtop coming out this Fall. '100's of exomes/d' #NGDx15
3:27pm August 18th 2015 via Hootsuite
Smith: (PacBio promised $100 by 2014 at AGBT 2008.) #NGDx15
3:25pm August 18th 2015 via Hootsuite
Smith: @PacBio - 85% accurate, output 'dismal and limited improvement becoming available'. Remembers the promise from 2008 at AGBT #NGDx15
Smith: Lower input for assay (AmpliSeq). Room for throughput improvement - hopeful #NGDx15
3:23pm August 18th 2015 via Hootsuite
Smith: Some weaknesses: ePCR, homopolymers, trying to play catchup. Strengths: turnaround time, Ion Chef, flexible output #NGDx15
Smith:Another issue: short instrument cycle time. @iontorrent potential competition. Explains chip technology based on pH change #NGDx15
3:22pm August 18th 2015 via Hootsuite
Smith: High throughput machines need sufficient samples. Feels that customer service lacks due to 'lack of competition' #NGDx15
3:21pm August 18th 2015 via Hootsuite
Smith: Scaling output from 15GB to 120GB to 1000GB to 1800GB. @illumina 'completely controls the seq space' #NGDx15
3:20pm August 18th 2015 via Hootsuite
Smith:Replacement instruments: from 1GB/run, to 80GB/run, to 1TB/run. 'They should have focused on the $100 genome' #NGDx15
3:19pm August 18th 2015 via Hootsuite
Smith: HiSeq 2000 (2009). Next improvement was patterned flowcells (2015) HiSeq 4000/5000. 5y depreciation not helpful every 2-3y #NGDx15
3:18pm August 18th 2015 via Hootsuite
Smith: The Genome Analyzer: barely 1Gb, short 25bp, bridge amplification easy to do. Blocked nucleotides. Runs took several days. #NGDx15
3:17pm August 18th 2015 via Hootsuite
Smith: Showed 191bp reads, Watson genome for about $1M. 20Mb/run expanded to 500Mb/run 'then stopped'. #NGDx15
3:15pm August 18th 2015 via Hootsuite
Smith: 454: 'It was Star Trek'. "Now in the Smithsonian, next to a cave man". Only 2y later. Reviews ePCR, pyrosequencing #NGDx15
3:13pm August 18th 2015 via Hootsuite
Smith: Picotitre plates borrowed tech from telecom industry; clusters on slides a second strategy. And: massively parallel seq #NGDx15
3:12pm August 18th 2015 via Hootsuite
Smith: Only a portion of the genome was mapped. 10^13 molecules/reaction. 10uL reactions and attendant reagents. #NGDx15
3:10pm August 18th 2015 via Hootsuite
Smith: The AB 3700 'was a big deal'. In 1978, pBR322 wasn't sequenced yet. 330 at Celera. 99.99% accurate. 3 mo sequencing. #NGDx15
3:09pm August 18th 2015 via Hootsuite
David Smith (Mayo Clinic MN) "Next-Generation Sequencing Platforms: where we are and where we are going" #NGDx15
3:07pm August 18th 2015 via Hootsuite
Velculescu: Moving from tissue to liquid; from single point mutations to dynamic genomes; from clinical to molecular response #NGDx15
3:02pm August 18th 2015 via Hootsuite
Velculescu: Approaches for early detection of cancer - 0.75% circulating tumor DNA. #NGDx15 2014 paper: http://t.co/fnXFO4DbRT
3:01pm August 18th 2015 via Hootsuite
Velculescu: Somatic rearr associated with MET amplification detected in PGDx assays. #NGDx15
3:00pm August 18th 2015 via Hootsuite
Velculescu:Detection of genetic resistance or sensitivity after targeted therapy. 2013 ref: http://t.co/B8Z7l8wgML #NGDx15
2:58pm August 18th 2015 via Hootsuite
Velculescu: Can detect six months earlier for pancreatic cancer Sausen 2015 Nature Comm http://t.co/6LDiBeItbL #NGDx15
2:57pm August 18th 2015 via Hootsuite
Velculescu: Fig. from Diehl et al Nature Med 2008 http://t.co/eLKwBRKSji No plasma detection - disease-free. In plasma - poor prog #NGDx15
2:55pm August 18th 2015 via Hootsuite
Velculescu: Dev a panel of 60 genes, and about 12 rearr's. About 10% detection in blood. NSCLC can be ID'd in sputum too. #NGDx15
2:54pm August 18th 2015 via Hootsuite
Velculescu: (Data in same Leary 2012 paper.) ERBB2 ampl. observed in a Colorectal cancer pt. Observed rearr in tumor and plasma #NGDx15
2:53pm August 18th 2015 via Hootsuite
Velculescu: Actionable mutations via cell-free DNA (where 1/4 of lung ca fall - not enough tissue). ERBB2 amplification via plasma #NGDx15
2:52pm August 18th 2015 via Hootsuite
Velculescu: Monitoring tumor progression over time - can be done with CNV, point mutations, or rearr's #NGDx15
2:51pm August 18th 2015 via Hootsuite
Velculescu: Found large-scale rearrangements via PARE.Detectable across tumor types, and variety of structural alterations #NGDx15
2:49pm August 18th 2015 via Hootsuite
Velculescu: Looked at 10 pts directly in blood, Science Trans Med 2012 looking at chromosome arms http://t.co/X0bS72w951 #NGDx15
2:46pm August 18th 2015 via Hootsuite
Velculescu: The challenge is finding the rare mutation in blood, including digital karyotyping and PARE; tumor-spec alterations #NGDx15
2:45pm August 18th 2015 via Hootsuite
