RT @frapaport: BR : mirrored subclonal CNAs (some cells have 2 copies of 1 allele, 1 or the other, while it’s flipped in another population…
6:06pm February 27th 2019 via Hootsuite Inc.
Raphael #AGBT19 Single-cell technology - 10X for CNA: using HATCHet-sc, copy number, allele-specific.
6:05pm February 27th 2019 via Hootsuite Inc.
Raphael #AGBT19 Able to get integer copy number data across samples. Preprint https://t.co/LJACguYoMg HATCHet tool… https://t.co/FpaTQFapfF
5:58pm February 27th 2019 via Hootsuite Inc.
Raphael #AGBT19 Every method for CNA - looks locally across the genome, and read-depth frequencies, indiv for each… https://t.co/iE0tKfVWx6
5:53pm February 27th 2019 via Hootsuite Inc.
Raphael #AGBT19 In Pancreatic Cancer, the opposite (10 samples, zero CNA) https://t.co/LhAx6QCLzV
5:52pm February 27th 2019 via Hootsuite Inc.
Raphael #AGBT19 Most of cancer sequencing is bulk. '15 Nature ref https://t.co/xY8s4YkJsF 50 samples, subclonal CNS, shared CNAs in 50/50.
5:50pm February 27th 2019 via Hootsuite Inc.
Raphael #AGBT19 Copy number Tree Mixutre deconvolution - fractional copy number data. '18 ref… https://t.co/5ElydyhE2p
5:48pm February 27th 2019 via Hootsuite Inc.
Raphael #AGBT19 Infer the past, reconst phylogenetic trees. SNVs easy to analyse. But CNAs? Multiple locations '17… https://t.co/KJITI7TQ5z
5:45pm February 27th 2019 via Hootsuite Inc.
Raphael #AGBT19 CNA's and WG duplications are ubiquitous - WGD 30% in advanced cancers. The past: in an individ. tu… https://t.co/waD8bPDESr
5:43pm February 27th 2019 via Hootsuite Inc.
Raphael #AGBT19 From SNVs to WG duplications and everything in-between - Nature Gen '03 https://t.co/Ksrr325hjq
5:42pm February 27th 2019 via Hootsuite Inc.
Ben Raphael (Princeton) #AGBT19 Copy number aberratoins in cancer: past, present and future
5:40pm February 27th 2019 via Hootsuite Inc.
Q: What function does this gene have via KO's? Kenstis #AGBT19 Mental disorders, dev disorders. Expressed only in n… https://t.co/4DiMxei1to
5:37pm February 27th 2019 via Hootsuite Inc.
Kenstis #AGBT19Childhood cancer 'as a disorder of developmental somatic DNA rearrangements'. '18 ref… https://t.co/8Q1SMcoULQ
5:35pm February 27th 2019 via Hootsuite Inc.
Kenstis #AGBT19 Shows Circos plot from '16 ref https://t.co/mAYZQXf2NW '17 ref https://t.co/NkziOaSl7c Targeting m… https://t.co/9neOxdWhZj
5:31pm February 27th 2019 via Hootsuite Inc.
Kenstis #AGBT19 WGS of these tumors: Two different methods (local assembly, and different k-mers) found translocati… https://t.co/hxxngcrcVn
5:23pm February 27th 2019 via Hootsuite Inc.
Kenstis #AGBT19 '15 eLife ref https://t.co/uSuaxx00vS A developmental mutator hypothesis. '17 Nature Gen… https://t.co/krhKxf1aXE
5:20pm February 27th 2019 via Hootsuite Inc.
Kenstis #AGBT19 PGBD5: BiggyBac Transposable Element 5; shows ears of corn; and now 1/2 of the human genome have SI… https://t.co/OhICbtvFWv
5:17pm February 27th 2019 via Hootsuite Inc.
Kenstis #AGBT19 Clue from lymphoblastic leukemias - chr translocations of a DNA recombinase RAG1/2. Unexplained fea… https://t.co/q84GnltVcH
5:14pm February 27th 2019 via Hootsuite Inc.
Kenstis #AGBT19 Subtitle: Domesticated DNA transposase PGBD5 and other developmental oncogenic mutations.
5:11pm February 27th 2019 via Hootsuite Inc.
Alex Kentsis (Memorial Sloan Kettering Cancer Center) #AGBT19 Why do young people get cancer?
5:10pm February 27th 2019 via Hootsuite Inc.
Vickovic #AGBT19 Another driver (for adoption) will be ease-of-use.
3:44pm February 27th 2019 via Hootsuite Inc.
Moffitt #AGBT19 Showing the biological worth of these measurements; other aspects are critical: benchmarking against other techniques.
3:43pm February 27th 2019 via Hootsuite Inc.
Beechem #AGBT19 Dev bio have been doing spatial biology forever; I-O another driver. Chen: discovery will be a driv… https://t.co/4JK5g38Sqx
3:42pm February 27th 2019 via Hootsuite Inc.
Q: a few years ago lots of hesitation around sc genomics; same today wrt spatial? #AGBT19 Rimkunas A different mind… https://t.co/Fm3Clj0TVo
3:40pm February 27th 2019 via Hootsuite Inc.
Moffitt #AGBT19 There needs to be new methods of statistical analysis. High-dimensional data; before computation vi… https://t.co/f5IsjHXw6B
3:36pm February 27th 2019 via Hootsuite Inc.
Chen #AGBT19 It takes time to show something is possible (taking a couple of technologies and combining them) befor… https://t.co/x3xbmp70rh
3:33pm February 27th 2019 via Hootsuite Inc.
Moffitt #AGBT19 Sample preparation and storage and affects on the assay are very important. Thanks to high multiple… https://t.co/R5BCFlORho
3:28pm February 27th 2019 via Hootsuite Inc.
Chen: #AGBT19 You need simple-to-run, low-cost, scalable metrics at the beginning. And then add'l controls, like ERCC.
3:26pm February 27th 2019 via Hootsuite Inc.
Beechem: #AGBT19 IHC 1-plex: can put into a panel 'and it won't fail', only 2 out of a thousand that have failed. A… https://t.co/ASk0WwSTpI
3:25pm February 27th 2019 via Hootsuite Inc.
Q: Varying degrees of sample quality? #AGBT19 Rimkunas For protein, you need a valid IHC study, cold ischemic time.… https://t.co/HvdWHiXFT6
3:23pm February 27th 2019 via Hootsuite Inc.
Q: What do you think of all this spatial technologies? #AGBT19 Rimkunas: H3 all about I-O and microenvironment; IHC… https://t.co/zCmRaGgGjZ
3:14pm February 27th 2019 via Hootsuite Inc.
Q: Any plans to dive into up-regulated luminal markers? Rimkunas #AGBT19 Yes, PPARg is expressed but unk effect on immune system.
2:59pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 Volcano plot shows luminal markers in tumor enriched side. DSP 'has been a game-changer' - from 15… https://t.co/1M2bs2rImT
2:57pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 PPARg low have high TIS (shows data), high degree of TIL using CD3. Shows PPARg hi - low TIS, lower degree of TIL.
2:56pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 Used illustration from '13 ref https://t.co/pzIWmMkAaw Hypothesis: immune markers in space, what's… https://t.co/VVsGQfSj8p
2:53pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 PPARg - mutated, ampl, amplified in muscle-invasive bladder ca. PPARg knockdown does not impact ce… https://t.co/klJQdKrGjj
2:51pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 DSP in patient paired biopsies - standard gene exp profiling confirmed.
2:49pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 Measurement of tumor content: vary widely. Added spec probes (5 custom genes to @nanostringtech I-… https://t.co/JahThcp4CX
2:47pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 Goal for DSP: look at pharmacodynamic markers, look at ER expression. 'Majority of clinical trial… https://t.co/Cj5aFEUtaW
2:45pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 In Ph 1, H3B-6545 suppresses both ERaMUT and ERaWT activity. Called a Selective Estrogen Receptor… https://t.co/96dKQwY32U
2:44pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 Using DSP for target engagement and tumor immunity. ER+ br cancer: aromatase inh relapse may be due to ESR1 gene mutations.
2:43pm February 27th 2019 via Hootsuite Inc.
RT @TPU_ICR: The next talk. H3 company. #agbt #agbt19 https://t.co/Eqk7HlqQ1C
2:41pm February 27th 2019 via Hootsuite Inc.
Rimkunas #AGBT19 Has 3 small molecules in PhI clinical trials. Uses data from FMI and others; H3 mission to generat… https://t.co/YNO2Yanbb7
Vicki Rimkunas (Eisai / H3) #AGBT19 Utilizing digital spatial profiling to guide drug development
2:40pm February 27th 2019 via Hootsuite Inc.
Okay #AGBT19 tweeps - send Stephane some love via retweeting this handy map! https://t.co/jCEi9vZggB
2:36pm February 27th 2019 via Twitter Web Client
Vickovic #AGBT19 Plans: combine with Mass Cytometry (sc); deconvolve ST with scRNAseq in tumors via machine learnin… https://t.co/RrwctLcJ3V
2:34pm February 27th 2019 via Hootsuite Inc.
Vickovic #AGBT19 Cross validation - combining spatial transcriptomics (ST) and scRNAseq data. In ALS - look at vent… https://t.co/oPxDb04PWq
2:32pm February 27th 2019 via Hootsuite Inc.
Vickovic AGBT19 20K - 30K UMI's spot, 5-6K genes. Morphology / exp profile. BioRxiv preprint https://t.co/YtgcAoMmDc
2:28pm February 27th 2019 via Hootsuite Inc.
Vickovic AGBT19 Position fresh-frozen tissue; cells are permeabilized; cDNA synthesis is done in-situ. Digest tissu… https://t.co/6jZLvX30gH
2:24pm February 27th 2019 via Hootsuite Inc.
Vickovic AGBT19 A 100um spot - millions of copies of barcodes, UMI, polydT. In 100um spot: between 3 and 30 cells,… https://t.co/nnDr5eLAfq
2:22pm February 27th 2019 via Hootsuite Inc.
