Smith: Size-based separation shown of exosomes. Can do viruses but have not done that work yet. #Tricon
6:26pm February 22nd 2017 via Hootsuite
Smith: docetaxel-resistant prostate ca-derived exosomes (collab with Mt Sinai) found to be smaller than sensitive ones #Tricon
6:25pm February 22nd 2017 via Hootsuite
Smith: Air-driven pump, for the fluid to push it through. Finishes with ability to subfractionate the exosome population #Tricon
6:24pm February 22nd 2017 via Hootsuite
Smith: How to use it, a way to get fluid into the chip itself? Decoupling via chip into a cartridge, up to 1mL input #Tricon
6:23pm February 22nd 2017 via Hootsuite
Smith: Covers technology for extracting sample from the chip. 50-100uL/hr per layer with stackable ability #Tricon
6:22pm February 22nd 2017 via Hootsuite
Smith: Dealing with clogging: use filtration before loading at 0.2um. Developed sorting pillar array, to run to full clog w/beads #Tricon
6:20pm February 22nd 2017 via Hootsuite
Smith:Thus they can create a device to separate on size but overcome dilution problems. Full-width injection. #Tricon
6:16pm February 22nd 2017 via Hootsuite
Smith: Posts can be changed in ordering, diameter. Simulated model w/predictions, verify experimentally. Showed micrographs, data #Tricon
6:15pm February 22nd 2017 via Hootsuite
Smith: Integrated the Gaussian distribution curves. Can get almost perfect separation of 200bp difference. #Tricon
6:14pm February 22nd 2017 via Hootsuite
Smith: Can do multimodal - shows clean separation of the 100bp, to 1kb, to 10kb. Borrowed chromatography resolution curves #Tricon
6:12pm February 22nd 2017 via Hootsuite
Smith: Shows at 10kb all aligned on the side of the channel. Thus opportunities for DNA seq prep. #Tricon
6:11pm February 22nd 2017 via Hootsuite
Smith: Shows cool movies - 100bp, 1kb, and 10kb DNAs in the inlet and the outlet. Gap size the same; shows zig-zag 100bp #Tricon
Smith: Biomarker separation down to 20ng - first beads, then exosomes, then 10kb from 100kb DNAs #Tricon
6:09pm February 22nd 2017 via Hootsuite
Smith: Can subfractionate, get compartimentalization. https://t.co/Y5lSTSBjbj Shows '16 ref https://t.co/BLdxE4urM2 #Tricon
6:08pm February 22nd 2017 via Hootsuite
Smith: Exosomes are 30-150nm; DNA is 2nm; viruses is 20-200nm. Streamlines among pillars: larger particles go to assymetry #Tricon
6:05pm February 22nd 2017 via Hootsuite
Smith: DLD is Deterministic Lateral Displacement. It is continuous flow, can separate different sized molecules, simple design #Tricon
6:04pm February 22nd 2017 via Hootsuite
Smith: Workflow for manual extraction for ctDNA shown. Microfluidics have many papers, many techniques and approaches #Tricon
6:03pm February 22nd 2017 via Hootsuite
Smith: Shows 1-2h Ultracent at 10k xg; then 2-3h at 100k xg, then 15h sucrose gradient, then anti-CD63 2-3h #Tricon
6:02pm February 22nd 2017 via Hootsuite
Smith: Shows figure from '15 rev https://t.co/V8aBglOBTC on importance of exosomes and involvement with disease #Tricon
6:01pm February 22nd 2017 via Hootsuite
Smith: Nanofabrication strategy includes flexible electronics, quantum computing, IoT, neuromorphic computing, nanobiotech #Tricon
5:59pm February 22nd 2017 via Hootsuite
Smith: IBM Research synonymous with Watson. nanoDLD on-chip separation of exosomes and nucleic acids. #Tricon
5:58pm February 22nd 2017 via Hootsuite
Joshua Smith (IBM Nanobiotechnology Group NY): Sample prep for liquid biopsies on a chip: exosomes, DNA and beyond #Tricon
5:57pm February 22nd 2017 via Hootsuite
Q: Does read-until affect nanopore life? A: ONT says it doesn't affect the pore. Sandia can't confirm - sees some variability. #Tricon
5:54pm February 22nd 2017 via Hootsuite
Q: How to deal with tubing contamination? Patel: Use disposable tubing. #Tricon
5:53pm February 22nd 2017 via Hootsuite
Q: Miniaturizing involves smaller volumes? Patel: Volumes are on the order of 10-100uL just making equipment smaller #Tricon
5:47pm February 22nd 2017 via Hootsuite
Patel: Library prep takes 3h manually. #Tricon
5:46pm February 22nd 2017 via Hootsuite
Q: ASPIRE starting material? Time? Patel: Purified DNA. Time hasn't been optimized. #Tricon
5:45pm February 22nd 2017 via Hootsuite
Patel: Working on more complex samples; can sequence DNA and RNA directly. Methods dev to deconvolute messy data #Tricon
5:44pm February 22nd 2017 via Hootsuite
Patel: ONT is constantly improving; 2nd strand can be lower quality; 1D squared may improve. Selective seq: Cas9-based selection #Tricon
5:43pm February 22nd 2017 via Hootsuite
Patel: Higher stringency, fewer reads. Can imagine bacterial DNA and host DNA where the host DNA is rejected #Tricon
5:40pm February 22nd 2017 via Hootsuite
Patel: Since read-until is in real-time, able to get higher rDNA mappability depending on level of stringency #Tricon
5:39pm February 22nd 2017 via Hootsuite
Patel: Modified version - a local base-calling to match against reference. Did Cas9-based selection of rDNA, enrich for spec size #Tricon
Kirshnakumar: Read-until allows for pruning of data in real-time. '16 Nature Methods https://t.co/nnG8lmStyC Can reject reads #Tricon
5:36pm February 22nd 2017 via Hootsuite
Kirshnakumar: Then looked at Kmer calls - Shows a plot of all 1024 5-mer possible calls, and expected vs observed ratios #Tricon
5:29pm February 22nd 2017 via Hootsuite
Kirshnakumar: The % that the next base will be similar to the score of that base; but remember, these are 5-mer calls. #Tricon
5:28pm February 22nd 2017 via Hootsuite
Kirshnakumar: Looked at contiguous base calls and Qscores; binned into deciles, shows base calling mistakes are non-deterministic #Tricon
5:27pm February 22nd 2017 via Hootsuite
Kirshnakumar: QC span, shows violin plots of GC content (B.thail 68%, C.diff 28%, E.coli 51%). #Tricon
Kirshnakumar: Population of reads <1kb w/low Qscores; above 1kb a cloud, scores range from 7-15. #Tricon
5:26pm February 22nd 2017 via Hootsuite
Kirshnakumar: Get 80-90% identity to the genomes in terms of alignment. 2D histograms show Qscore not related to read length #Tricon
5:25pm February 22nd 2017 via Hootsuite
Kirshnakumar: For Dx, Poreminion, Poretools, in-house scrips. 3 orgnsms, E.coli, C.diff., B.thail. Pie charts of 1D Q>6, 2D Q>9 #Trico
5:24pm February 22nd 2017 via Hootsuite
Kirshnakumar: Raw squiggle data (Metrichor, Nanonet is @oxfordnanopore callers. Mapping via LAST, BWA-MEM, GraphMap #Tricon
5:23pm February 22nd 2017 via Hootsuite
Kirshnakumar: Ideal for rapid bacterial ID in the field, wanted to develop an end-to-end pipeline. #Tricon
5:22pm February 22nd 2017 via Hootsuite
Kirshnakumar: Windows are called as 5-mers; oppy to use on both template and complement ("2D") #Tricon
5:21pm February 22nd 2017 via Hootsuite
Kirshnakumar: Data is different; shows squiggle plot, and neural network basecallers looking at 5-mers. #Tricon
Kirshnakumar: Field sequencing already - ISS, Ebola, ZiBRA (Zika virus in razil) #Tricon
5:20pm February 22nd 2017 via Hootsuite
Kirshnakumar: Very interested in its long reads, real-time data, interactive 'read-until', field-read and small footprint #Tricon
5:19pm February 22nd 2017 via Hootsuite
Raga Kirshnakumar (Sandia NL): Real-time diagnostics using nanopore sequencing #Tricon
Patel: Miniaturization of rotary pump, actuator; auto placement of magnet; perhaps lyophilization. Wants to include DNA extraction #Tricon
5:18pm February 22nd 2017 via Hootsuite
Patel: Volume of reagents are the same as in bench protocol. Can be hands-off; load from capillary to load. #Tricon
5:17pm February 22nd 2017 via Hootsuite
Patel: Can do automated 2D prep 'for field-portable sequencers'. Simple to make, disposable components, semi-automated #Tricon
5:16pm February 22nd 2017 via Hootsuite
