Freeman: Seeing democratization, as they've gone from a few genes and up-scaled; great training of 'next gen of scientists' #AGBT14
1:37pm February 15th 2014 via Hootsuite
RT @westr: #AGBT14 current analytics: 7.5M impressions - http://t.co/D0BohlPFWy #pm101 #genomics
1:33pm February 15th 2014 via Hootsuite
Freeman: Correlated to RNA-Seq data; rate-limiting is bisulfite primer design. #AGBT14
1:30pm February 15th 2014 via Hootsuite
Freeman: Bisulf. Amplicon Sequencing (BSAS) analyzed via GUI, in-silico reference conversion. Nice data across several CpC sites #AGBT14
1:28pm February 15th 2014 via Hootsuite
Freeman: Co-isolated DNA and RNA (Q); TruSeq/HiSeq; CLCbio; IPA. Needed targeted methylation; 2-20kb, invented Bisulf. amplicon #AGBT14
1:27pm February 15th 2014 via Hootsuite
Freeman: Using rat model (less genome annotation, no capture reagents, limited tissue); small effects, hetergeneous tissue #AGBT14
1:24pm February 15th 2014 via Hootsuite
RT @will_fitzhugh: Alan Williams from @iontorrent: v4.2 of Ion Reporter will support gene fusion detection and reporting #AGBT14
1:23pm February 15th 2014 via Hootsuite
QIAGEN: Poor glycemic control - cause complications years afterward. Large studies over a 10y timeframe. May be epigenetic. #AGBT14
1:22pm February 15th 2014 via Hootsuite
Freeman: Diabetic retinopathy is leading cause of vision loss (12k - 24k in US lose some vision/ year) #AGBT14
1:20pm February 15th 2014 via Hootsuite
Up next at the Q workshop: William Freeman, Univ OK HSC: Metabolic memory and transcriptomic signatures in diabetic retinopathy #AGBT14
1:18pm February 15th 2014 via Hootsuite
QIAGEN: 1-20 independent runs on the GeneReader (GR); hotspot panel throughput x 250 samples/day #AGBT14
1:16pm February 15th 2014 via Hootsuite
QIAGEN: New GeneRead FFPE kit for small-scale purification; REPLI-g single-cell portfolio. #AGBT14
1:15pm February 15th 2014 via Hootsuite
QIAGEN GmbH Workshop:Used the words 'dominant player'; '14 plans include 12 new tech kits; 14 new gene panels; GeneReader #AGBT14
1:14pm February 15th 2014 via Hootsuite
QIAGEN GmbH Workshop: >80% of NGS runs use Q sample-prep; 2.3k inst. using CLCbio; 15K use Ingenuity tools, including IPA (10y old) #AGBT
1:12pm February 15th 2014 via Hootsuite
QIAGEN GmbH workshop: illustrating the largest bottlenecks, and the large number of paraffin-embedded sample collections #AGBT14
1:11pm February 15th 2014 via Hootsuite
Williams: Hi-Q data now avail; universal 200 / 400 bp kit; 70% red. in deletion error, 30% reduction in insertion error #AGBT2014
1:00pm February 15th 2014 via Hootsuite
Williams: Chef: For PGM in late Mar, for Proton soon after. 79% loading, 80-90M PI reads/run. 1.5% run failure rate #AGBT2014
12:58pm February 15th 2014 via Hootsuite
Williams: Room to improve, target early acces in 'May or June', full launch of PII in 2nd half of 2014 #AGBT2014
12:55pm February 15th 2014 via Hootsuite
Williams: L. Moroz data, 342M extrapolated reads. Cp. the PI to PII, r^2 of 0.99 across different samples #AGBT2014
12:54pm February 15th 2014 via Hootsuite
Williams: 91bp human frag lib data shown, extrapolated 291M reads. Are where we are in 3w w/PII what took 4mo with PI #AGBT2014
12:52pm February 15th 2014 via Hootsuite
Williams: Now 3w with new PII design; biggest risk was 5Gb/s data output. #AGBT14
12:50pm February 15th 2014 via Hootsuite
RT @lexnederbragt: Radovich: early access data by new Ion AmpliSeq Exome RDY - dried down primer pools in plates for easier workflow #AGBT14
12:47pm February 15th 2014 via Hootsuite
RT @iontorrent: Radovich: Using combo of Ion PGM System and Open Array qPCR in CLIA lab for PGx #AGBT14
12:46pm February 15th 2014 via Hootsuite in reply to
RT @OmicsOmicsBlog: Boland: Had Chef since mid-Nov; 37 runs. 200 bp chemistry. Challenge: titrating library. Uses 1 Chef for 2 PGMs #AGBT14
12:45pm February 15th 2014 via Hootsuite
Nice #AGBT14 crowd in the Palms Ballroom to hear about @iontorrent Chef and Proton updates. http://t.co/gHX4NrfPhe
12:12pm February 15th 2014 via Hootsuite
Tang: Q: SNP analysis from indiv cells? A: de novo point muts - need 3 cells. Several oocytes each with 2 PB's (same donor) #AGBT14
11:57am February 15th 2014 via Hootsuite
Tang: scRRBS of indiv. cells shows considerable var; also looking at haploid cell methylation status (sperm): 92% of sites 100%/0% #AGBT14
11:55am February 15th 2014 via Hootsuite
Tang: Single-cell RRBS publication in Genome Res here. http://t.co/ceJQOshNFG #AGBT14
11:54am February 15th 2014 via Hootsuite
Tang: RRBS development to the single-cell level: remove pur steps, combine to single-tube reaction, only heat #AGBT14
11:53am February 15th 2014 via Hootsuite
Tang: Discussion of a method called Super-Seq (alas missed any ref, can't locate) for lncRNA analysis for single-cell #AGBT14
11:52am February 15th 2014 via Hootsuite
Tang: PCA of 120 cells for single-cell transcr.: can separate 3 distinct celltypes. Nature Struct Biol ref: http://t.co/F9UyFQPnpE #AGBT14
11:49am February 15th 2014 via Hootsuite
Tang: Illus. a method of NIPT for post-fertilized embryos. First MALBAC-based implantation is underway (presum. in China) #AGBT14
11:47am February 15th 2014 via Hootsuite
Tang: Able to deduce maternal SNVs of indiv. zygotes; validated via Sanger 32/33 alleles. 1: amplification via MALBAC allele dropout #AGBT14
11:45am February 15th 2014 via Hootsuite
Tang: After micromanipulation, use MALBEC with 8 donors. Cell publication of 8 human embryo's in Cell 2013 http://t.co/IPVqqGwE3w #AGBT14
11:44am February 15th 2014 via Hootsuite
Tang: Illus. meiosis of human oocytes, 1st polar body (2N); then 2nd polar body (1N). Looking for euploidy from polar bodies #AGBT14
11:40am February 15th 2014 via Hootsuite
Tang: Major Q is what det. early cell fate? Early embryos in dev. - uses MALBEC for WGS, others. Science PDF: http://t.co/dQUv9NtGOg #AGBT14
11:39am February 15th 2014 via Hootsuite
Up next: Fuchou Tang, Peking Univ.: The Transcriptome and DNA Methylome Landscapes of Human Preimplantation Embryos and ESC's #AGBT14
11:35am February 15th 2014 via Hootsuite
OMG the US beat Russia in the hockey game in a 3-2 shootout. Back to live-tweeting a scientific meeting.
11:32am February 15th 2014 via Hootsuite
Burton: 1K rhododendron spp., only 660MB but near-perfect 10kb repeats. Was able to isolate intact rhododen. nuclei #AGBT14
11:30am February 15th 2014 via Hootsuite
Burton:Hi-C has mainly been done in cell lines; now looking at new world monkeys, hops, and rhododendron (next) #AGBT14
11:29am February 15th 2014 via Hootsuite
Burton:Test of how small a short contig size does the method fail? ~ 50kb #AGBT14
11:28am February 15th 2014 via Hootsuite
Burton: Review of Lachesis software method published in 2013 Nature Biotech http://t.co/8WVXrWhpLy #AGBT14
11:24am February 15th 2014 via Hootsuite
Burton: Hi-C and refers to Lieberman-Aiden's work in 2009 http://t.co/NBRlmFPEuc #AGBT14 (Note - a hero to me- see http://t.co/oPankrrbOS )
11:23am February 15th 2014 via Hootsuite
Burton: Incomplete as there are no BACs, no genetic & physical maps to build on as with the HGP #AGBT14
11:21am February 15th 2014 via Hootsuite
Burton: De novo solely from short reads: cheap de novo assy's lack chromosome-scale assy -Hard to align/compare; gene model incompl #AGBT14
11:20am February 15th 2014 via Hootsuite
Next up: Joshua Burton, Univ. WA: Chromosome-Scale Scaffolding of de novo Genome Assemblies Based on Chromatin Interactions #AGBT14
11:17am February 15th 2014 via Hootsuite
Listening to Carlos reminds me of how entertaining and informative an excellent presenter can be. #AGBT14
11:16am February 15th 2014 via Hootsuite
Bustamante: Concl: Goal is a WGS of an ancient genome at only 2-3x the cost of a modern human. #AGBT14
11:15am February 15th 2014 via Hootsuite
Bustamante: Bias? 92%-96% correlation; all the correct spp. taxonomy per location #AGBT14
Ehrich: Looking at different env. samples (saliva, cheek swab, human soil): 50-70% microbial, enriched to 70-97% #AGBT14
11:13am February 15th 2014 via Hootsuite
