February 2015

Richard Leggett, The Genome Analysis Centre UK “Towards Real-Time Surveillance Approaches Using Nanopore Sequencers” #AGBT15

8:49pm February 26th 2015 via Hootsuite

BW: Mainly gene bodies, promoters and fn elements; tissue-spec, sometimes not the proper cell types avail. #AGBT15

8:42pm February 26th 2015 via Hootsuite

BW: Used Agilent methyl-seq capture (84Mbp), >10x increase in diff methylated C's. 80% hypomethylation agrees w/previous obs. #AGBT15

8:41pm February 26th 2015 via Hootsuite

BW: See up-regulation; example of 2 genes shown, NXF3 and RUFY4. Data suggested epigenetic priming in vitro #AGBT15

8:40pm February 26th 2015 via Hootsuite

BW: Cp of model data to pt data: filtered consistent genes against normal RNA-Seq data, potential biomarkers & therapeutic targets #AGBT

8:39pm February 26th 2015 via Hootsuite

BW: Exp signatures recapitulated; showed changes in AML reg networks. #AGBT15

8:38pm February 26th 2015 via Hootsuite

BW: Barabe et al Science 2007 paper: http://t.co/QoRfuCydjl Model in mice; less noice than in original pts. #AGBT15

8:38pm February 26th 2015 via Hootsuite

BW: Adapt human cord blood model system; healthy cord blood from single donor, use retrovirus, expanded, xenografted #AGBT15

8:36pm February 26th 2015 via Hootsuite

BW: Celton 2014 ref: http://t.co/QRcim8XMLz for GATA2. 'Complex recomb. of SNVs are not experimentally tractable' #AGBT15

8:35pm February 26th 2015 via Hootsuite

BW: 430 adult AML, RNA-Seq. 'Long tail is more like a deep pool' Many examples of germ-line contributions - GATA2 example #AGBT15

8:33pm February 26th 2015 via Hootsuite

BW: Begins with figure from 24 br ca samples from Stratton's 2009 Nature paper http://t.co/SqLlJJgn5o 'long tail' of mutations #AGBT15

8:31pm February 26th 2015 via Hootsuite

Brian Wilhelm, Univ Montreal “Integrated Genetic and Epigenetic Analysis of Model and Patient Acute Myeloid Leukemias” #AGBT15

8:30pm February 26th 2015 via Hootsuite

JK: 10 AML samples; no normal tissue; low-coverage WGS and RNA-Seq. Unpublished data, will honor request #AGBT15

8:15pm February 26th 2015 via Hootsuite

JK:Chr banding most common for cytogenetics; another method multiplex FISH; third is aCGH '05 Nature Rev Gen http://t.co/g9xbef4M03 #AGBT15

8:14pm February 26th 2015 via Hootsuite

JK: Listed common translocations; 2013 NEJM piece: http://t.co/ChKYOTdqWt #AGBT15

8:12pm February 26th 2015 via Hootsuite

JK:Can we use NGS to complement or replace trad methods? Leukemia - ALL is blockage of certain differentiation; blasts result #AGBT15

8:10pm February 26th 2015 via Hootsuite

Jaeseung Kim, Ontario Inst Cancer Res “Identification of Cryptic Genomic Lesions in Complex Karyotype Leukemia” #AGBT15

8:09pm February 26th 2015 via Hootsuite

(Foundation) Q:Did you look at structure overall? A:No, mut freq for targeted approach similar tho #AGBT15

8:04pm February 26th 2015 via Hootsuite

(Foundation) Bargraph of genomic landscape of PACC's distinct from other panc tumors #AGBT15

7:59pm February 26th 2015 via Hootsuite

(Foundation) IHC for p-ERK:6/7 positive; neg samples 6/28 stain positive. 4 had other MAPK activating events #AGBT15

7:58pm February 26th 2015 via Hootsuite

(Foundation) Vanderbilt's W. Pau - functional char of SND1-BRAF activates MAPK pathway; tested MEK inhibitor, pan-RAF inh in models #AGBT15

7:57pm February 26th 2015 via Hootsuite

(Foundation) Also BRAF fusions w/novel upstream partners. (Kinase domains in BRAF always intact.) #AGBT15

7:56pm February 26th 2015 via Hootsuite

(Foundation) In their db of 15k samples; found 1 Cancer of Unk Primary #AGBT15

7:55pm February 26th 2015 via Hootsuite

(Foundation) 11 samples for RNA, for 33 genes. Found recurring SND1-BRAF fusion; fusion partners the same, breakpoints differ #AGBT15

7:54pm February 26th 2015 via Hootsuite

(Foundation) Difficult to target this tumor type - common drivers not there. 44 samples 287- or 485-genes on DNA, then RNA #AGBT15

7:53pm February 26th 2015 via Hootsuite

(Foundation Med) "Pancreatic Acinar Cell Carcinomas Harbor Recurrent RAF Fusion and Frequent Inactivation of DNA Repair Genes” #AGBT15

7:52pm February 26th 2015 via Hootsuite

DJ: 2x250 PCR-free + DISCOVAR de novo (tool built); tool for 10x ('tool building') #AGBT15

7:49pm February 26th 2015 via Hootsuite

DJ: 'Remarkably, it works!' Shows 160kb on one chromosome; DISCOVAR branching graphs: 'some resolvable if close enough' #AGBT15

7:48pm February 26th 2015 via Hootsuite

JF: Describes 10X Genomics tool. 200K droplets, each w/own barcode, each w/100kb long molecules (slide says '100' but it's 100kb) #AGBT15

7:42pm February 26th 2015 via Hootsuite

JF: 8 Ewing Sarcoma samples; EWSR1 'poking' the assembly to illus how easy to assemble and learn things #AGBT15

7:40pm February 26th 2015 via Hootsuite

DJ: Describing DISCOVAR and 'crazy-quilt' rearrangement. 2014 Nature Genetics http://t.co/yF1HpRY9zg #AGBT15

7:37pm February 26th 2015 via Hootsuite

David Jaffe (Broad Inst) "De novo identification of somatic mutations in cancer" #AGBT15

7:35pm February 26th 2015 via Hootsuite

RT @splon: J Bradner #AGBT15 lymphoma enhancer landscape studies show how poorly cell lines represent tumors. Tumors closer to lymph nodes.

5:06pm February 26th 2015 via Twitter Web Client

JB:Pleads for an 'outstanding bioinformatics post-doc' - apply http://t.co/C3ewHrjl0f @jaybradner #AGBT15

5:05pm February 26th 2015 via Hootsuite

JB:Also looking at super-enhancers for studying medullo-blastoma in press. #AGBT15

4:59pm February 26th 2015 via Hootsuite

JB:Their super-enhancers: more readily displaced; short xcr and protein half-life of myc shown. #AGBT15

4:56pm February 26th 2015 via Hootsuite

JB: About 10x the size of regular enhancers; 2014 Nature Biotech http://t.co/Yvhu88cSMd Different than locus ctrl regions. #AGBT15

4:54pm February 26th 2015 via Hootsuite

JB: Cell 2013 http://t.co/5WB7SkSoGR #AGBT15

4:52pm February 26th 2015 via Hootsuite

RT @obahcall: Join our @NatureRevGenet @illumina TweetUp TONIGHT 930pm Lobby Bar. Meet in person, chat science, publications, social media …

4:50pm February 26th 2015 via Twitter Web Client

JB: Developed BRD4 to study MYC. Thought it could facilitate MYC's effect to turn off gene exp #AGBT15

4:49pm February 26th 2015 via Hootsuite

JB: Nature '10 paper: http://t.co/AFJ0f0ZMfX Can test BRD4 compound w/ primary xenografts #AGBT15

4:47pm February 26th 2015 via Hootsuite

JB: 3D figure - large patch for a landing zone; H3K27ac binding site illustrated. BrDr4 (small molecule) called JQ1 described #AGBT15

4:45pm February 26th 2015 via Hootsuite

JB: Shows Lys27 neutralized via HAT adding an acetyl 'cap'. Shows bromodomains - disrupt the readers of lys acetylation #AGBT15

4:44pm February 26th 2015 via Hootsuite

JB: Illus RNAPII that seed recruitment; mentioned Brad Bernstein and Stam group at UW - H3K27me3 a repressor. H3K27ac activation #AGBT15

4:43pm February 26th 2015 via Hootsuite

JB: His bias: cancer a disease of regulatory regions, and regulatory factors. c-myc, TP53 work at the enhancer regions #AGBT15

4:41pm February 26th 2015 via Hootsuite

JB: Discovery chemistry lab: ability to measure genome-wide gene exp and protein measurements; new insights to cell biology #AGBT15

4:40pm February 26th 2015 via Hootsuite

James Bradner, Dana Farber Cancer Institute. “Disruption of Super Enhancers” #AGBT15

4:39pm February 26th 2015 via Hootsuite

JA:Found many types of reg variation; gene dupl. and protein-coding change at longer timescale. #AGBT15

4:36pm February 26th 2015 via Hootsuite