ICYMI: #AACR18 video interview with Pillar Biosciences' poster presenter on targeted NGS down to 2% MAF from FFPE https://t.co/C8t66V76e7
11:54am April 20th 2018 via Hootsuite
Great to meet new friends and catch up with familiar ones at #AACR18 - see you in Atlanta at #AACR19 !
5:04pm April 18th 2018 via Hootsuite
Spira: #AACR18 Intralesional inj of anti-PD-1 w/DCIS. 'Field effect' as an approach - cancers as gene x env. May extend to liquid biopsy
1:34pm April 18th 2018 via Hootsuite
Spira: #AACR18 Slide from Eva Szabo from NCI: immunopreventions 'will be the future of this field'. Finn: MUC1 Ag as prev. vaccine for CRC
1:30pm April 18th 2018 via Hootsuite
Spira: Also RNAseq of pre-cancerous lesions of immune microenv - down-reg genes lesions progressed. FISH showed mphage low, CD8 low #AACR18
1:28pm April 18th 2018 via Hootsuite
Spira: #AACR18 Feasibility - '15 ref https://t.co/t8yyHn1Me3 squamous lung premalignant lesions. Campbell here: showing CNV mod to severe
1:26pm April 18th 2018 via Hootsuite
Spira: #AACR18 Look at cancer as a chronic disease; the case for a pre-cancer atlas (PCA), very difficult to collect pre-malignant tissue
1:24pm April 18th 2018 via Hootsuite
Spira: #AACR18 Cardiogists are now intercepting cancer '17 ref https://t.co/8gAVIGXSGw 67% reduction in lung ca due to inflamm
1:21pm April 18th 2018 via Hootsuite
Spira: #AACR18 Vogelstein con't "50% of our efforts directed to early detection and prevention".
Spira: #AACR18 Quotes Volgelstein '17 in ASCO Post "Cardiologists are doing it right - the focus has been on prevention' of massive infarcts
1:19pm April 18th 2018 via Hootsuite
Avrum Spira (Boston Univ MA) Prevention and Survivorship/Precision Prevention and Interception #AACR18
1:18pm April 18th 2018 via Hootsuite
Mardis: Layout is four talks: Prevention (Spira), Basic Research (Mardis), Clinical, and Look to the Future talks. #AACR18
1:17pm April 18th 2018 via Hootsuite
Elaine Mardis giving the closing introduction at #AACR18 https://t.co/WZU3pi33Y2
Shah: #AACR18 Can now do CNV analysis on thousands of cells. Shows graph of increase from 4/17 to now: 167k cells, 216 libraries
12:34pm April 18th 2018 via Hootsuite
Shah: #AACR18 Have worked on opening up from microfluidic platform (cumbersome) to robotic pin nano-well, 5K-well arrays, can pool and seq
12:33pm April 18th 2018 via Hootsuite
Shah: #AACR18 Can bin reads across intervals, to get CNV inferred from low-coverage sc genomes. Can pool and get higher resolution (SNVs)
12:32pm April 18th 2018 via Hootsuite
Shah: #AACR18 Interested in rare poplns, want statistical power. Tagmentation - '17 https://t.co/NeOHTPt3Ub but only get sparse represent.
12:31pm April 18th 2018 via Hootsuite
Shah: #AACR18 sc measurements at scale:decomposing cancer into its constituent parts; errors are present. Thus scWGS and phase and haplotype
12:30pm April 18th 2018 via Hootsuite
Shah: #AACR18 Points out individual clones from original tumor, led to brain met, and secondary recurr. Visual '17 https://t.co/GgPgTzple7
12:29pm April 18th 2018 via Hootsuite
Shah: #AACR18 Modeling: an ov ca cell map (metastatic to brain) and secondary relapse and sequenced clones '16 ref https://t.co/j362nPV2sY
12:28pm April 18th 2018 via Hootsuite
Shah: #AACR18 What cell popln's constitute a tumor? Can trajectories be predicted? What is their behavior?
12:26pm April 18th 2018 via Hootsuite
Shah: #AACR18 Now onto the genome of malignant cells; WGS and working with Sam Aparicio at BCCA. Cancer as dynamic raises Q's.
12:25pm April 18th 2018 via Hootsuite
Sohrab Shah (BC Cancer Agency CA) Scalable single cell whole genome sequencing: Towards population genetics of cancer #AACR18
12:24pm April 18th 2018 via Hootsuite
Q: Any way to do spatial hi-dimensional methods? Shields: Will lose info w/dissociation of cells. Will go that way #AACR18
Q: Always see 3 populations? Shields: Likely at day 11; looking at other cancer types as well #AACR18
12:22pm April 18th 2018 via Hootsuite
Q: Spatial imptc? Shields: Likely, what these cells are producing in local environment, if populations affect each other #AACR18
12:20pm April 18th 2018 via Hootsuite
Shields: #AACR18 Id'd 'inflammatory CAFs' - CXCL12-expressing CAFs that recruit macrophages.
12:19pm April 18th 2018 via Hootsuite
Shields: #AACR18 Shows progression of CD8 T-cell expansion from naive, to active, to exhausted over time. 309 CAFs over time points: 3 clust
12:13pm April 18th 2018 via Hootsuite
Shields: #AACR18 Remove tumor cells (mCherry+), narrow immune populations. Shows immune cell subpopulations; also by site, and over time
12:10pm April 18th 2018 via Hootsuite
Shields: #AACR18 Thus scRNASeq; explore CAF heterogeneity in tumor microenv. Subcut inj of B16 melanoma, 3 time points
12:09pm April 18th 2018 via Hootsuite
Shields: #AACR18 Feig et al and Ozdemier et al had different results. Depleting CAFs decr / incr tumor growth? https://t.co/uUV9XKWeRV
12:08pm April 18th 2018 via Hootsuite
Shields: #AACR18 Not universal CAF marker (carcinoma assoc'd fibroblast). They are hetergeneous population of cells. What roles?
12:07pm April 18th 2018 via Hootsuite
Shields: #AACR18 Lymphatic biology: podoplanin in tumor stroma related to poor prognosis. Immune cell direct interact. Fibroblast role?
12:06pm April 18th 2018 via Hootsuite
Shields: #AACR18 Growth factors, angiogenesis, lymphangiogenesis, invasion and metastasis, ECM remodeling. Recent: immune infiltration
12:03pm April 18th 2018 via Hootsuite
Shields: The tumor microenv - blood vessels, lymph vessels, macrophages, fibroblasts, neutrophils, lymphocyte, extracell matrix #AACR18
12:02pm April 18th 2018 via Hootsuite
Jacqui Shields (Univ Cambridge UK) Exploiting single cell approaches to define the evolving tumor microenvironment #AACR18 (All unpubl work)
12:01pm April 18th 2018 via Hootsuite
Shain: #AACR18 Shows p14 not indicative for invasion. Zheng Judson Cancer Cell (in revision), bi-allelic los of CDKN2A init mel invasion
11:54am April 18th 2018 via Hootsuite
Shain: #AACR18 Cell cycle disruption too: CDKN2A encodes p16/INK4A and p14/ARF, produce two products. Shows p16 low-level w/invasive
11:53am April 18th 2018 via Hootsuite
Shain: #AACR18 Shows clear expr. clustering data, between nevus and invasive. A shift forward to polycomb repressive complex 2.
11:51am April 18th 2018 via Hootsuite
Shain: #AACR18 SWI/SNF and PRC2 are antagonistic; reviews benign vs malignant polycomb targets, H3K27me3 blocked in benign.
11:50am April 18th 2018 via Hootsuite
Shain: #AACR18 TERT promoter mut status correlated w/progression stage. Now onto Chromatin remodeling gnees (ARID2, 1A,1B, SMARCA4, PBRM1)
11:49am April 18th 2018 via Hootsuite
Shain: #AACR18 Melanomas and MAP-Kinase gene exp signature - early during progression, subsequent ampl. Up-reg of telomerase TERT next
11:48am April 18th 2018 via Hootsuite
Shain: #AACR18 From 82 cases, 430 areas. 2 publ: https://t.co/dcO2iH2yBM and one new one in Cancer Cell. MAPK-mut alleles: high levels in mM
11:47am April 18th 2018 via Hootsuite
Shain: #AACR18 By the time invasive melanoma detected, it has spread already. ID'd 82 cases w/remnant precursor lesions. Microdissected.
11:44am April 18th 2018 via Hootsuite
Shain: Melanoma starts on one side w/melanocytic nevi (mole), then lesioins, T1-T4 then metastatic melanoma (mM). Idea:full spectrum #AACR18
11:43am April 18th 2018 via Hootsuite
Hunter Shain (UCSF CA) Genomic, transcriptomic analysis reveals incremental disrupt. of key signaling pathways during melanoma evol #AACR18
11:42am April 18th 2018 via Hootsuite
A2: Landau #AACR18 500K CpGs with modest 1M reads. More seq doesn't provide much more. About 10% overlap between cells as epimut rate high
11:41am April 18th 2018 via Hootsuite
Q: Sparsity, missing data? Landau: Treat as an ally. RRBS limits target to 5M CpGs. Thus sparse info still gives chance to reconstr. #AACR18
11:40am April 18th 2018 via Hootsuite
RT @mtmdphd: #AACR18 Wed am Plenary #cagenome - Griffith - Opportunities/ Challenges - mission not completed https://t.co/VfWwi79plQ
11:38am April 18th 2018 via Twitter Web Client
Q: Does sc data capitulate CLL bulk? Landau: In unmut CLL, epimut is lower; later mut forms (B-cells) branch lengths are longer #AACR18
11:34am April 18th 2018 via Hootsuite
