Mangion: Torrent Variant Caller has block polymorphism feature, although turned off by default (computationally intensive) #IWT14
4:20am September 12th 2014 via Hootsuite
John Mangion (Thermo Fisher Scientific) "Variant calling, mutation analysis and data integration" #IWT14
4:18am September 12th 2014 via Hootsuite
Sharkey: Ex.: for Colon/Lung v2, >700 samples worth of data compiled among the collaborators #IWT14
4:15am September 12th 2014 via Hootsuite
Sharkey: Implementation networks are three or more labs that he coordinates; a flexible, adaptable approach, 8-12w timeframe #IWT14
4:14am September 12th 2014 via Hootsuite
Sharkey: List of early FALCON in development: RASopathies, MDS, others #IWT14
4:13am September 12th 2014 via Hootsuite
Sharkey: A single AmpliSeq Colon/Lung run (16 barcoded samples on a 318 chip) is 1472 CE reactions #IWT14
4:09am September 12th 2014 via Hootsuite
Sharkey: How to remove the barriers? A jigsaw puzzle of cost, workflow, throughput, performance, bioinformatics. #IWT14
4:07am September 12th 2014 via Hootsuite
Sharkey: Helpful reminder that NGS is only <10 years old. Listed many of the applications on CE from MLPA, fragment analysis, etc. #IWT14
Freddie Sharkey (Thermo Fisher Scientific) "CE to NGS on the PGM and the role of implementation networks" #IWT14
4:06am September 12th 2014 via Hootsuite
Wood: PGM Torrent Server 12TB, Proton TS 24TB. http://t.co/FNfOkmEe8C gives 100GB data free #IWT14
4:01am September 12th 2014 via Hootsuite
Wood: Data structure is DAT, WELLS, BAM, Aligned BAM, VCF: files to backup are BAM and VCF's #IWT14
4:00am September 12th 2014 via Hootsuite
Wood: Amplicon coverage visuallized with a click - on any gene of interest across samples #IWT14
3:54am September 12th 2014 via Hootsuite
Wood: Filter chain automation in Ion Reporter: from 54K var's (exome sample) to 1 with 3 filters shown #IWT14
3:52am September 12th 2014 via Hootsuite
Wood: Variant lists can be saved - to either quickly filter in (a quick check) or filter out (common polymorphisms, possible FPs) #IWT14
3:50am September 12th 2014 via Hootsuite
Wood: Day to day, setup of workplan template (with barcodes), Oxford found that Ion's param. optimizations were already 'very good' #IWT14
3:49am September 12th 2014 via Hootsuite
Up next: Joe Wood (Thermo Fisher) "Bioinformatics for Clinical Research" #IWT14
3:43am September 12th 2014 via Hootsuite
With genetic testing, I gave my parents the gift of divorce - Vox http://t.co/ZsQ1ArIXlN HT @notsojunkdna 'a must-read' about @23andMe
10:00pm September 11th 2014 via Hootsuite
Apple's Steve Jobs was concerned about his children's gadget use - Telegraph http://t.co/hBNmdTRdtX
9:01pm September 11th 2014 via Hootsuite
The Internet Probably Isn't Ruining Your Teenager's Brain | WIRED http://t.co/I1wuiGHLc5
8:01pm September 11th 2014 via Hootsuite
The newest sequencer on the block: Base4 goes public | CoreGenomics http://t.co/qz9b0fwnU9
7:00pm September 11th 2014 via Hootsuite
RT @genome_gov: 10 NIH investigators will be awarded exome sequence data needed for their clinical research studies. http://t.co/4uMlFspQE6
6:00pm September 11th 2014 via Hootsuite
RT @Biotechnology: Can Your Blood Type Affect Your Memory? University of Vermont Study: http://t.co/vu0oVeyzXf
5:00pm September 11th 2014 via Hootsuite
RT @HarvardBiz: The future of capitalism is already here http://t.co/utzHU5jU38
4:02pm September 11th 2014 via Hootsuite
Friendships and Natural Selection | PubMed http://t.co/XbANaDi0wh The genotyping research showing friends' genetic resemblance
3:15pm September 11th 2014 via Hootsuite
"Your friends... resemble you genetically" | Huffington Post http://t.co/qjP29Df20u
3:02pm September 11th 2014 via Hootsuite
RT @drbachinsky: What the humble worm might tell us about doubling our lifespan http://t.co/XsPAeqCX4q via @ConversationUK
2:02pm September 11th 2014 via Hootsuite
RT @drbachinsky: Ebola Then and Now — NEJM http://t.co/YgmUZRu3fR
1:02pm September 11th 2014 via Hootsuite
Tanzi: Comparing dis-aggregated FFPE + DEPArray to 'regular' FFPE: a sensitivity to extraction method (dis-aggregation) #IWT14
12:31pm September 11th 2014 via Hootsuite
Tanzi: Disaggregated from FFPE, 300 cells collected and AmpliSeq - nice results; moved to 20, 10, 8 cells; some drop in uniformity #IWT14
12:28pm September 11th 2014 via Hootsuite
Tanzi: For FFPE samples, disaggregate, direct AmpliSeq without WGA. Sorted via marker (vimentin, stromal) (cytokeratin, cancer) #IWT14
12:27pm September 11th 2014 via Hootsuite
Tanzi: Fixation shown to introduce some FP’s, as a function of base changes in single cells #IWT14
Tanzi: Added add’l hotspots and CNV to the Cancer Hotspot panel, fixed/unfixed single cells got 84-86% coverage >20x #IWT14
12:26pm September 11th 2014 via Hootsuite
Tanzi: Joining single-cell isolation w/NGS: In 100d with Ion PGM, did WGA from fixed cells via 'Ampli1', a single-primer based method #IWT14
Tanzi: Fluidics can do basic sorting, one cell at a time based upon morphology, label. Can solve heterogeneity from samples. #IWT14
12:18pm September 11th 2014 via Hootsuite
Tanzi: Can step through these 9-tile cages across the surface of the chip. Can observe fluorescence, brightfield also #IWT14
Tanzi: 300K tiles of electrodes, creating de-electrophoretic 'cages' with an energy minima on the center, where the cell stays #IWT14
12:14pm September 11th 2014 via Hootsuite
Tanzi: Semiconductor-based DEP Array - moves cells in and out of the device, digital selection, isolation, using a flow cell 90um #IWT14
12:12pm September 11th 2014 via Hootsuite
Raimo Tanzi, Silicon Biosystems "Combining Ion with DEPArray digitalized samples to resolve heterogeneity on solid tumors & CTCs" #IWT14
12:11pm September 11th 2014 via Hootsuite
Guttery Q: Size of amplicon? A: 125-175bp Comment: nucleosomes around 160bp, would like to go smaller (helping some dropouts) #IWT14
12:10pm September 11th 2014 via Hootsuite
Guttery: Was able to call copy number reproducibly down to 1ng on a custom CNV AmpliSeq panel they designed #IWT14
12:06pm September 11th 2014 via Hootsuite
Guttery: Points out this recent paper on patterns, analysis of false-positives using the AmpliSeq Cancer panel http://t.co/ZcBLYKw4ha #IWT1
12:05pm September 11th 2014 via Hootsuite
Guttery: Can get down to 3% MAF ‘which we’re delighted with’. AS Designer: “a really neat tool’. Now supplementing for Br ca resrch #IWT14
12:01pm September 11th 2014 via Hootsuite
Guttery: Was able to do mixing experiments of 5% var freq, 98% detection, replication at 5ng and 1ng input #IWT14
12:00pm September 11th 2014 via Hootsuite
RT @pushingsocial: Consumers Rank Video as Trusted, Most Personable and Authentic Brand Marketing Experience http://t.co/ISTNqYOpai
Guttery: Varying yield, fragments <500bp, 'sequencing is VERY sample-dependent'. Library preps can 'fail' QC and still work, rev too #IWT
11:55am September 11th 2014 via Hootsuite
Guttery: Mentioned this Science Trans Med 2012 paper http://t.co/JlWsQjnjeU #IWT14
11:54am September 11th 2014 via Hootsuite
Guttery: Amts vary widely. Typically 1-10ng/mL; extraction should be <2h after venipuncture; 3 spins rec'd; process immed or -80C #IWT14
11:52am September 11th 2014 via Hootsuite
Guttery: Makes the case for cfDNA as a 'liquid biopsy': acccessibility, ability to monitor over time, ability to assess heterogeneity #IWT14
11:49am September 11th 2014 via Hootsuite
David Guttery (Univ Leicester) "Targeted sequencing of cell-free DNA using the Ion AmpliSeq Cancer Hotspot and Custom Gene Panels" #IWT14
11:48am September 11th 2014 via Hootsuite
Gerrard: Work published in Br J Haematol 2013 http://t.co/kvZZBh5kGa Using AmpliSeq was able to show nice CNV data, verified #IWT14
11:42am September 11th 2014 via Hootsuite
