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
Cottrell #AGBT19 n=59, 23 new Dx. Thinking of N of 1 approach - paired tumor/normal WES, RNA-Seq, can also do micr… https://t.co/O16K6aWsBg
7:35pm February 28th 2019 via Twitter Web Client
Cottrell #AGBT19 Comprehensive protocol - to ID targeted Rx, ID clinical trial, make Dx, establish prognosis, det c… https://t.co/18kIXntmCF
7:33pm February 28th 2019 via Twitter Web Client
Catherine Cottrell (Nationwide Children's Hosp) #AGBT19 Design and implementation of a comprehensive genomic profi… https://t.co/pY53h4WEvS
7:30pm February 28th 2019 via Twitter Web Client
Nelson #AGBT19 PTEN, splice variants in Pr ca of the AR receptor readily detected, whether that variant is consiste… https://t.co/joHdFEFEJt
5:21pm February 28th 2019 via Twitter Web Client
Beechem #AGBT19 Points out that the slides are reusable, a useful thing. Also that these studies were done quickly.
5:20pm February 28th 2019 via Twitter Web Client
Q: Pt mgmt in earlier stage? Nelson #AGBT19 Localized has made progress, but problem is sampling (whether aggressiv… https://t.co/XH5beKeKPt
5:17pm February 28th 2019 via Twitter Web Client
Q: Can vast hetergeneity allow further subsets for Rx? Nelson #AGBT19 First cut will clarify whether it's the same… https://t.co/MD158cmd5S
5:15pm February 28th 2019 via Twitter Web Client
Nelson #AGBT19 Concl - CRPC molecular landscape indicates 'many subtypes with therapeutic implications'. DSP to ass… https://t.co/nAWWSMRGXn
5:13pm February 28th 2019 via Twitter Web Client
Nelson #AGBT19 Shows transition data from AR+/NE-, to different states of genes from different ROI's, illustrating… https://t.co/RlBNbIMwVO
5:08pm February 28th 2019 via Twitter Web Client
Nelson #AGBT19 Series of experiments on 5 FFPE sections: RNA, protein. Reprod between 108-plex and 1412-plex, r2=0.… https://t.co/2AihKnv9Tf
5:04pm February 28th 2019 via Twitter Web Client
Nelson #AGBT19 Prostate ca cell states - double neg look like squamous cells, some molecular classification by gene… https://t.co/wNsVM40YmL
5:01pm February 28th 2019 via Twitter Web Client
Nelson #AGBT19 New Rx - potent pressure on lineage of AR. Prior to 2012 - tumor progressoin on AR+; seeing much mor… https://t.co/TWmDPhVHZE
5:00pm February 28th 2019 via Twitter Web Client
Nelson #AGBT19 Their focus on prostate cancer. 26K deaths in US, due to mPC. Reduce mortality by early det or preve… https://t.co/zChutQQQQj
4:59pm February 28th 2019 via Twitter Web Client
Peter Nelson (Fred Hutch CC) #AGBT19 Mapping the microenvironment composition in metastatic prostate cancer by mul… https://t.co/0uGgksGZAu
4:57pm February 28th 2019 via Twitter Web Client
McPherson #AGBT19 Shows other genes down-reg 'made sense'. Cp melanocytes, epidermis, and immune-rich. Concl: known… https://t.co/makzLT3zzN
4:55pm February 28th 2019 via Twitter Web Client
McPherson #AGBT19 Shows volcano plots - PRAME gene up-regulated. Shows piece of tape - PRAME and LINC00518 by qPCR.… https://t.co/1Eo64Bz89X
4:54pm February 28th 2019 via Twitter Web Client
McPherson #AGBT19 Serial sections of same regions: R2 = 0.96. For technical replicates R2 = 0.98. Melanocytes, staining.
4:51pm February 28th 2019 via Twitter Web Client
McPherson #AGBT19 Four classes (from common nevi to melanoma), and look at 108 genes. Illustrated 200 um ROI's ID'd… https://t.co/YBGffalkkL
4:50pm February 28th 2019 via Twitter Web Client
McPherson #AGBT19 Tissues are small, lots of areas of interest, lots of LCM and trying to sequence. Shows lots of d… https://t.co/YqTs3jxqhk
4:49pm February 28th 2019 via Twitter Web Client
McPherson #AGBT19 Shows KM curve for melanoma, common nevi (moles) are mimics. Molecular tests - IHC. Thought: gene… https://t.co/OBvEWkHjIb
4:48pm February 28th 2019 via Twitter Web Client
John McPherson (UC Davis) #AGBT19 Spatially resolving RNA biomarkers using GeoMx Digital Spatial Profiler for earl… https://t.co/ZAscUNv6pf
4:47pm February 28th 2019 via Twitter Web Client
Beechem #AGBT19 Hyb&Seq: full-blown, 4096 seq chem working, contract mfr done, much faster, three posters (908...)… https://t.co/bfhwynx
4:45pm February 28th 2019 via Twitter Web Client
