CA: Oncogenes - ER has overexp of HER2; Ser119 '01 ref http://t.co/XtakNVVDKm #AACR15
5:38pm April 19th 2015 via Hootsuite
CA:Subtypes of br ca: 75% endocrine therapy, 20% Her2, rest TNBC 15%. ER+ br ca exhibit long-term risk of recurrance #AACR15
5:36pm April 19th 2015 via Hootsuite
Carlos Arteaga (Vanderbilt Univ TN) “Mech of resist. to endocrine therapy: Insights from translational studies in breast cancer” CA #AACR15
5:34pm April 19th 2015 via Hootsuite
JB: Collecting systematic data at-scale, dependencies validate pt-specific mutations. #AACR15
4:22pm April 19th 2015 via Hootsuite
JB: (Cell Line Factory homepage at Broad Inst: http://t.co/bo4x2f95Ur ) and they are looking for more participants. #AACR15
4:21pm April 19th 2015 via Hootsuite
JB:Next: create new models to test genome-nominated dependencies called 'Cancer Cell Line Factory'. >30 co-PI's, 8 inst, 16 ca types #AAC
4:20pm April 19th 2015 via Hootsuite
JB: Called TumorPlex screen; can distinguish rare var's that distinguish between drivers & passengers. Tested w/ 5 known oncogenes #AACR
4:18pm April 19th 2015 via Hootsuite
JB: Next: High-TP, barcoded array of 256 pathway activators, all comb. of 16 unique cDNA into RAS-minus cell lines #AACR15
4:16pm April 19th 2015 via Hootsuite
JB: #AACR15 Figure of 334 ling ca somatic variation impact: GOF, LOF, and Impactful. http://t.co/UhAHW2BZwU
4:14pm April 19th 2015 via Hootsuite
JB: Changes in gene exp can predict variant impact. Ex: ARAF L96Q, cp WT to MUT alleles. GOF, LOF, no effect, 'impactful' ambiguous #AACR15
4:12pm April 19th 2015 via Hootsuite
JB: Gene exp, morphologic profiling. L1000 gene exp - Luminex-based profiling of 1000 transcripts ("cost effective") from Golub lab #AACR15
4:11pm April 19th 2015 via Hootsuite
JB: Lentiviral clones with perturbation tools. For lung ca/pan-cancer, gene-agnostic info-rich bioassays. #AACR15
4:10pm April 19th 2015 via Hootsuite
JB:Majority of variation in ca genomes: 'exceedingly rare'. #AACR15 '14 Nature fig http://t.co/v2WMS0g6XG Have dev 'Target Accellerator'
4:09pm April 19th 2015 via Hootsuite
Jesse Boehm (Broad Inst MA) “Towards precision functional genomics via next-gen functional mapping of cancer variants” JB #AACR15
4:07pm April 19th 2015 via Hootsuite
GG:Q:Possible heterogeneity of primary sites for met-met transmission? A:Sample-limited, only 10 samples 1 primary #AACR15
4:06pm April 19th 2015 via Hootsuite
GG: This work just published in Nature http://t.co/LFOsxvXrrI TS commonly deleted before metastasis. AR ampl after spread #AACR15
4:04pm April 19th 2015 via Hootsuite
GG: Observed 'met to met transmission' - all tumors at that site have all the same mut's. 7/10 individs. #AACR15
4:02pm April 19th 2015 via Hootsuite
GG: Mets are 'more similar to each other than to the original prostate cancer', 5/5 samples. #AACR15
4:01pm April 19th 2015 via Hootsuite
GG:Shows another pair where it appears that there were multiple 'seeds' on secondary site. (Beauty of having multiple smpls/individ) #AACR15
3:59pm April 19th 2015 via Hootsuite
GG: Reconstructed phylogeny of subclones looking at clusters of mutations; cp 2 samples from same indiv. (called nD-DP) #AACR15
3:58pm April 19th 2015 via Hootsuite
GG: AR signalting - usu. specific to indiv. samples, likely convergent evolution ('off-trunk') already metastasized. #AACR15
3:55pm April 19th 2015 via Hootsuite
GG: Timing of events on or off 'trunk' - TS 'common to all samples, likely present in the prostate primary'. #AACR15
GG: WGS 51 samples from 10 individ's. Insertions, deletions, substs. Classed as 'trunk' (100% of cells), 'leaf' (one site) 'branch' #AACR15
3:54pm April 19th 2015 via Hootsuite
GG: Looking at evolution in metastatic prostate ca Fig from Yates paepr http://t.co/LpYwTVhmOj PELICAN data #AACR15
3:52pm April 19th 2015 via Hootsuite
Gunes Gundem (Wellcome Trust) The life history of lethal metastatic prostate cancer GG #AACR15
3:50pm April 19th 2015 via Hootsuite
CG:Q:Any common genes for metastasis? A:Many genes involved, but focused on KRAS-driven cancers #AACR15
3:49pm April 19th 2015 via Hootsuite
CG:Moving to human HBEC iKRAS^G12D tumorigenesis; their screened hits are invasive in HBEC's #AACR15
3:48pm April 19th 2015 via Hootsuite
CG: Chart of genes by abundance of barcodes per gene by number of mice. MYC as reference. 80% genes at 0. #AACR15 http://t.co/k2fVxQ58Mk
3:46pm April 19th 2015 via Hootsuite
CG: One mouse - detect relative abundance of barcode for a given gene. THRA drives tumor for both sub-cut and for lung met #AACR15
3:43pm April 19th 2015 via Hootsuite
CG: Lentivirus, got 225 barcoded tumor candidate lines. Doing in vivo metastatis screening, then look for NGS barcode enrichment #AACR15
3:42pm April 19th 2015 via Hootsuite
CG: HiTMMoB - high-tp mutagenesis + molecular barcoding. >35K seq annotated ORF clones. Mouse model from MD Anderson KRAS^G12D tumor #AAC
3:40pm April 19th 2015 via Hootsuite
CG: NSCLC 85-90% have common drivers. Their fn genomics have many tools - tumorigenicity/metastasis in mouse models. #AACR15
3:39pm April 19th 2015 via Hootsuite
Caitlin Grzeskowiak (Baylor TX) "High-throughput functional screening for metastasis drivers of lung cancer" CG #AACR15
3:38pm April 19th 2015 via Hootsuite
NS:Q:Able to get AF to assess clonality? A:RNA-Seq data, so balance betw. normal & fusion may not be consistent. #AACR15
3:35pm April 19th 2015 via Hootsuite
NS: Summary: 6 add'l #TCGA types surveyed for fusions. Novel ALG14-JAK1, 2 new FGR fusions, New NTRK1/3/2 pan-ca fusions #AACR15
3:33pm April 19th 2015 via Hootsuite
NS: Novel MET & PIK3CA fusions - in solid tumors where muts and ampl are already driver events. High copy number, highest w/fusion #AACR
3:30pm April 19th 2015 via Hootsuite
NS: Red - new fusion; Orange - Known kinase, novel partner. #AACR15
3:29pm April 19th 2015 via Hootsuite
NS: The landscape of novel fusions; purple= known fusion, novel indication http://t.co/N90nWeZELz #AACR15
3:28pm April 19th 2015 via Hootsuite
NS: Shows >20 fusion partner genes by cancer type; new partners, known existing fusions recapitulated, novel fusions #AACR15
3:26pm April 19th 2015 via Hootsuite
NS: Algorithm: ID's gene-gene fusions from RNA-Seq data, reports supporting evidence. Filters out passenger events, FPs (artifacts) #AACR15
3:23pm April 19th 2015 via Hootsuite
Nicolas Stransky (Blueprint Medicines Cambridge MA) The landscape of kinase fusions in cancer NS #AACR15
3:22pm April 19th 2015 via Hootsuite
RS: Making a vaccine for T3-tumor bearing mice, and cure them 'almost as good as the checkpoint inhibitors' #AACR15
11:34am April 19th 2015 via Hootsuite
RS: Confirmed in-vivo; detected by MS proteomics; det. accumulation of two peptides; long peptides can be used as prophyl vaccine #AACR15
RS: Showed H-2Kb epitope binding dozens of mutations; CD8+ TILs from T3 mice recognize the two predicted peptides. #AACR15
11:32am April 19th 2015 via Hootsuite
RS: Looked at exome of tumor/normal, apply prediction, synth peptides, make p-MHC-I tetramers / pepide-pulsed splenocytes #AACR15
11:29am April 19th 2015 via Hootsuite
RS:Edited T3 MCA sarcoma, with mAb can cure mice against immune checkpoints Nature '14 ref http://t.co/57ct5T3y6A cDNA cap-seq #AACR15
11:28am April 19th 2015 via Hootsuite
RS: Asks tumor-spec mutant neoantigens;. Nature '12 http://t.co/5nQ1EbRQcL used prediction for tumor-spec rejection antigens #AACR15
11:25am April 19th 2015 via Hootsuite
RS: WT are exposed to immune system, typical of what is seen in cancer cases. Current view Science '11 ref http://t.co/u40GKhzeWs #AACR15
11:23am April 19th 2015 via Hootsuite
RS: Unedited, RAG2 -/- mice have high immunogenicity, good models for nascent tumor cells (prior to immune interaction) #AACR15
11:19am April 19th 2015 via Hootsuite
RS: Immunoediting - Elimination, Equilibrium and Escape; 15y ago, fig from '01 Nature ref http://t.co/hzK3pcO7TX RAG2 unedited vs WT #AACR15
