US=Land of the geo-ignorant RT @conradhackett: US adult guesses about the location of Ukraine http://t.co/znrNWX9uJm http://t.co/j11KK7NQrb
8:20am April 9th 2014 via Hootsuite
RT @GenomicsEngland: Come & talk abt 100,000 Genomes Proj.,Cambridge 30 April - participants, clinicians, researchers http://t.co/DG1aQe
7:20am April 9th 2014 via Hootsuite
RT @THebertMcGill: CRISPR-mediated cures! Cool!... http://t.co/UXJKTTjiUV
6:20am April 9th 2014 via Hootsuite
RT @k8hert: My emerging truth about bioinformatics is that more work goes into organizing and archiving data than analyzing it.
5:20am April 9th 2014 via Hootsuite
The Race To Locate Twitter Users - WSJ http://t.co/Vw7jx3GlRC
4:20am April 9th 2014 via Hootsuite
RT @AACR: Free #AACR14 webcast: View presentations from the Opening Plenary Session. http://t.co/20O9R2fz3a
3:20am April 9th 2014 via Hootsuite
RT @drsam: Love this. Should be posted at every Pharma. http://t.co/biIiD0oEck
2:20am April 9th 2014 via Hootsuite
Hutch biotech spinoff Adaptive Biotech snags $105 million | Seattle Times http://t.co/8AXAysAQBL They are doing NGS on immune repertoire
1:20am April 9th 2014 via Hootsuite
.@cwvhogue David H said later that all the majors (Amazon etc.) were all involved (they have engaged already).
12:23am April 9th 2014 via Hootsuite in reply to
(Genepeeks) offering DNA screening of 'hypothetical babies' raises fears over designer children | Guardian http://t.co/AG83NM6d2d
12:20am April 9th 2014 via Hootsuite
RT @LeighGTurner: NIH Center for Regenerative Medicine is shut down; Mahendra Rao resigns. http://t.co/ndw7RpGzJt @NatureNews
11:20pm April 8th 2014 via Hootsuite
RT @MIT: New study finds nanoparticles commonly added to consumer products can damage DNA. http://t.co/VTGWEvgoE8
10:20pm April 8th 2014 via Hootsuite
Getz: After subsampling, determeined about 2K samples / tumor type needed for 90% power for 90% genes at >2% freq #AACR14
8:59pm April 8th 2014 via Hootsuite
Getz: Know there are more genes to be found; looked at 5K cancer genomes from 21 tumor types, Lawrence 2014: http://t.co/Oosoqya5C3 #AACR14
8:58pm April 8th 2014 via Hootsuite
Getz: Charts from several TCGA papers - genes mutated more often than by chance; the long tail ends b/c lack stat power #AACR14
8:56pm April 8th 2014 via Hootsuite
Next: Gad Getz, Broad Inst. Why do we need a cancer data and knowledge commons? A place to store & share; need to harmonize results #AA
8:54pm April 8th 2014 via Hootsuite
Haussler: 2 months of YouTube is 100PB. 'We can do this." "We must head off the dev. of genomic information silos" #AACR14
8:47pm April 8th 2014 via Hootsuite
Haussler: Need machine-aided ways for pattern recognition: gather data, preprocess, train + eval., store + display, then predict #AACR14
8:46pm April 8th 2014 via Hootsuite
.@obigriffith Whoops - too fast on the <ctrl>-c. (And a looong day - I'm just about 'done'!)
8:44pm April 8th 2014 via Hootsuite in reply to
Hudson:Venn diagram of same BAM, different centers calling var's. Link to UC Berkeley's SMaSH website http://t.co/dTincSvLbK #AACR14
8:42pm April 8th 2014 via Hootsuite
Hudson: But cancer is the 'high water mark for genomics' due to its complexity; other diseases cost less for data stor & analysis #AACR1
8:39pm April 8th 2014 via Hootsuite
Hudson: In 2014, est cost is $50/genome/yr for 1M genomes (~100PB); includes 25K disks plus 100K cores incl. operating costs #AACR14
8:38pm April 8th 2014 via Hootsuite
Hudson: Not monolithic geographically, nor architecture: read-layer db (100PB); variation layer db (1PB); interpret layer (1TB) #AACR14
8:37pm April 8th 2014 via Hootsuite
Hudson: Individual, uniform consent process for 1M genomes; 'it's API's, not file formats' "we have to get beyond that" #AACR14
8:34pm April 8th 2014 via Hootsuite
Haussler: Computation needs to be provided close to the data. Dave Patterson's '1M genomes warehouse' link http://t.co/G3l71KD2Uv #AACR14
8:33pm April 8th 2014 via Hootsuite
Haussler: A task team is working on development a next-gen human genetic variation including known variation + API to access it #AACR14
8:29pm April 8th 2014 via Hootsuite
Haussler: Need API's and computational procedures on top of that (where the innovation occurs). But API standards needed first #AACR14
8:27pm April 8th 2014 via Hootsuite
Haussler: File formats - BAM, CRAM and VCF's. But inevitably - will need to add future enhancements for clinical applicability #AACR14
8:26pm April 8th 2014 via Hootsuite
Haussler: Example of a driver project: "Genomic Matchmaker" - Heidi Rehm, expert sharing of rare genetic variants #AACR14
8:25pm April 8th 2014 via Hootsuite
Haussler: Founding partners 70 institutes, 40 countries; several working groups; also several driving projects #AACR14
8:24pm April 8th 2014 via Hootsuite
Haussler: 'Major medical centers... create Balkanized, incompatible, inadequate systems'; 'reinforces barriers to data sharing' #AACR14
8:22pm April 8th 2014 via Hootsuite
Haussler: The future needs multiple CGHubs worldwide - major cloud providers (AMZN, GOOG, MISFT) should be engaged #AACR14
8:21pm April 8th 2014 via Hootsuite
Haussler: Used commodity HW, now has served >1M total files; 15PB transferred; has 1.4PB data; 4 Gb/s bandwidth (!) peak 15 Gb/s #AACR14
Haussler: CGHub is ~$100/yr/genome at 50K genomes; growing to 2.5PB in near future; scalable to 20PB (20 x10^15 bytes) #AACR14
8:19pm April 8th 2014 via Hootsuite
Haussler: TCGA is scaling to 10K tumors from 20 adult cancers; ICGC will hit 25K tumors; Cancer Genomics Hub in San Diego CA #AACR14
8:18pm April 8th 2014 via Hootsuite
Next: David Haussler, UCSC. One key difference between HIV and cancer: it isn't passed onto cancers of our children #AACR14
8:17pm April 8th 2014 via Hootsuite
Hudson: Modeled after the W3C, 12 on the transitional steering committee. List of steering committee: http://t.co/MJhXkYg5ri #AACR14
8:15pm April 8th 2014 via Hootsuite
Hudson: Global Alliance: a startup began in Jan 2013; white paper Link to UCSF (PDF) http://t.co/f9WErjIh6n #AACR14
8:12pm April 8th 2014 via Hootsuite
Hudson: ICGC datasets too large to handle due to sheer size; want a commons database to query across datasets #AACR14
8:10pm April 8th 2014 via Hootsuite
Hudson: ICGC has standardized datasets. Portal launched Oct 2013, homepage here: http://t.co/V2RSl7ZRX9 #AACR14
8:09pm April 8th 2014 via Hootsuite
Forum: How to Achieve a Cancer Knowledge Commons Database of Cancer Genetics, moderator Tom Hudson, OICR
8:07pm April 8th 2014 via Hootsuite
Bass: Conclude TCGA offers 'numerous opportunities for further detailed mechanistic and translational studies' #AACR14
7:57pm April 8th 2014 via Hootsuite
Bass: ID gene RHOA plays role in invasion, highly recurrent mutations. Tyr42 - RHOA is a GTP-ase protein, like Ras; RHOA + Rock1 #AACR14
7:56pm April 8th 2014 via Hootsuite
Bass: Moving onto Stable type: genomically-stable. Used Mut-Sig tool to find mutations higher than chance #AACR14
7:54pm April 8th 2014 via Hootsuite
Bass: Greet et al Hum Cancer Biol 2012 ref. http://t.co/lptslLeIKj confirms similar effect of EBV+ in lymphomas inducing PD-L1 #AACR14
7:52pm April 8th 2014 via Hootsuite
Bass: TCGA-enabled wide analysis (esp. methylation data) helped define EBV+ group; CNV found 9p ampl; exp data showed PD-L1/L2 #AACR14
7:50pm April 8th 2014 via Hootsuite
Bass: Strong T-cell infiltration in EBV+ gastric ca: expression signature of enriched signalling. #AACR14
7:49pm April 8th 2014 via Hootsuite
Bass: PDL1/2: immune checkpoint markers. Found EBV+ gastric ca had much higher expression of PD-L1/L2. #AACR14
7:48pm April 8th 2014 via Hootsuite
Bass: For EBV+ gastric ca, found focal amplification at 9p24.1, JAK2 locus. Other genes nearby - DC274 & PDCLILG2 (PDL1 and PDL2!) #AACR
7:47pm April 8th 2014 via Hootsuite
Bass: Found dramatic rates of PIK3CA mutation in EBV+ gastric ca - on the order of 80% #AACR14
7:45pm April 8th 2014 via Hootsuite
