Swanton: Ploidy analysis of primary nephrectormy cp to lung wall, very different allelic imbalance between the two #ncistg14
9:24am March 21st 2014 via Hootsuite
Swanton: Diag. of bottlenecking at metastatic sites - is there a subst. for diversity? #ncistg14
9:22am March 21st 2014 via Hootsuite
Swanton: 1960: macroevolution figure and quote - chromosomal structure, rearrangements, genome doubling etc. #ncistg14
9:21am March 21st 2014 via Hootsuite
Swanton: Challenge is cancer 'macroevolution'. Points to Goldschmidt book called 'hopeful monsters', rare events -> change #ncistg14
9:20am March 21st 2014 via Hootsuite
Swanton: Some complex tumors, illustrating very recent work in Nature Genetics ref: http://t.co/q1dSh0YOWR #ncistg14
9:19am March 21st 2014 via Hootsuite
Swanton: 1/3 of the mut's were non-synon. Showed branched evolution in ccRCC Ref: http://t.co/ME1mtg3JDy #ncistg14
9:18am March 21st 2014 via Hootsuite
Swanton: Implications of hetergeneity in cancer, ref: http://t.co/16vQ53WvFy #ncistg14
9:17am March 21st 2014 via Hootsuite
Charles Swanton, University College London. Tumour Heterogeneity and Cancer Evolution #ncistg14
9:16am March 21st 2014 via Hootsuite
Church: Original Cas9 Science paper had 190K guide RNAs, many more possible. Ref: http://t.co/Hdpknwy5bK #ncistg14
9:15am March 21st 2014 via Hootsuite
Church: Q: Can mtDNA be edited? A: Working on it, looks promising #ncistg14
9:14am March 21st 2014 via Hootsuite
Church: Synthetic epigenomics, with orthogonal Cas9 proteins, many more in the pipeline http://t.co/kipsMv7osP #ncistg14
9:12am March 21st 2014 via Hootsuite
Church: CRISPR can be in the MB range, also between chromosomes #ncistg14
9:10am March 21st 2014 via Hootsuite
Church: Improving Cas9 Nature Biotech ref: http://t.co/i8H6umYzt8 Now showing 3 to 83kb deletions #ncistg14
Church:CRISPR was in '87 considered junk DNA. As of 2013: 20 organisms modified #ncistg14
9:08am March 21st 2014 via Hootsuite
Church: Slide with many ways of genome targeting - 8 methods illustrated. Meganuclease, Recombinase, lamba bet/exo MAGE, RecA CAGE #ncistg14
9:07am March 21st 2014 via Hootsuite
Church: Making double-null CCR5 with ZFN - ex-vivo deletion for HIV resistance #ncistg14
9:06am March 21st 2014 via Hootsuite
Church: Gene therapy now has been revived - ~1970 clinical trials going on. Using ZnF nuclease (ZFN, Sangamo) using FokI dimers #ncistg14
Church: 3D imaging using OligoPaints method, like x-ray crystallography 2012 PNAS ref: http://t.co/7BTThiNwpE #ncistg14
9:05am March 21st 2014 via Hootsuite
Church: Technique enables resolution to go from 400nm to 10nm #ncistg14
9:03am March 21st 2014 via Hootsuite
Church: 10nm resolution uses small labeled nt with barcoded tags to get more color space. Ref here: http://t.co/m2CeSDNoxq #ncistg14
Church: Stratification uses a subset of RNAs - not a random primer (select out certain subset of RNAs) 1/4 or 1/16th the pop. #ncistg14
9:01am March 21st 2014 via Hootsuite
Church: Resolving crowded RNA sequences - thin sections, deconvolution, super-res (10nm), molecular stratification #ncistg14
Church: Applied to iPS cells, brain tissues, fibroblast, embryos #ncistg14
9:00am March 21st 2014 via Hootsuite
Church: Depth of fibronectin example is 0 to 15 reads along the exons; 8.9kb and 527 total reads #ncistg14
Church: Not looking at 3' end, it is full-length; showed data from fibronectin mRNA incl. alt splicing and alleles #ncistg14
8:59am March 21st 2014 via Hootsuite
Church: <50% from rRNA, per-base error 0.07% shows good reprod. via r-value vs # of observations #ncistg14
8:58am March 21st 2014 via Hootsuite
Church: Entire section is now a hydrogel; rigid enough to hyb over an over, 10nm resolution. Does SOLiD sequencing, by ligation #ncistg14
8:56am March 21st 2014 via Hootsuite
Church: FISSEQ - just came out in Science (here: http://t.co/BV5W1gGp0I ) 3D RNA in-situ sequencing. Diagrammed out method #ncistg14
8:55am March 21st 2014 via Hootsuite
Church: Done in 10 cells in 384 wells; the right number to use. What about 1 cell? <1 cell? #ncistg14
8:54am March 21st 2014 via Hootsuite
Church: Real accuracy: "clinical diplotype accuracy", pointing to the CGI/Harvard paper Nature July 2012 '1 error per 10M bp' #ncistg14
Church: Oops, that should be Jay Shendure Science 2005 #ncistg14
8:52am March 21st 2014 via Hootsuite
Church: Photo of Rob Mitra, Jay Shurdure, Drmanac and their seminal contributions to NGS #ncistg14
Church: Chart with exponential quality improvement - 10^9 (Q90 quality). Haplotype phase length - on the order of 3E06 #ncistg14
8:51am March 21st 2014 via Hootsuite
Church: HGP costs and Moore's law - Affordable genome would have been 60y from 2004. Turned out to be 6y. #ncistg14
8:50am March 21st 2014 via Hootsuite
Church: "What's next for sequencing?" single-cell and sub-cellular genetics. #ncistg14
8:49am March 21st 2014 via Hootsuite
Church: Cohort with NIST+FDA http://t.co/xbCiP2kWEe project (8 trios), along with ENCODE & GTEx perfectly consented etc. #ncistg14
Church: Personal Genomes project - http://t.co/1OI2rypeha is the only open access #WGS dataset + stem cell biobank #ncistg14
8:47am March 21st 2014 via Hootsuite
Church: Pivot to CRISPR organ-on-a-chip at Wyss. Referred to Ingber's work http://t.co/JBQPe3zmtn #ncistg14
8:46am March 21st 2014 via Hootsuite
Church: Rare alleles myostatin double null example. N=1, MSTN, can do causality analysis in bovine, canine, low atheroclerosis #ncistg14
8:44am March 21st 2014 via Hootsuite
Church: Supercentenarian study - listed 9 rare protected gene variants for low coronary, low Alzhemiers, low T2D, many double-null #ncistg14
8:43am March 21st 2014 via Hootsuite
Church: Began by referencing mutations that confer extreme radiation resistance in eLife http://t.co/LL9nfH11eC #ncistg14
8:42am March 21st 2014 via Hootsuite
George Church (Harvard) at the #NCI Translational Genomics #ncistg14 meeting http://t.co/1z2XfAAzGT
8:40am March 21st 2014 via Hootsuite
George Church, Harvard: New Technologies for Disease Prevention #ncistg14
8:31am March 21st 2014 via Hootsuite
Today's agenda at the #NCI 3rd Symposia on Translational Genomics #ncistg14 http://t.co/Da2qaZUWdG Church, Staudt, Baylin
8:16am March 21st 2014 via Hootsuite
Farnham: CRISPRs "are so much quicker and easier to clone" (Available from @LIFECorporation http://t.co/s1CUsefq6C )#ncistg14
4:11pm March 20th 2014 via Twitter Web Client
Farnham: Now look at stable repression - of 3K promoters, 30 bound promoters stay repressed, one of which was SOX2 #ncistg14
4:10pm March 20th 2014 via Twitter Web Client
Farnham: Showed by turning on the switch, ~3K promoters methylated. But H3K4me3 unaffected (!) #ncistg14
4:08pm March 20th 2014 via Twitter Web Client
Farnham: 'It went to 25k places in the genome'. Alt usage of the six ZNF's. 'Kind of crazy.' But tested it - look at bisulf. WGS #ncistg14
4:07pm March 20th 2014 via Twitter Web Client
Farnham: Using DNMT3a and a ZNF can toggle methylation of SOX2, or SKD to do the same #ncistg14
4:06pm March 20th 2014 via Twitter Web Client
Farnham: Toggling using more genome engineering - instead of deletion, engineer signals to turn genes on/off #ncistg14
4:05pm March 20th 2014 via Twitter Web Client
