Rahman: VUS - she receives 'several emails per day' about this (VUS = variant of unknown significance) #AACR14
4:47pm April 5th 2014 via Hootsuite
Rahman: The new bottleneck - what does it mean, how to deliver it. Interpretation tool developed. #AACR14
4:46pm April 5th 2014 via Hootsuite
Rahman: 96 samples / 8h found 100% sensitivity / specificity for BRCA #AACR14
4:45pm April 5th 2014 via Hootsuite
Rahman: Analysis is called GAMA, much more complicated than anticipated; 'you will need to tailor it for your setting' investment #AACR14
4:44pm April 5th 2014 via Hootsuite
Rahman: They helped developed the ILMN TruSight Cancer, 50ng input, 95% of samples 95% target at least 50x, median 1000x coverage #AACR14
Rahman: MCG 'likely to change to WES / WGS in time' but a few years before it happens #AACR14
4:43pm April 5th 2014 via Hootsuite
Rahman: The MCG effort focuses on targeted, HTP assays. "Must be at least equiv. to existing ones" #AACR14
4:42pm April 5th 2014 via Hootsuite
Rahman: Mainstreaming Cancer Genetics website http://t.co/kYF6ssMF0B #AACR14
4:40pm April 5th 2014 via Hootsuite
Rahman: (By the way, the speaker can be found on Twitter here: http://t.co/Dh6oeDMJjy ) #AACR14
4:39pm April 5th 2014 via Hootsuite
Rahman: Pedigree example shared; look at the potential for cancer prevention where future generations would be aware of status #AACR14
4:38pm April 5th 2014 via Hootsuite
Rahman: CPG's have impacts on management - co-risk of other cancer types with BRCA. PARP inh, as example for personalized effort #AACR14
4:35pm April 5th 2014 via Hootsuite
.@splon You are so generous!
4:33pm April 5th 2014 via Hootsuite in reply to
Rahman:Looking at germline predisposition in cancer. >100 Cancer Predisposition Genes (CPG) #AACR14 PubMed http://t.co/hqOpBZlz2b
4:33pm April 5th 2014 via Hootsuite
Next: N Razman Inst Cancer Res "Implementing large-scale testing of cancer predisposition genes: Maximising benefits, minimising harms"
4:31pm April 5th 2014 via Hootsuite
Strong: Showed KRAS amplification example from this Mohan et al PLoS Genet 2014 PubMed http://t.co/uAxbhzgotX #AACR14
4:29pm April 5th 2014 via Hootsuite
Strong: Looking at ctDNA - Bettegowda Sci Trans Med 2014 paper PubMed http://t.co/SZMRhqmo9R 'could be nice proof of principle' #AACR14
4:27pm April 5th 2014 via Hootsuite
Strong: Showed varying results across 12 WGS samples reported in Dewey et al JAMA PubMed http://t.co/97DymBl42w #AACR14
4:25pm April 5th 2014 via Hootsuite
Strong: Lack of consensus, lack of std'ized processes with NGS (laundry list incl. pipelines, curation, phenotype/genotype DBs #AACR14
4:22pm April 5th 2014 via Hootsuite
Strong: Other barriers are primary care provider attitudes, education Strong et al 2014 PubMed http://t.co/3NWVvOHxog #AACR14
4:19pm April 5th 2014 via Hootsuite
Up first: session chair Louise Strong, UT MD Anderson Barriers to NGS in the clinical research setting - public attitudes #AACR14
4:16pm April 5th 2014 via Hootsuite
Educational session: "Clinical Cancer Genetics in the Next Generation Sequencing Era" #AACR14
4:14pm April 5th 2014 via Hootsuite
Zender: Upon knockdown, decrease in Raf1, MEK, Erk indicating cross-signalling #AACR14
2:35pm April 5th 2014 via Hootsuite
Zender: p38 MAPK signalling: suppression plus sorafenib, used @ingenuity IPA with gene expression for analysis #AACR14
2:34pm April 5th 2014 via Hootsuite
Zender: Used 250 shRNAs of 100 human HCC's with focal genome amplifications #AACR14
2:28pm April 5th 2014 via Hootsuite
Zender: Use mouse liver cancer mouse model and stable RNAi to directly conduct in-vivo work on Sorafenib sensitizers #AACR14
2:27pm April 5th 2014 via Hootsuite
.@mucociliary Thank you for the kind words, Ian.
2:20pm April 5th 2014 via Hootsuite in reply to
Zender: Mouse model for hepatocellular carcinoma. Tn vector, a few weeks to (end-point) #AACR14
2:18pm April 5th 2014 via Hootsuite
Zender: >90% of all oncology Phase I trials fail; 'the pre-cliinical bar should be higher' #AACR14
2:16pm April 5th 2014 via Hootsuite
Next up: Lars Zender Univ Hosp Tuebingen "In vivo functional genetic screens" #AACR14
2:13pm April 5th 2014 via Hootsuite
Root: Q:P53 and MDM4 dependency? A: Have seen non-intuitive direction, inverse directions than expected #AACR14
2:12pm April 5th 2014 via Hootsuite
Root: A: CRISPR can also have other off-target effects, yet to be fully known. Also: what fx has the knockout? +/- selelection... #AACR14
2:10pm April 5th 2014 via Hootsuite
Root: Q:CRISPR vs RNAi in med term? A: Haploinsufficiency different than knockout; anectdotally - different effects (CYCLOPS) #AACR14
2:09pm April 5th 2014 via Hootsuite
Root: Also other tools include mouse in vivo xenografts, growth in agar, co-cultured cells #AACR14
2:07pm April 5th 2014 via Hootsuite
Root: Can use other tools - CRISPR, used for both + and - selection screens, they are doing that but in progress how well it works #AACR14
2:06pm April 5th 2014 via Hootsuite
Root: Achilles is available - find genes that have shown dependencies per shRNA screen http://t.co/YfRI4SVN36 #AACR14
2:04pm April 5th 2014 via Hootsuite
Root: This 'CYCLOPS' work described here in 2012 Cell (PubMed) http://t.co/9buNt1lV1J #AACR14
2:03pm April 5th 2014 via Hootsuite
Root: Dependency ass'd with copy number loss: CYCLOPS: a subset of hemizygously deleted genes that are highly essential #AACR14
2:02pm April 5th 2014 via Hootsuite
Root: Looked at Wnt active vs non-active across 102 cell lines. "Genes to pathways to networks"; codependency examples #AACR14
2:01pm April 5th 2014 via Hootsuite
Root: Looked at ARID1B as essential for ARID1A mutant tumor cells Refers to Helming PubMed ttp://ow.ly/vsZ6L #AACR14 h
1:58pm April 5th 2014 via Hootsuite
Root: PIK3CA mut's, many others - found 9 known and 5 new discoveries, Q-values <10^5, using Achillles 2.4 #AACR14
1:57pm April 5th 2014 via Hootsuite
.@zmadak Have to think pretty fast too - esp when looking up stuff on the web. Love the 'Wang et al PLoS One 2012' reference. 2400 found!
1:56pm April 5th 2014 via Hootsuite in reply to
.@zmadak No, just Firefox on an old XP machine, use Hootsuite (could use Twitter's main interface, just preference). And I type pretty fast.
1:55pm April 5th 2014 via Hootsuite in reply to
Root: Ceveloped a gene scoring method. Citation: Tsherniak Ataris tool PubMed http://t.co/eqymzpjILY #AACR14
1:53pm April 5th 2014 via Hootsuite
Root: Use about 5 shRNA's/gene, effects vary in terms of off-target, varying suppression level. Can't just average out signal #AACR14
1:52pm April 5th 2014 via Hootsuite
Root: But also found idiosyncratic genes in their cell lines as well. #AACR14
1:51pm April 5th 2014 via Hootsuite
Root: In 12 lines also ID's cell-line-specific essential genes. BCR / ABL in K562 line (CML leukemia line) #AACR14
Root: Project Achillles - how the pooling shRNA libraries is impt; http://t.co/riKQ0qL5Lt ID'd 8 commonly essential genes (12 lines) #AACR14
1:50pm April 5th 2014 via Hootsuite
Root: Cancer Cell Line Encyclopedia resource at the Broad Inst here: http://t.co/vySZqIPqyv #AACR14
1:48pm April 5th 2014 via Hootsuite
Root: Approach - large # of ca cell lines, activation of pathways, link dependencies and genetic features; then assess these #AACR14
1:47pm April 5th 2014 via Hootsuite
Next up: David Root Broad Inst "Large-scale screens for cancer cell genetic dependencies " #AACR14
1:43pm April 5th 2014 via Hootsuite
