DT: CTC need to intravasate (go into circ.), then extravasate (get out). CTC's implies heterogeneity. Liquid biopsy; localized ca #AACR15
2:32pm April 18th 2015 via Hootsuite
David Ting (Mass Gen Hospital MA) “Single cell RNA sequencing of circulating tumor cells” DT #AACR15
2:30pm April 18th 2015 via Hootsuite
CZ: They are working on exact linearity for WGA method; also low-level single-cell RNA-Seq, and single-cell ChIP-Seq. #AACR15
2:27pm April 18th 2015 via Hootsuite
CZ: First-strand error is 1e-4; thus one genome has 1e5 false-positives (!). Used 3 cells of very similar lineage to eliminate FP's #AACR15
2:22pm April 18th 2015 via Hootsuite
CZ: Method is not linear; called quasi-linear. Get 93% coverage at 25x depth. Cp to MDA (Genomiphi v2). Much better CNV resolution #AACR15
2:19pm April 18th 2015 via Hootsuite
CZ: Schematic from 2012 Science paper http://t.co/P4QwmDdrp0 explaining MALBAC. Sets of semiamplicons & full amplicons looped out #AACR1
2:17pm April 18th 2015 via Hootsuite
CZ: The Big Bang theory - 2015 Nature Gen ref http://t.co/2LWHw6mj6O argument for single-cells. Problem: Uniform amplification #AACR15
2:15pm April 18th 2015 via Hootsuite
Chuck Zong (Baylor, Houston TX) “MALBAC whole genome amplification of single cancer cells” #AACR15
2:13pm April 18th 2015 via Hootsuite
PVL: Single br ca cells: used Rubicon PicoPlex, MDA and PCR. Data from 2013 Nucl Acids Res ref http://t.co/EFiVopa9d3 #AACR15
1:58pm April 18th 2015 via Hootsuite
RT @DebGrainger: Prob. one of the most "out there" slides I've seen at a scientific meeting. Ever. Found at #AACR15 http://t.co/7FbecQWUV5
1:53pm April 18th 2015 via Hootsuite
PVL: Shows fig 2010 PNAS allele-spec copy number variation http://t.co/3wIb4eTKth TGP phasing, clear changes 'Battenberg' cake-like #AACR15
1:47pm April 18th 2015 via Hootsuite
PVL: 'Most recent common ancestor' cell, 2012 Yates ref Nature Gen Rev http://t.co/hlfUSQIKOf #AACR15
1:43pm April 18th 2015 via Hootsuite
PVL: SKY karyotypes shown; genomes are clearly v. aberrant. Nice figure from '13 Stratton EMBO ref http://t.co/l8LvnM42Hw #AACR15
1:41pm April 18th 2015 via Hootsuite
Peter Van Loo (Francis Crick Inst London) “Molecular archeology of cancer” PVL #AACR15
1:38pm April 18th 2015 via Hootsuite
NN:Q:Any animal model data? A:Only starting, no data yet. #AACR15
1:36pm April 18th 2015 via Hootsuite
RT @LAbizar: #AACR15 Navin, tumor evolution by single cell seq shows punctuated evolution http://t.co/F2J9N85LSu
RT @LAbizar: #AACR15 Navin, MD Anderson, future directions in single cell sequencing http://t.co/Xu1dSgwg2s
1:35pm April 18th 2015 via Hootsuite
NN:Q:How consistent? A:Var between pts much higher than within individual. SC - all common lineage #AACR15
1:34pm April 18th 2015 via Hootsuite
NN: Shows evidence for punctuated evolution fig from 2014 Nature http://t.co/gnxbLTSKvL Barcoding 'shows many subclonal muts at <1%' #AAC
1:32pm April 18th 2015 via Hootsuite
NN: Doing molecular barcoding and ultra-deep (118K-fold) seq, to sequence in bulk but validate single-cell exome seq Can see 1/5,000 #AACR15
1:30pm April 18th 2015 via Hootsuite
NN: From 16 cells from same individual: some substructure there, huge diff between tumor & normal. #AACR15
1:29pm April 18th 2015 via Hootsuite
NN: Sometimes - muts in normal cells, could be mosaicism in norm dev. Onto TNBC: ER-/PR-/Her2-, two major populations by CNV #AACR15
1:28pm April 18th 2015 via Hootsuite
NN: ER+ single-cell seq for br ca: showed CNV heatmap, exomes show much more diversity. PIK3CA in almost all; CASP3 about 80% #AACR15
1:26pm April 18th 2015 via Hootsuite
NN: Looking at tumor evolution: 2011 Nature http://t.co/gwuAnjGR7N Single nucleus sequencing 2015 Genome Biol http://t.co/D5KxUVZMhG #AACR15
1:25pm April 18th 2015 via Hootsuite
NN: 'Lots of commercial solutions' - Fluidigm's C1, Nanostring, SiliconBiosystems, Clontech, BD, QIAGEN listed #AACR15
1:22pm April 18th 2015 via Hootsuite
NN: Coverage uniformity 'still a big issue'. Validation is a need. Concern: microbial contamination. Very pure reagents needed. #AACR15
1:21pm April 18th 2015 via Hootsuite
NN:Errors: allelic dropout 10-50%; FP 1e-5 to 1e-6; FN coverage 10-50%. Tech variation / errors 'can be falsely interpreted' #AACR15
1:19pm April 18th 2015 via Hootsuite
NN: @iontorrent Proton shown, among other platforms. 'Emerging technologies' (single-molecule) can be useful for single microbes #AACR15
1:18pm April 18th 2015 via Hootsuite
NN: Whole transcriptome: oligo-dT anchor, template switching. New method: random index (http://t.co/oJmuO5c3HU) #AACR15
1:17pm April 18th 2015 via Hootsuite
NN: WGA: DOP-PCR is degen. primers, mostly used for copy-number. MALBAC mentioned. #AACR15
1:16pm April 18th 2015 via Hootsuite
NN: For rare cells (<1%): CellSearch, DEPArray, CellCelector (microcapillary), MagSweeper, Nanofilters (size-exclusion, 7um pores) #AACR1
1:14pm April 18th 2015 via Hootsuite
NN: Methods: isolating can be by mouth pipetting, serial dilution, flow-sorting (we use 'quite a lot'), microfluidics (C1), LCM. #AACR15
1:13pm April 18th 2015 via Hootsuite
NN: Mentions 2013 Nature Methods 'method of the year' issue as a nice overview (although not focused on cancer). #AACR15
1:12pm April 18th 2015 via Hootsuite
NN: Future directions - single cell epigenome, multiplexing, RNA & DNA from same cell. #AACR15
NN: 2014 review http://t.co/ehY6mI1JoR A diversity index can be calculated to guide therapy, predict response, monitor, early det. #AACR15
1:10pm April 18th 2015 via Hootsuite
NN: Publication numbers and distribution - most pubs are on cancer. Navin & Wang review Mol Cell in press #AACR15
1:08pm April 18th 2015 via Hootsuite
NN: Leeuwenhoek & Hook 1600's; Virchof's cell theory, considered 'father of pathology'. Karyotyping, FISH http://t.co/LCYOHvYvgt #AACR15
1:06pm April 18th 2015 via Hootsuite
NN: Why single cells? Resolving diverse genomes in populations, rare cells, and substructure. Bulk tissue view of basal carcinoma #AACR15
1:04pm April 18th 2015 via Hootsuite
Nicholas Navin (MD Andersen) ‘Cancer genomics: one cell at a time’ NN #AACR15
1:03pm April 18th 2015 via Hootsuite
RT @fluidigm: The #AACR workshop on #SingleCell sequencing is about to start in room 115! http://t.co/KIp3njlkQi
For the next 5 days expect a flood of #AACR15 tweets thru 4/22 from 7am-6pm all about #cancer http://t.co/eNLrb64DCu
9:00am April 18th 2015 via Hootsuite
RT @vocativ: Science says your altruism is just evolution trying to make you attractive http://t.co/dnKR6OKr6i http://t.co/ODNXRtDw40
8:15am April 18th 2015 via Hootsuite
RT @iGEM: Many thanks to @Google for their sponsorship of #iGEM2015!!
7:15am April 18th 2015 via Hootsuite
RT @omespeak: San Diego to be featured in Nat Geo's 'World's Smartest Cities' program http://t.co/BZSe4Ai4WT
6:55am April 18th 2015 via Hootsuite
RT @Lee_Flea: Lion Torrent at the National Zoo, South Africa. See what I did there :) #IonMiniTour @iontorrent http://t.co/IzLTcA3RTh
5:55am April 18th 2015 via Hootsuite
RT @Xilouw: Ion Torrent Mini driving through Golden Gate @LifeTech #ionminitour #Travel #nature http://t.co/r7LhzQqtkH
4:50am April 18th 2015 via Hootsuite
RT @GENbio: Human pluripotent stem cells can be primed to enter a self-renewing state with trophoblast potential. http://t.co/f1hDGxe0LU
10:50pm April 17th 2015 via Hootsuite
Healthcare Information and Management Systems Society Keynotes Highlight the Speed of Innovation - Bio-IT World http://t.co/alE6iZOoEl
9:45pm April 17th 2015 via Hootsuite
RT @AACR: #AACR15 kicks off tomorrow in Philadelphia: http://t.co/Trf5YUGtLL http://t.co/zqeUMk6kJP
9:12pm April 17th 2015 via Hootsuite
RT @ale_miele: How to Turn Ph.D.s into Data Scientists and Data Engineers http://t.co/KBwuKNVQce by @bigdata - @advskills #datascience
8:00pm April 17th 2015 via Hootsuite
