Gerrard: HaloPlex needed 225ng, got a bargain price, but 'fiddly' workflow (1 week), 'expensive to scale' #IWT14
11:40am September 11th 2014 via Hootsuite
Gerrard: But req'd 3ug DNA, 'horrible' workflow, cost also a concern. Adopted HaloPlex + Ion PGM #IWT14
Gerrard: Many ribosomal proteins involved with syndrome, perfect candidate for targeted. Started with SureSelect and MiSeq #IWT14
11:39am September 11th 2014 via Hootsuite
Gareth Gerrard, Imperial Molecular Path, ICL "Custom Ion AmpliSeq Panels for research in Diamond-Blackfan Anaemia research" #IWT14
11:37am September 11th 2014 via Hootsuite
RT @lexnederbragt: Keith Robison, @OmicsOmicsBlog, has a post-publication review up on the Mol Ecol Res MinION paper: http://t.co/e1y2AKSSoO
11:01am September 11th 2014 via Hootsuite
Henderson: Showed 2/5 samples where cfDNA mutations detected but nothing in the primary #IWT14
10:39am September 11th 2014 via Hootsuite
Henderson: Comment on cell free DNA: not only low-levels, samples need to be fresh, and 'more work needs to be done' to know signif. #IWT14
10:37am September 11th 2014 via Hootsuite
Henderson: For multi-gene controls, is excited about the AcroMetrix Oncology Hotspot Controls http://t.co/5UYIwiE6PZ #IWT14
10:31am September 11th 2014 via Hootsuite
Henderson: 'We are now evaluating Ion Chef and have great hopes for that.' #IWT14
10:21am September 11th 2014 via Hootsuite
Shirley Henderson (John Radcliffe Hospital, Oxford): Sees a 5-7% FFPE sample failure rate in her hands, comparable to prior methods #IWT14
10:19am September 11th 2014 via Hootsuite
RT @Genomicsnew: Genomics market in the US to grow at a CAGR of 7.28 percent by 2018 - WhaTech http://t.co/jC5vbY9q54
10:03am September 11th 2014 via Hootsuite
Nelen: Q: Analysis? A: Torrent Suite for base calling, JSI for variant calling / analysis. Didn't want to change software on top #IWT14
9:20am September 11th 2014 via Hootsuite
Searching for mutant genes: The Resilience Project, a search for protective mutations | Canada AM TV Video http://t.co/lzDurGOJg3
9:00am September 11th 2014 via Hootsuite
Nelen: Q: Bottlenecks? A: Amplicon dropouts need to be done via Sanger. #IWT14
8:54am September 11th 2014 via Hootsuite
Nelen: Q: For pooling, sample conc concern? A: Found that it doesn't matter - they don't even purify product (library prep cleans up) #IWT14
8:52am September 11th 2014 via Hootsuite
Nelen: Their costs have gone from 4.45 euro to 1.45 euro (60%) Sanger compared to NGS per gene sequenced (only reagent cost) #IWT14
8:44am September 11th 2014 via Hootsuite
Nelen: Thus they lower the # of barcodes needed by insuring no two samples have the same gene sequenced on the same PGM run #IWT14
8:43am September 11th 2014 via Hootsuite
Nelen: When doing different genes from different samples, the gene can be unique in that pool for ID for the sample. #IWT14
8:40am September 11th 2014 via Hootsuite
Nelen: Laid out their automated pipeline, from sample receipt onward. Only nuance is the barcode / pooling step w/ the PGM #IWT14
8:38am September 11th 2014 via Hootsuite
Nelen: Had 2 FP, looked at them closely. (I missed the TP number) Was able to calculate sens rate of 99.86%, and 99.98% specificity. #IWT14
8:36am September 11th 2014 via Hootsuite
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
