Ragoussis #AGBT19 Cycling cells ID'd by scRNA-seq signature.
9:29pm February 28th 2019 via Twitter Web Client
Ragoussis #AGBT19 Integrate RNA-seq with scCNV data: Shows good correspondence. But CN events in sc assays only in… https://t.co/LDep5rVWBF
9:26pm February 28th 2019 via Twitter Web Client
Ragoussis #AGBT19 One sample - BDGFRA on Chr 4 on the branch, 0.22 allele frequency, other genes 1.0 on the trunk.
9:24pm February 28th 2019 via Twitter Web Client
Ragoussis #AGBT19 Early events in phylogenetic tree: Chr10 deletion, then Chr7 amp. Integrating CNVs - did WGS and… https://t.co/CRmaMz7rvI
9:22pm February 28th 2019 via Twitter Web Client
Ragoussis #AGBT19 Did scDNA CNV with 10X Genomics, also phylogenetic tree construction. Sometimes can find CNAs, others none.
9:20pm February 28th 2019 via Twitter Web Client
Ragoussis #AGBT19 3 mins signatures found by PCA: astrocytic, stem and neuronal genes, with a conserved lineage. An… https://t.co/1nahfkk50C
9:18pm February 28th 2019 via Twitter Web Client
Ragoussis #AGBT19 Find transcriptomic hetergeneity in GBM. Find expected TCGA subtypes (Proneural, neural, classical, one other).
9:16pm February 28th 2019 via Twitter Web Client
Ragoussis #AGBT19 Dissoc 100,000 cells from 30 pts and 20K fetal brain cells, to scRNA-seq. Chose CD31- and CD45- cells, did enrichment.
9:15pm February 28th 2019 via Twitter Web Client
Ragoussis #AGBT19 GBM has mean survival of 14 months with current Rx. Multiforme - hetergeneous. Thus - hierarchy,… https://t.co/qlSQ3FquiU
9:14pm February 28th 2019 via Twitter Web Client
Jiannis Ragoussis (McGill Univ) #AGBT19 Single cell DNA-seq and single cell RNA-seq of 20,000 Glioblastoma cells i… https://t.co/5Xz8CFX9z3
9:13pm February 28th 2019 via Twitter Web Client
Q: can it be turned into cfDNA test? McNamara #AGBT19 Morbidity of cancer treatment, it may be worth it.
9:10pm February 28th 2019 via Twitter Web Client
Q: Can markers be combined into a single metric? McNamara #AGBT19 With immune markers that may be possible with predictive power.
9:09pm February 28th 2019 via Twitter Web Client
McNamara #AGBT19 Future: interrogating immune changes w/targeted Rx.
9:08pm February 28th 2019 via Twitter Web Client
McNamara #AGBT19 DSP RNA data vs bulk - significant difference with DSP, in bulk signal clearly lost. Concl: archiv… https://t.co/GG1dqUSHqp
9:07pm February 28th 2019 via Twitter Web Client
McNamara #AGBT19 Effects of 1 cycle of Rx: tumor prolif decreases from baseline to run-in. Her2 protein also decrea… https://t.co/IEctnnTuM8
9:05pm February 28th 2019 via Twitter Web Client
McNamara #AGBT19 The DSP technology - can look at many markers. Coeff of var by protein probe - Her2 varies higher.… https://t.co/PYiwdftemQ
9:03pm February 28th 2019 via Twitter Web Client
McNamara #AGBT19 How consistent is Her2 levels from various regions? Staining - mean squared error 0.124 But betwee… https://t.co/kUfreoVmDv
9:02pm February 28th 2019 via Twitter Web Client
McNamara #AGBT19 PD-1, PD-L1 access as well as CTLA-4 on the RNA. Q's: what can they learn about spatial heterogene… https://t.co/3urv7DOqeU
8:59pm February 28th 2019 via Twitter Web Client
McNamara #AGBT19 Shows image masks, profiled PanCK+ and - regions, chose four regions across three time points. Pro… https://t.co/ltSdMG5G57
8:57pm February 28th 2019 via Twitter Web Client
McNamara #AGBT19 Working with archival samples impt. Both protein 43-plex, and RNA 108-plex. ROI's ID'd under flour… https://t.co/B9DHEHS2ed
8:56pm February 28th 2019 via Twitter Web Client
McNamara #AGBT19 Heterogeneity in the tumor and microenvironment in the course of Rx - resp and non-resp. Looking a… https://t.co/yySMhwGSFI
8:54pm February 28th 2019 via Twitter Web Client
Katherine McNamara (Stanford) #AGBT19 Spatial and temporal profiling of protein and RNA in the tumor-immune microe… https://t.co/ysBviPk2Qg
8:51pm February 28th 2019 via Twitter Web Client
Manojlovic #AGBT19 Note: slides are noted confidential, will no longer tweet (sorry)..
8:39pm February 28th 2019 via Twitter Web Client
Manojlovic #AGBT19 Ancestry can influence disease risk; looking at admixture, multi-ethnic intratumor heterogeneity… https://t.co/O8QAEbTd81
8:37pm February 28th 2019 via Twitter Web Client
Manojlovic #AGBT19 Low volume=lymph node mets, lower mortality. Hi volume=escape to bone or visceral mets. Aggressi… https://t.co/rjXCnANGET
8:35pm February 28th 2019 via Twitter Web Client
Manojlovic #AGBT19 Prostate cancer - racial disparities. Lethal mPC in AA pts. CTC expression profiling. metastatic… https://t.co/BvWdk7qbhn
8:34pm February 28th 2019 via Twitter Web Client
Zarko Manojlovic (USC) #AGBT19 Comprehensive molecular profiling of metastatic disease in prostate cancer
8:30pm February 28th 2019 via Twitter Web Client
Boland #AGBT19 Using custom AmpliSeq panels - with E2 dropouts that indicate cancer. Some controls also show some loss.
8:25pm February 28th 2019 via Twitter Web Client
Boland #AGBT19 Shows four interesting Circos plots with integrations. 54 'genes of interest'; SV's; but not practic… https://t.co/zF63JDVaXi
8:24pm February 28th 2019 via Twitter Web Client
Boland #AGBT19 Shows chart from '08 https://t.co/3wUDJbZMzR Used 10X Genomics for fused reads with human / viral in… https://t.co/xH3bbIiOEo
8:19pm February 28th 2019 via Twitter Web Client
Boland #AGBT19 HPV 18kb, 2 genes E6 and E7 known oncogenes, impacting p53 and Rb. High Risk type - HPV 16 and HPV 1… https://t.co/6z8Ftmi0IV
8:14pm February 28th 2019 via Twitter Web Client
Boland #AGBT19 '12 cervical cancer mortality rate: in africa, 20x-30x higher than in the US. 6y later: unchanged. S… https://t.co/NGOSdztnUL
8:12pm February 28th 2019 via Twitter Web Client
Boland #AGBT19 Created assays for low-resource countries. HPV typing, targeted methylation assay. Washington Post h… https://t.co/Eprc8osGPf
8:11pm February 28th 2019 via Twitter Web Client
Joe Boland (NCI) #AGBT19 Understanding the role of HPV Integration on the stability of the human genome from pre-cancer to cancer
8:10pm February 28th 2019 via Twitter Web Client
Aganezov #AGBT19 RCK Github here: https://t.co/xwaNt8aF5U Credits @mike_schatz and Timp labs
8:06pm February 28th 2019 via Twitter Web Client
Aganezov #AGBT19 Concl: both short and long reads are complementary; 'please try to use several different technolog… https://t.co/xZUPRrekL0
Aganezov #AGBT19 Looking at allele-spec copy number profile inference; looking at haplotype-specific karyotype anal… https://t.co/8CNx4KAhms
8:03pm February 28th 2019 via Twitter Web Client
Aganezov #AGBT19 Shows ONT, PacBio recall of 80%, precision of 90%, at 30x coverage.
7:58pm February 28th 2019 via Twitter Web Client
Aganezov #AGBT19 Looked at only sample 51: COSMIC genes affected by SVs, and # of SVs affecting COSMIC genes, short… https://t.co/gpCnNTYAMk
Aganezov #AGBT19 photo if SV callers and inferences. https://t.co/kDtNyOx3cd
7:57pm February 28th 2019 via Hootsuite Inc.
Aganezov #AGBT19 Yields on ONT PromethION now up to 80GB per run. Using NGMLR https://t.co/YaZsjyYrAi SVs used lots of methods.
7:56pm February 28th 2019 via Twitter Web Client
Aganezov #AGBT19 They are using both methods: SKBR3 lines, matrigel-grown organoids, and two other individuals. Use… https://t.co/0Xbjjse6Tj
7:54pm February 28th 2019 via Twitter Web Client
Aganezov #AGBT19 Cancer genomes - looking at clonal level for disease drivers, and help Rx. Tech shortcoming on sho… https://t.co/dZihLpN7V2
7:52pm February 28th 2019 via Twitter Web Client
Sergey Aganezov (Johns Hopkins) #AGBT19 Reconstructing haplotype-specific cancer genome karyotypes with multiple sequencing technologies
7:50pm February 28th 2019 via Twitter Web Client
Q: Scalability? Cottrell #AGBT19 They are scaling but interpretation remains a challenge. Refining algorithms but a… https://t.co/7VHVrAc75c
7:49pm February 28th 2019 via Twitter Web Client
Cottrell #AGBT19 Congenital cancer cases among newborns - 3 findings, novel fusions, etc. 59 accepted, 53 consented… https://t.co/C18shWCAcO
7:47pm February 28th 2019 via Twitter Web Client
Cottrell #AGBT19 Case 2. 18yo male, medulloblastoma. Resection, chemo, radiation. Recurrent medulloblastoma after 2… https://t.co/yJg7hWdkh9
7:43pm February 28th 2019 via Twitter Web Client
Cottrell #AGBT19 Also transloc - constitutional. In non-genic region. t(X;16); X-chr, can have inactivation. Put in… https://t.co/U6JYgu4CJI
7:41pm February 28th 2019 via Twitter Web Client
Cottrell #AGBT19 Chose 60x WGS found GNAQ oncogene 'activating', BAP1 tumor suppressor, late event.
7:39pm February 28th 2019 via Twitter Web Client
Cottrell #AGBT19 Stats and breakdown of types of tumors sequenced so far. Case 1: 17yo female, meningeal melanoma,… https://t.co/Ai83WYsmVF
7:38pm February 28th 2019 via Twitter Web Client
