RT @nytimesscience: There are as many as 4,500 clinical trials involving stem cells underway in the U.S. right now http://t.co/Ar1vL8wc0V
1:05am September 17th 2014 via Hootsuite
MT @iontorrent: Human populations have grown since the Stone Age, so have the # of rare disease-related genetic var's http://t.co/7l4C9a1KT7
12:05am September 17th 2014 via Hootsuite
Physicians' Genomics Knowledge, Basic Skills Still Barrier to Adoption | GenomeWeb http://t.co/TjZFmtVNM0
11:00pm September 16th 2014 via Hootsuite
Behind the Bench: Fishing for Rare Pathogenic De Novo Variants in a Sea of SNVs http://t.co/hQThITT14m
10:00pm September 16th 2014 via Hootsuite
New post: Human Identification by NGS | Behind the Bench http://t.co/V5nSvrFm9A
9:00pm September 16th 2014 via Hootsuite
The missing piece to changing the university culture : Nature Biotech http://t.co/GN3WFnDJGP A depressing figure of PhDs vs. acad. positions
8:01pm September 16th 2014 via Hootsuite
RT @SwedishCanary: This salad tastes like I'd rather be fat.
7:00pm September 16th 2014 via Hootsuite
MT @sritchie73: Lee Hood advocating a holy trinity: biology, technology and computation. Seems to miss the final key: statistics #icsb2014
6:00pm September 16th 2014 via Hootsuite
Almost one-half of wealthy Chinese plan to leave | WSJ http://t.co/oURAy5KiNY
11:02am September 16th 2014 via Hootsuite
Vanhatalo: (Points out why the usable key signal is only 3 bp) #IWT14
10:11am September 16th 2014 via Hootsuite
Vanhatalo: Ion Chef library amts range from 50-100pM, 5x more than the rec'd 11pM for OT2 #IWT14
9:59am September 16th 2014 via Hootsuite
Vanhatalo: Qubit, BioAnalyzer, qPCR all good for library quant. No to nanodrop or a gel - not helpful #IWT14
9:56am September 16th 2014 via Hootsuite
Vanhatalo: "Covaris and Biorupter have less variability across sample types, compared to enzymatic methods" #IWT14
9:52am September 16th 2014 via Hootsuite
Vanhatalo: Qualifying starting DNA with RNAseP real-time PCR (document on Ion Community: http://t.co/tS5LKrBgYf ) #IWT14
9:47am September 16th 2014 via Hootsuite
Vanhatalo: Best practices document at Ion Community (free reg) http://t.co/K7OwkAifOW #IWT14
9:43am September 16th 2014 via Hootsuite
Last: Jussi Vanhatalo (Thermo Fisher Scientific): "Best practices, quality control along the Ion Workflow and more" #IWT14
9:42am September 16th 2014 via Hootsuite
Tyrelle:Q:What is common signal shift? A:The key sequences, shifted up (or down) along the read, a parameter #IWT14
9:33am September 16th 2014 via Hootsuite
Tyrelle: Alllele=no call: hotspot DEL filtered due to 'common signal shift'. Can dig back in and look at how close to threshold #IWT14
9:30am September 16th 2014 via Hootsuite
Tyrelle: Source=hotspot, Type=MNP: a hotspot file generated. Contrast: missing SNV in hotspot. 0.0% freq. 3rd: not-called novel Del #IWT14
9:27am September 16th 2014 via Hootsuite
Tyrelle: In essence, going back to data the bases were called originally, now in the context of all the other signals at that base #IWT14
9:19am September 16th 2014 via Hootsuite
Tyrelle: TVC looks at the underlying raw data; signal properties in the aggregate examined (these are flowspace signals) #IWT14
9:18am September 16th 2014 via Hootsuite
Tyrelle: De-amination metric - not filtered on, just a parameter for FFPE or other samples where effect can be seen #IWT14
9:16am September 16th 2014 via Hootsuite
Tyrelle: MNP=multi-nucleotide polymorphism. COMPLEX=block-substitutions. #IWT14
9:14am September 16th 2014 via Hootsuite
Tyrelle: TVC (Torrent Variant Caller) is available at GitHub under GPLv2 located here: http://t.co/MEERCfqf7y #IWT14
9:13am September 16th 2014 via Hootsuite
Greg Tyrelle (Thermo Fisher Scientific) "Variant Calling, Mutation Analysis, and Data Interpretation" #IWT14
9:12am September 16th 2014 via Hootsuite
Sartori: 'Further developments for Hematology currently under evaluation'; open for discussion and input for the next project #IWT14
9:01am September 16th 2014 via Hootsuite
Sartori: Can call most mutations, still needs more tuning, confident that with more data will finish work on the Reporter plug-in #IWT14
8:57am September 16th 2014 via Hootsuite
Sartori: Uniformity 94.3%, mean depth 2218x, average on-target mapping 88%; 90% of bases at 500x. #IWT14
8:54am September 16th 2014 via Hootsuite
Sartori: Verification testing begun, 120 total samples, 6 samples on 318. From about 40 samples: 1 amplicon <100x (DNMT3A), 4 <500x #I
8:53am September 16th 2014 via Hootsuite
Sartori: Poorest prior performing amplicons: now significantly improved numbers for CEBPA (9 amplicons) Lowest one still >500x #IWT14
8:51am September 16th 2014 via Hootsuite
Sartori: 3&4 modified conditions for G/C-rich templates; after amplifying combine 1&3, 2&4 for library prep. 'Everyone was nervo
8:50am September 16th 2014 via Hootsuite
Sartori: Without a new design, they added two more pools to the first 234 amplicons. 3&4 have only 12 & 15 primer pairs #IWT14
8:49am September 16th 2014 via Hootsuite
Sartori: 2 panel pool had low performance including CEBPA, DNMT3A. Many in the list were along CEBPA gene #IWT14
8:47am September 16th 2014 via Hootsuite
Sartori: For AML, collaborators from UCL (London), CHRU (Lille, France), CHUV (Lausanne) #IWT14
8:42am September 16th 2014 via Hootsuite
Sartori: Consortium proposed list, tested performance, verified with known samples, demo'd workflow #IWT14
8:41am September 16th 2014 via Hootsuite
Sartori: FALCON organizes consortia around applications; helps with analytical verification; tailor workflow dev't; share experience #IWT14
8:36am September 16th 2014 via Hootsuite
Sartori: Melanie Baumann from the FALCON team, a clinical consortium development facilitation group. Lab in Darmstadt #IWT14
8:34am September 16th 2014 via Hootsuite
Alexander Sartori (Thermo Fisher Scientific) "Ion AmpliSeq AML Research Panel" #IWT14
8:31am September 16th 2014 via Hootsuite
Gunther: Project: + / - cells, 50-200K cells (proliferated). r around 0.88-0.94. FACS takes time, primary culture affect r values #IWT14
8:22am September 16th 2014 via Hootsuite
Gunther: (cont) SAMTools, feature Counts, mergeCounts, correlation, DESEQ2 (more relaxed) for genes / isoforms) #IWT14
8:20am September 16th 2014 via Hootsuite
Gunther: Their bifx workflow: FASTQ, add’l quality trimming by Reaper (EBI Q20/20, 30-200bp), use STAR (Encode) for mapping... #IWT14
Gunther: Size-selected vs non-SS samples not to be mixed; less mappable reads. Readlengths >20-30% longer, better for de novo ass’y. #IWT
8:19am September 16th 2014 via Hootsuite
Gunther: Small input results in high duplications; reduce # of cycles cut dupl. rate from 60-70% to below 40%. Fewer PCR dup's in IGV #IWT14
8:18am September 16th 2014 via Hootsuite
Gunther: Changes to protocol: RNA frag to 1 min for up to 4ug starting amt. Need to aliquot ligation buffer (as the ATP is labile). #IWT14
Gunther: Tested sample preps for small RNA: Best results are PureLink miRNA; Q RNeasy Micro + on-column DNase #IWT14
8:17am September 16th 2014 via Hootsuite
Gunther: FACS muscle stem cells: Min input 10-20K cells (100ng total RNA input, more is better) #IWT14
8:16am September 16th 2014 via Hootsuite
Gunther: Proton, 2/3 of almost 100 runs RNA-Seq or miRNA-Seq. Use RiboMinus Eukaryote v2, also Dynabeads mRNA Direct Micro (polyA) #IWT14
8:15am September 16th 2014 via Hootsuite
Dr. Stephan Gunther (MPI Bad Nauheim) "Transcriptome analysis on Ion Proton™ Sequencer" #IWT14
8:11am September 16th 2014 via Hootsuite
Kurth: (Gave credit to the OncoNetwork Consortium, and to Rosella Petraroli of Thermo Fisher Scientific) #IWT14
6:41am September 16th 2014 via Hootsuite
Kurth: RNA fusion: 20k reads/sample, 16/318 chip, fusion positive if >20 reads across junction. Sens 97% by imbalance or by fusion #IWT14
6:36am September 16th 2014 via Hootsuite
