Nelen: They use SeqNext software from JSI #IWT14 Highly stringent: need at least 15% of the reads in both dirs. http://t.co/FqAiEDOzIH
8:33am September 11th 2014 via Hootsuite
Nelen: From 981 samples, had 1224 amplicons with known muts; uses '% coverage <40x' as a measure of coverage (typically ~3%) #IWT14
8:29am September 11th 2014 via Hootsuite
Nelen: Proof of principle went smoothly (2bp ins, 17bp deletion). But how to verify the PGM and the quality of the data? #IWT14
8:28am September 11th 2014 via Hootsuite
.@iontorrent Thanks for the shout-out (live from Ion World 2014 #IWT14 )
8:26am September 11th 2014 via Hootsuite in reply to
Nelen: A 'simple' idea (in quotes): take PCR primers for their Sanger assays (with M13 tails); shear + ligate to beads + PGM seq #IWT14
8:24am September 11th 2014 via Hootsuite
Nelen: Wanted to get away from batching (due to turnaround time); wanted to move it to the PGM for cost-effectiveness #IWT14
8:23am September 11th 2014 via Hootsuite
Nelen: Another gene: RYR1 gene has 106 exons, too expensive for Sanger. Both mtDNA and RYR1 'very successful' now #IWT14
8:19am September 11th 2014 via Hootsuite
Nelen: Testing different enrichment: look at entire 16.5kb mtDNA, including >5% heteroplasmy detection. (MitoChip about 15%) #IWT14
8:18am September 11th 2014 via Hootsuite
Nelen: Used SOLiD at Nijmegen since 2011 for WES; heavily involved with BRCA1/2 AmpliSeq panel develop. "If we can sequence BRCA..." #IWT14
8:16am September 11th 2014 via Hootsuite
Next at #IWT14 - Marcel Nelen Radboud UMC (Netherlands) "Sanger Sequencing, the end of an era" (how clinical research is evolving)
8:10am September 11th 2014 via Hootsuite
Allen: A new environmental master mix is included with the Ion 16S Metagenomics kit - lowers effect of inhibitors, V2-4-8, V3-6, 7-9 #IWT14
7:16am September 11th 2014 via Hootsuite
Allen: Ion 16S Metagenomics Kit to be released soon; showed 20 known species detected in a mock BEI sample #IWT14
7:13am September 11th 2014 via Hootsuite
Allen: (Note: Here is the original 2012 SPAdes paper in J Comp Biol http://t.co/Hm1AqRVbTz ) #IWT14
7:04am September 11th 2014 via Hootsuite
Allen: De novo ass'y tools: SPAdes has support (de bruijn graph-based) for @iontorrent, unlike Velvet or Mira #IWT14 http://t.co/BKNzfq88Us
7:01am September 11th 2014 via Hootsuite
A Massive Quest Begins To Find Good Genes That Protect Us | Forbes http://t.co/63LwXnr5OD Matthew Herper on the Resilience Project
7:00am September 11th 2014 via Hootsuite
Allen: For TrueMate, 1-5ug for 3kb inserts; 10-20ug for 10kb inserts. 'Worth the extra work given the quality of the mate-pairs' #IWT14
6:59am September 11th 2014 via Hootsuite
Allen: Have used Tn-based MuSeek library prep from 50-100ng; have gone down to 20ng #IWT14
6:57am September 11th 2014 via Hootsuite
Chris Allen (@iontorrent): 'Ion Torrent Supporting Microbiology'; long reads, easy workflow, for public health, clin microbiology #IWT14
6:51am September 11th 2014 via Hootsuite
Chris Allan (@iontorrent): 'Ion Torrent Supporting Microbiology'; long reads, easy workflow, for public health, clin microbiology #IWT14
Q&A: More barcodes for GBS? We have 96 commercial, 384 designed, and are working on 'thousands for GBS' (Watson) #IWT14
6:46am September 11th 2014 via Hootsuite
Dowds: Can choose prior version (IR 4.0 or 4.2) of the Ion Reporter software, much requested feature. #IWT14
6:44am September 11th 2014 via Hootsuite
Dowds: Showing all the variant details in Ion Reporter, how quickly to get down to annotated variant lists #IWT14
6:35am September 11th 2014 via Hootsuite
Dowds: For AmpliSeq transcriptome, a new Ion Reporter plug-in offers gene expression analysis #IWT14
6:32am September 11th 2014 via Hootsuite
Carl Dowds (@iontorrent): Ion Software Updates: Ion Reporter allows automated data analysis. Panel design has advice for CNV design #IWT14
6:24am September 11th 2014 via Hootsuite
Shah: Announces AmpliSeq Any Genome, four add'l animal genomes, four plant ones. #IWT14
6:17am September 11th 2014 via Hootsuite
Anjali Shah (@iontorrent): AmpliSeq, to-date 116 publications. AmpliSeq RNA lung fusion panel: 98.4% concordance with FISH, ISH & qPCR
6:09am September 11th 2014 via Hootsuite
Watson: @iontorrent 16S metagnomics kit and informatics workflow launches. Also TrueMate mate-pair libraries. Blog: http://t.co/azi6irDNJo
5:57am September 11th 2014 via Hootsuite
Watson: @iontorrent AmpliSeq Transcriptome fits between targeted RNA-Seq with AmpliSeq and regular RNA-Seq. 20,802 genes in 1 pool.
5:50am September 11th 2014 via Hootsuite
Watson: PGM Hi-Q on @iontorrent Chef to launch 1H 2015, with improvement in both AQ20 and loading metrics. Also improved Proton Hi-Q Chef.
5:36am September 11th 2014 via Hootsuite
Watson: Announces @iontorrent Hi-Q sequencing kit for the OneTouch 2, equivalent or improved indel rates for targeted panels
5:34am September 11th 2014 via Hootsuite
Clues from the resilient | Science (May 30 2014) http://t.co/2k5M2wIQKb TIL about what Stephen Friend / Eric Schadt are working on
5:00am September 11th 2014 via Hootsuite
How Apple Will Convince You to Buy a Smartwatch -- NYMag http://t.co/79ys8ZRpm4
4:00am September 11th 2014 via Hootsuite
RT @hollybik: The @Storify of tweets from #BaltiAndBioinformatics - thanks to @pathogenomenick for organizing! http://t.co/ZLm7H4RGt4
10:01pm September 10th 2014 via Hootsuite
RT @hollybik: "Comfortable with NGS? It's all about to change again." - ominous (in a good way) signoff from C Brown #BaltiAndBioinformatics
9:01pm September 10th 2014 via Hootsuite
Jurassic Farm: Bringing back an ancient cattle breed, extinct since 1627 - Modern Farmer http://t.co/uLRVdeteJX
8:00pm September 10th 2014 via Hootsuite
Army's New Laser Cannon Blasts Drones Out of the Sky, Even in Fog | WIRED http://t.co/2c0U0V30Go
7:01pm September 10th 2014 via Hootsuite
Millennials Are Out-Reading Older Generations: Imagine That! - The Atlantic http://t.co/2cdna92dSB
6:01pm September 10th 2014 via Hootsuite
Why Apple Devices Will Soon Rule Every Aspect of Your Life | WIRED http://t.co/1imnvKseGn
5:01pm September 10th 2014 via Hootsuite
Look up. Great reminder of what’s truly important. | YouTube http://t.co/Xhx87XUMIp
4:02pm September 10th 2014 via Hootsuite
5M Google Gmail accounts hacked | http://t.co/X2z5KUIHN8
3:00pm September 10th 2014 via Hootsuite
Single animal to human transmission event responsible for 2014 Ebola outbreak | NIH http://t.co/gAkBckcwUy
2:02pm September 10th 2014 via Hootsuite
Uli Broekel (Med Coll WI) examines miRNAs using @iontorrent 318 on PGM for cardiac disease. Known and novel miRNAs AAAS Webinar
12:41pm September 10th 2014 via Hootsuite
A. Papp: Differential expressed gene calling at 94% concordance comparing @iontorrent AmpliSeq Transcriptome to RNA-Seq AAAS Webinar
12:31pm September 10th 2014 via Hootsuite
A. Papp AAAS Webinar: "We love the ERCC controls"; esp. useful for NuGEN's Ovation amplification variability on @iontorrent Proton RNA-Seq
12:29pm September 10th 2014 via Hootsuite
Audrey Papp in AAAS webinar (sponsored by @iontorrent): 90% RNA-Seq read mappability; Proton platform 'highly accurate in our hands'
12:28pm September 10th 2014 via Hootsuite
RT @iontorrent: Ulrich Broeckel, MD discusses #transcriptome sequencing to identify genes in complex diseases at Science webinar 9/10 http:…
11:59am September 10th 2014 via Hootsuite
RT @ConversationUK: Sequencing 100k #genomes is exciting but how will it transform care for patients? http://t.co/9hKcYH7AWb #genomics
10:00am September 10th 2014 via Hootsuite
MT @iontorrent: Hypothesis-experiment cycle shortened, expedition sequences marine microbial genomes onboard yacht: http://t.co/yhdlVepSXp
8:59am September 10th 2014 via Hootsuite
ISIS declares war on Twitter | Mail Online http://t.co/cUYRyCt61m
7:30am September 10th 2014 via Hootsuite
Electric buses: Proterra wants to rid America of emission-spewing buses | Slate http://t.co/lRJkcZ0vvo
6:16am September 10th 2014 via Hootsuite
