Shapiro: Nature Comm. horse reference (2011) http://t.co/HDS3lCzL3a #AGBT14
3:14pm February 13th 2014 via Hootsuite
Shapiro: Interesting history of horses - equus caballus - originating in NAm, gone extinct ~13K y ago, migrated to Asia via land #AGBT14
3:13pm February 13th 2014 via Hootsuite
Shapiro: Today - only 2 spp, horses and bison (yet unpubl) #AGBT14
3:11pm February 13th 2014 via Hootsuite
Shapiro: A day of collecting, 20 bags of bones from this period. 9 different megafauna #AGBT14
3:10pm February 13th 2014 via Hootsuite
Shapiro: Nice timelapse of on-site work, a gold mining site near Dawson City, digging in permafrost #AGBT14
Shapiro: Beringia - locale of shallow sease across the Bering, one land mass; cold, vegetative, ice age megafauna #AGBT14
3:09pm February 13th 2014 via Hootsuite
Shapiro: Can look at a 4C temp rapid warming period 20K - 10K y ago and look for changes #AGBT14
3:08pm February 13th 2014 via Hootsuite
Shapiro: 3M years of oscillating climate change Nature reference (08) http://t.co/3ZVuvodn8F #AGBT14
3:07pm February 13th 2014 via Hootsuite
Shapiro: 15y project - use DNA from the past to see how climate change affected species int eh past. #AGBT14
3:05pm February 13th 2014 via Hootsuite
Up next: Beth Shapiro (UCSC) Paleogenomes, ice-age megafauna, and rapid warming #AGBT14
3:04pm February 13th 2014 via Hootsuite
Gilbert:Q: Museum material? A: Often mis-identified, you want rare and hard-to-get. Want to get 3 or 4 samples #AGBT14
3:03pm February 13th 2014 via Hootsuite
Gilbert: Q: Discoveries? A: Novel rabbit never caught in years of camera trapping. And the equivalent 'unicorn' #AGBT14
3:02pm February 13th 2014 via Hootsuite
Gilbert: Next may look at vampire bats, also vulture stomach. #AGBT14
3:01pm February 13th 2014 via Hootsuite
Gilbert: The dream: portable in-field monitoring. On-site extraction, sequencing and informatics. (MinION 'isn't cool enough') #AGBT14
2:58pm February 13th 2014 via Hootsuite
Gilbert: British folks' humor: Kissing for Conservation, which famous person do you want? #AGBT14
2:56pm February 13th 2014 via Hootsuite
Gilbert: Discussion of tools - Schuster's, QIIME. But the real problem is cost for the conservation folks. #AGBT14
2:55pm February 13th 2014 via Hootsuite
Gilbert: Madagascar example - only 84% of their mammals no reference available for OTU assignment. #AGBT14
2:54pm February 13th 2014 via Hootsuite
Nice to meet @salisburymw, @obahcall, and @topoisomerase at #AGBT14
2:50pm February 13th 2014 via Hootsuite
RT @salisburymw: It's only day 2, but I think Tom Gilbert wins the prize for funniest presentation of #agbt14.
2:49pm February 13th 2014 via Hootsuite
Gilbert: Willerslev's work Mammoth's from 3K years ago Nature 2014 http://t.co/hEdKHZRAjD #AGBT14
2:48pm February 13th 2014 via Hootsuite
Gilbert: Looking for DNA in old locations - sediment, permafrost. 2003 Science http://t.co/9A9jO6bCRy #AGBT14
2:47pm February 13th 2014 via Hootsuite
Gilbert: Other substrates? (Photo of elephant's urine - 20-50L / day!) #AGBT14
2:45pm February 13th 2014 via Hootsuite
Gilbert: 20 leeches: rabbit and deer only discovered in last 10y (from Vietnam) #AGBT14
Gilbert: (He's a great, funny and interesting speaker.) #AGBT14
2:44pm February 13th 2014 via Hootsuite
Gilbert: Feed the leech, find out how long it is there (>4 mos.) Slowly uses up food supply, a microbiome preservative #AGBT14
Gilbert: Leech study in Current Biol 2012 http://t.co/BbnPcpLbI1 #AGBT14
2:42pm February 13th 2014 via Hootsuite
Gilbert: But cameras also weak. Then markets - discovered 'for dinner' but heretofore undiscovered. #AGBT14
2:41pm February 13th 2014 via Hootsuite
Gilbert: Pretty photos of tropical forests - not easy to work in and access. Looking at scat, footprints, camera tracks work best #AGBT14
2:40pm February 13th 2014 via Hootsuite
Gilbert: 25% 'assessable' under threat - but what about 'data deficient' and 'not evaluated'? #AGBT14
2:39pm February 13th 2014 via Hootsuite
Gilbert: About 5.5k species of mammals. 76 spp. extinct in 50y; 29 add'l might be; 40% threatened by habitat loss #AGBT14
2:38pm February 13th 2014 via Hootsuite
Up next: Thomas Gilbert (Univ Copenhagen) Next-gen eDNA in biodiversity monitoring - potential and problems #AGBT14
2:37pm February 13th 2014 via Hootsuite
Morrison: Q: Cross-platform concordance? A: See his poster, "Parallel sequencing on the PGM and MiSeq for max. sensitivity and PPV"
11:57am February 13th 2014 via Hootsuite
Morrison: Q: Any germline variants reported as well? A: Not at present, and 'intriguing question'. 24 genes, ave of 1 non-act/gene #AGBT14
11:55am February 13th 2014 via Hootsuite
Levy: Q: What about outcomes fed back? A: SNaPshot for melanoma, CR, 40 vars in metastatic mel, 60% went onto a gene-dir therapy #AGBT14
11:54am February 13th 2014 via Hootsuite
Levy: Q: Links to Clinical Trials db? A: Yes, worldwide links avail on the site #AGBT14
11:53am February 13th 2014 via Hootsuite
Levy: Q: Is the API available publicly? A: No, licensing via GenomeOncology for content #AGBT14
11:51am February 13th 2014 via Hootsuite
Levy (now Morrison): Q:how easy to map to GRCh38? A: A problem but we'll 'have to do it' #AGBT14
11:50am February 13th 2014 via Hootsuite
Levy: 'Actionable target summary'; 'Alteration Failed Testing'. Reporting all variants detection #AGBT14
11:46am February 13th 2014 via Hootsuite
Levy: Helped develop 'genomics workbench' tool (GenomeOncology) for merging MiSeq and PGM data; output a summary report #AGBT14
11:45am February 13th 2014 via Hootsuite
Levy: More than test validation: order entry via EHR, with links to exist within EHR. Major effort, many other reporting functions #AGBT14
11:42am February 13th 2014 via Hootsuite
Levy: Goal highest sens and highest PPV, using both MiSeq and @iontorrent PGM with same gene panels #AGBT14
11:41am February 13th 2014 via Hootsuite
Levy: KB management: diagram illustrates 'actionable for tumor type tested', '... for other tumor type' and 'non-actionable' #AGBT14
11:40am February 13th 2014 via Hootsuite
Levy: RPCI test design Mar '13: used NGS, transloc by FISH, CNV by 'digital detection'. PPV, throughput, cost varies #AGBT14
11:39am February 13th 2014 via Hootsuite
Levy: Co-speaker Carl Morrison (Roswell Park Cancer Inst) brought to stage. API developed for daily content updates #AGBT14
11:37am February 13th 2014 via Hootsuite
Levy: Variance evidence levels, and levels of biomarker representation (gene var, exon, fusion, rearr., amplification, protein) #AGBT14
11:35am February 13th 2014 via Hootsuite
Levy: 'Actionable' means: large effect size, and strong evidence. Four effects: sensitivity, resistance, prognostic, diagnostic #AGBT14
Levy: http://t.co/LISd5gofaE first developed in '10 at Vanderbilt with SNaPshot testing. Now 22 Institutions, 19 cancers #AGBT14
11:33am February 13th 2014 via Hootsuite
Levy: Approach to use MyCancerGenome as a kb of clin relevant var's for design and validation. Phase 1: design, pipeline & report #AGBT
11:32am February 13th 2014 via Hootsuite
Levy: Collab with MyCancerGenome and Roswell Park - how to design an actionable panel, how to interpret and QC, and how to report. #AGBT14
11:30am February 13th 2014 via Hootsuite
Up next: Mia Levy (Vanderbilt): Design and validation of an oncology NGS laboratory-developed test focused on actionable mutations #AGBT14
11:28am February 13th 2014 via Hootsuite
