Harkins: Q&A - aneuploidy turnaround time could be done in 24h with a staggered shift. #NGS12
11:39am August 15th 2012 via HootSuite
Harkins: Clustering of 9 samples based on AF, heatmap shows more heterogeneity; tumorogenesis model highly complex. #NGS12
11:38am August 15th 2012 via HootSuite
Harkins: From the 9 samples; shared mutation for different metastatic samples; need to address allele freq. in primary then met. #NGS12
11:36am August 15th 2012 via HootSuite
Harkins: Comparing coverage at 50bp vs. 200bp, from 50-70% coverage to 90%+; readlength really matters for targeted seq. #NGS12
11:35am August 15th 2012 via HootSuite
Harkins: Looking for driver mutations, >99% mappable reads, shows good mean vs. median coverage stats. #NGS12
11:34am August 15th 2012 via HootSuite
Harkins: 4th application - ovarian cancer. Custom TargetSeq 2K gene panel, kinases, oncogenes, 9 samples from 1 individual. #NGS12
11:32am August 15th 2012 via HootSuite
Harkins: LifeTech claims 5% allele freq sensitivity. He shows down to 1.2% and 2.5%, but pipetting and biological sig. may confound. #NGS12
11:31am August 15th 2012 via HootSuite
Harkins: Using spike experiment with AmpliSeq, 1kb target + 6bp barcode, 5 different plasmids with specific mutated targets. #NGS12
11:28am August 15th 2012 via HootSuite
Harkins: Ampliseq R&D has gone up to 20K amplicons per tube. #NGS12
11:26am August 15th 2012 via HootSuite
Harkins: Amplicon sequencing via AmpliSeq; 46 cancer genes, >400 genes, >700 diseases, and custom offerings for up to 4K primer pairs
11:25am August 15th 2012 via HootSuite
Harkins: 3rd app - low freq somatic mutation detection, with Mickey Williams at the NCI. Looking at 5%, 1% MAF levels in cancer. #NGS12
11:24am August 15th 2012 via HootSuite
Harkins: Normalizing reads per chromosome length, can get copy number of the chromosome info. Whisker plots - convincing for T21. #NGS12
Harkins: 2nd app: detecting aneuploidy with 0.2x WGS coverage (1.5Gb data). 200bp fragment reads, single 318 chip used. #NGS12
11:23am August 15th 2012 via HootSuite
Harkins: SNP view missed an error-prone DNA replication gene, between 6 and 7 pandemic wave. #NGS12
11:22am August 15th 2012 via HootSuite
Harkins: Equivalent plot - four variables, space / habitat / time, with colors. CTX phage most virulent, but TCP allows adhering. #NGS12
11:20am August 15th 2012 via HootSuite
Harkins: Random forest with 30k variables 4h; PCA would take 3-4 d only on SNPs. #NGS12
11:19am August 15th 2012 via HootSuite
Harkins: From 38 genomes; added public data to get to 210 genomes, and analyzed a new way. 29.9k variables to analyze - random forest #NGS12
11:18am August 15th 2012 via HootSuite
Harkins: V. cholerae across geography and history: 38 genomes, 2 major scaffolds illustrated. #NGS12
11:17am August 15th 2012 via HootSuite
Harkins: 1st application example V. cholerea persistence across niches; 7th wave pandemic now. #NGS12
11:15am August 15th 2012 via HootSuite
T Harkins: Now running 400bp on #PGM, will cover four examples of applications. #NGS12
11:08am August 15th 2012 via HootSuite
RT @verge: Google promotes AdWords with print advertisement http://t.co/F04QZyZC
10:45am August 15th 2012 via HootSuite
Roever: Treatment of chip is done post-manufacturing in Taiwan, locally in Silicon Valley. #NGS12
10:15am August 15th 2012 via HootSuite
Roever: Q&A: Expects users to assemble bilayer on-site, synthetic polymers could be used instead of bilayer. #NGS12
10:14am August 15th 2012 via HootSuite
Roever: Other 4th gen SMS - Genia, Oxford, NABsys, IBM/Roche. #NGS12
10:04am August 15th 2012 via HootSuite
Roever: Compared to ~80% accuracy using same pore molecule. #NGS12
10:03am August 15th 2012 via HootSuite
Roever: Range of voltages, measure conductance. 98% accurate, single-base, alpha hemolysin pore. #NGS12
Roever: Four different molecules, showing single base differences between the four. 19 experiments, 2700 captures. #NGS12
10:02am August 15th 2012 via HootSuite
Roever: 30fA noise performance - detection of a few thousand electrons. 3.5 x 10^-12 A, x 1 second time-scale #NGS12
10:01am August 15th 2012 via HootSuite
Roever: Review of alpha hemolysin nanopore, looking at more than 1 base due to dimension of the read-head, engineering the protein #NGS12
10:00am August 15th 2012 via HootSuite
Roever: No fluidics, no optics, but making the chip is not trivial as they are not designed for salt solutions. #NGS12
9:57am August 15th 2012 via HootSuite
Roever: Current chip - 260 amplifiers on an active CMOS to make bilayer, insert pore. Placed into reader board. $1K board, $100 chip#NGS12
9:56am August 15th 2012 via HootSuite
Roever: Picture of prototypes - 'pipe bomb' with amplifier buried in ice. Signal proc done with other equipment. #NGS12
9:55am August 15th 2012 via HootSuite
Roever: Electronic assembly of bilayer, control of insertion of nanopore, capacitance measurement for sequencing. #NGS12
9:54am August 15th 2012 via HootSuite
.@justcoachit Thank you for the kind words!
9:48am August 15th 2012 via HootSuite in reply to
Roever: Criteria for MDx: Accuracy, Throughput, flexible panels, ease of use, cost. On flexibility - after WGS 'just a software Q' #NGS12
9:47am August 15th 2012 via HootSuite
Sens. ~90%; promising. MT @wagersscott: Omics technique that is easy and cheap #PersonalizedMedicine http://t.co/ix6njf0g @DrFens
9:45am August 15th 2012 via HootSuite
Rosentein: Here's his Nature Methods 2012 reference. http://t.co/CgsMdUjM #NGS12
9:44am August 15th 2012 via HootSuite
Roever: 3 assertions, first is 'DNA sequencing will dominate MDx', SMS will be the best approach, Genia's nanopore ICs ideal for MDx #NGS12
9:41am August 15th 2012 via HootSuite
S. Roever: "Solving the Challenges of DNA Sequencing for Molecular Diagnostics" #NGS12
9:39am August 15th 2012 via HootSuite
Rosenstein: Conclude: electronics + chemistry are complementary. Electronics can't keep up with signals. #NGS12
9:33am August 15th 2012 via HootSuite
Rosenstein: 10-15ms - 10x faster of measured events. 50bp oligos - can see diffusion, capture, threading, xloc via 1nA x 100us #NGS12
Rosenstein: Smaller interface, integration on the 10mm scale, refer to his Nature Methods 2012 paper. #NGS12
9:32am August 15th 2012 via HootSuite
Rosenstein: Aim to lower noise, raise bandwidth, via CMOS preamp optimized for nanopores. #NGS12
9:31am August 15th 2012 via HootSuite
Rosenstein: Noise density graph: Flicker, Thermal & Shot, Dielectic loss, Capacitance. Reducing parasitic loss - lower freq noise #NGS12
9:29am August 15th 2012 via HootSuite
Rosenstein: Ionic capacitance the problem with nanopore + membrane. Can't do fast when electrons are stored. #NGS12
9:27am August 15th 2012 via HootSuite
Rosenstein: Apply voltage, measure current ideal theory - problem is "parasitic capacitance". #NGS12
Rosenstein: Electrophysiology amplifiers - optimized for other uses. (Patch clamping, w/ pre-amp.) Nanopore signals are larger. #NGS12
9:25am August 15th 2012 via HootSuite
Rosenstein: Capture molecules, and slow enough to measure. Noise, signal, time, all problems. Faster = more noise. #NGS12
9:23am August 15th 2012 via HootSuite
Rosenstein: Protein vs. solid-state illustrated. Same idea - watching ion flux across the two sides of the pore. Transient signal. #NGS12
Rosenstein: Patch clamping - 1pA = 6M electrons per sec. Quantized unit is much smaller. SNR challenge is noise. #NGS12
9:21am August 15th 2012 via HootSuite
