Zenklusen: Announced 3rd annual TCGA symposium in May http://t.co/En6pe5NtvO #ncistg14
2:16pm March 21st 2014 via Hootsuite
Zenklusen: Huge datasets for TCGA (petabytes); downloadable but not very usable. Working on a 'genomics data commons' #ncistg14
2:14pm March 21st 2014 via Hootsuite
Zenklusen: They have 100d after 100 cases of a tumor type have data generated, analysis groups must work fast #ncistg14
2:12pm March 21st 2014 via Hootsuite
Zenklusen: Only request for TCGA is not to publish cross-platforms (what the major TCGA papers will do) #ncistg14
2:11pm March 21st 2014 via Hootsuite
Zenklusen: TCGA data is released under Ft. Lauderdale principles (PDF: http://t.co/p2YI2HHi2c ) #ncistg14
2:10pm March 21st 2014 via Hootsuite
Zenklusen: Top lesson: "It's about pathways and integrated analysis" #ncistg14
2:02pm March 21st 2014 via Hootsuite
Zenklusen: 3 Nature publications; 6 submitted and 1 more (lung adenocarcinoma) accepted #ncistg14
Zenklusen: Data collection is the bane; 3m to 2y, map of participating centers nationwide; data generation 45-180d #ncistg14
2:00pm March 21st 2014 via Hootsuite
Zenklusen: 'We will be available for followup forever". 132k samples of RNA/DNA/protein shipped since 2006 #ncistg14
1:59pm March 21st 2014 via Hootsuite
Zenklusen: Rare tumor project approved Mar 2012; 50-100 samples per type getting enough samples not easy http://t.co/xESCyQI8lo #ncistg14
1:55pm March 21st 2014 via Hootsuite
Zenklusen: Supplemental data would be 50x WGS, 7x WGS, Methylseq, RPPA (reverse phase protein arrays) #ncistg14
1:52pm March 21st 2014 via Hootsuite
Zenklusen: Core dataset includes histology images, pathology, WES, SNPs, mRNAseq, miRNAseq, methylation array #ncistg14
1:51pm March 21st 2014 via Hootsuite
Zenklusen: Biospecimen resource core, 6 genome char centers., 3 genome centers, 7 data analysis centers #ncistg14
1:49pm March 21st 2014 via Hootsuite
Zenklusen: Finished accruing 11K-12K samples; characterization through end of '14; analysis completion of 35 tumors total #ncistg14
1:48pm March 21st 2014 via Hootsuite
Zenklusen: "TCGA is science, but sometimes it's accounting" #ncistg14
1:46pm March 21st 2014 via Hootsuite
Jean Claude Zenklusen, Center for Cancer Genomics, NCI: The State of The Cancer Genome Atlas #ncistg14
1:45pm March 21st 2014 via Hootsuite
Staudt: ~17 compounds targeting AGC DLBCLwith ibrutinib #ncistg14
1:42pm March 21st 2014 via Hootsuite
Staudt: ABC DLBCL cell survival depends on particular IgVh region, Apoptotic dead cells release antigens that simulate BCR's #ncistg14
1:27pm March 21st 2014 via Hootsuite
Staudt: Antigen-induced B-cell receptor clustering visualized by TIRF microscopy. #ncistg14
1:25pm March 21st 2014 via Hootsuite
Louis Staudt, NCI. Using Genomics to Understand Response and Resistance to Targeted Therapy in Lymphoma #ncistg14
1:18pm March 21st 2014 via Hootsuite
Barrett: Breast Cancer Genome Guided Therapy study (BEAUTY) http://t.co/WpZ6XJtEti #ncistg14
12:02pm March 21st 2014 via Hootsuite
Barrett: Aneuploid peak can be further segmented into Vimentin +/-, Ki67, etc #ncistg14
11:48am March 21st 2014 via Hootsuite
Barrett: Ploidy is one parameter; can also use other parameters with cell surface markers or nuclear ones #ncistg14
11:47am March 21st 2014 via Hootsuite
Barrett: CNV analysis of a 3.8N, only 7.6% of the cell population. Can be done using FFPE tissue (!) #ncistg14
11:46am March 21st 2014 via Hootsuite
Barrett: Sorting on the basis of DNA content using a UV laser. 2.0N, 3.2N, 4N, 6.4N #ncistg14
11:45am March 21st 2014 via Hootsuite
Barrett: Photo of instruments used for solid tumor flow; an open system with low CV's, high discrimination using DNA content #ncistg14
Barrett: Can collect 4 streams, diploid, aneuploid, two smaller fractions. Optimized for downstream analysis #ncistg14
11:44am March 21st 2014 via Hootsuite
Barrett: Doing clonal profiling with flow sorting of neoplastic cells from biopsy. Solid tumors, to give cells or nuclei #ncistg14
11:43am March 21st 2014 via Hootsuite
Barrett: Pancreatic cancer has lots of stroma scarring; 'like a rock', only 20% tumor content #ncistg14
11:42am March 21st 2014 via Hootsuite
Barrett: Clonal evolution diagram from 1976 Science ref. http://t.co/F5nElkQYBB #ncistg14
11:41am March 21st 2014 via Hootsuite
Michael T. Barrett, Translational Genomics Research Institute: Clonal Heterogeneity and Clinical Phenotypes #ncistg14
11:38am March 21st 2014 via Hootsuite
Tlsty: Q: Circulating ePS? A: All have different markers, high CD90. ePS are CD90 negative. #ncistg14
11:35am March 21st 2014 via Hootsuite
Tlsty: A: Doesn't think it is unique to organ, as many tissues (incl esophagus) have been used. #ncistg14
11:34am March 21st 2014 via Hootsuite
Tlsty: Q:Have eye ePS have been tried? A: not yet, p16 repressed and then non-repressed (hallmark of differentiation) #ncistg14
11:32am March 21st 2014 via Hootsuite
Tlsty: Q:Future in translational? A: ePS in regenerative medicine - if they can be activated and controlled #ncistg14
11:31am March 21st 2014 via Hootsuite
Tlsty: Suggests that microenvironment can turn on cancer plasticity as a hallmark of cancer (Hanahan) #ncistg14
11:30am March 21st 2014 via Hootsuite
Tlsty: hESCs do not express CD73; no effect on SON expression in hESCs #ncistg14
11:25am March 21st 2014 via Hootsuite
Tlsty: CD73 inhibition: a 5' nucleotidase to create adenosine. CD73 knockdown affects SON #ncistg14
11:24am March 21st 2014 via Hootsuite
Tlsty: ePS are rare, 'reserve cells'. Found in other tissues (pancreas ePS cells can create ectodermal tissue) #ncistg14
11:21am March 21st 2014 via Hootsuite
Tlsty: ePS cells do not challenge concept of tissue-specific stem cells (exist side-by-side). May contribute to wound healing #ncistg14
11:20am March 21st 2014 via Hootsuite
Tlsty: Criteria of pleuripotency 2004 Cell ref: http://t.co/mZJUIeOjy4 Validated independently, indistinguishable #ncistg14
11:19am March 21st 2014 via Hootsuite
Tlsty: Telomerase activity confirms mortality, also normal karyotype after 59 doublings #ncistg14
11:18am March 21st 2014 via Hootsuite
Tlsty: ePS are mortal and genomically intact. Can be expanded - ~59 doublings; after 120d culture majority of cells in G1 #ncistg14
11:17am March 21st 2014 via Hootsuite
Tlsty: ePS compared to hESC and iPS and mesenchymal stem cells and mammary stem cells: ePS are different in expression, markers #ncistg14
11:16am March 21st 2014 via Hootsuite
Tlsty: Forensic analysis (STR) confirms lineage of tissue of ePS #ncistg14
11:15am March 21st 2014 via Hootsuite
Tlsty: R1 fx co-expresses pluripotency markers Oct3/4, Sox2, Nanog. Called ePS (endogenous Plastic Somatic cells) #ncistg14
11:14am March 21st 2014 via Hootsuite
Tlsty: All R1 cells were not cultured. Were they homogeneous however? A single cell does have the lineage diff. ability #ncistg14
Tlsty: R1 can create teratomas, three main derivatives and others; R2-R4 no growths. R1 cells are not malignant #ncistg14
11:12am March 21st 2014 via Hootsuite
Tlsty: Most difficult - endodermal lineage using published protocols; SOX17 and FOXA2, then pancreatic lineage #ncistg14
11:10am March 21st 2014 via Hootsuite
Tlsty: R1 also differentiate into CD31-pos HUVEC cells; R1 can also differentiate into cardiomyocytes -both molecular + functional #ncistg14
11:09am March 21st 2014 via Hootsuite
