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
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
