Rosenbaurm: ALK is consistent, not a lot of variability. In EML4 - dimerization domain always there but heterogeneous #NGDx17
12:06pm August 18th 2017 via Hootsuite
Rosenbaurm: ALK-EML4 translocation shown. ALK normally in neuroendocrine cells in development. In lung - constitutively dimerized #NGDx17
Jason Rosenbaum (U Penn) NGS reveals genomic heterogeneity of ALK fusion breakpoints in NSCLC #NGDx17
12:04pm August 18th 2017 via Hootsuite
Q: Done 'omics on the captured EVs? Hu: Yes, but here only using exosomes for the readout #NGDx17
11:59am August 18th 2017 via Hootsuite
Hu: Working on taking it from a microscope (fluorimetry) to a cellphone (!!) #NGDx17
11:55am August 18th 2017 via Hootsuite
Hu: PNAS manuscript (in press) for TB diagnosis as a detection platform. Shows data from that paper, showing HIV+TB+ v normal #NGDx17
11:54am August 18th 2017 via Hootsuite
Hu: This work published this year in Nature Biomed Eng https://t.co/GYuZZOy9o7 #NGDx17
11:52am August 18th 2017 via Hootsuite
Hu: NCI's EDRN is now sending samples for additional validation of their approach #NGDx17
11:49am August 18th 2017 via Hootsuite
Hu: Showed CA19-9 ELISA data for PancCa and their EV detection paltform. AUC curves look very favorable. 91%/85% sens/spec #NGDx17
Hu: nPES cost /1000wells is ~$1200 cp to ~$1650 for ELISA. 0.2 ng/uL cp to 30-77 ng/uL. 4-5 logs cp to 2 logs dyn range #NGDx17
11:43am August 18th 2017 via Hootsuite
Hu: Shows 1000-fold sensitivity compared to ELISA. Sample vol is also 1/100th (1uL input). At higher vol nPES signal too high #NGDx17
11:42am August 18th 2017 via Hootsuite
Hu: Glass slide coated w/anti-CD81 ab, EV-capture, detected by AuS-anti-CD63 and AuR-anti-CD9. Two different particles #NGDx17
11:39am August 18th 2017 via Hootsuite
Hu: Other methods w/polymers, antibody mag beads, ELISAs. Problem is unable to directly detect tumor EVs. Sample excludes mouse #NGDx17
11:37am August 18th 2017 via Hootsuite
Hu: Shows great video of exosome release from cells into the blood. Exosomes still depend on size-exclusion by ultracentrifugation #NGDx17
11:36am August 18th 2017 via Hootsuite
Tony Hu (Arizona State Univ) Nanoplasmonic quantification of tumor-derived extracellular vesicles in plasma microsamples #NGDx17
11:34am August 18th 2017 via Hootsuite
Q: Looking at cell-free? Murphy: Yes #NGDx17
11:33am August 18th 2017 via Hootsuite
Q: Can this be applied to RNA? Murphy: Hard to do along a few dimensions #NGDx17
Q: Easy to implement? Murphy: There are concerns by others for WGA, but have shown data is consistent #NGDx17
11:31am August 18th 2017 via Hootsuite
Q: Picking up rearr - how prevalent in the core? Murphy: Showing less conservative filtering. More noise - but low amt of sample #NGDx17
11:28am August 18th 2017 via Hootsuite
Murphy: Not only FNAs but also other cases where small samples are impt - bile brushes etc #NGDx17
11:26am August 18th 2017 via Hootsuite
Murphy: Touch Prep already in the clinic. (FYI here's a '12 ref that describes method w/MatePair NGS https://t.co/AHciyh4FyV ) #NGDx17
11:23am August 18th 2017 via Hootsuite
Murphy: Shows differences in observed heterogeneity between core vs touch prep. Shows Alk rearr, and complex MP (why FISH failed) #NGDx17
11:21am August 18th 2017 via Hootsuite
Murphy: Show results from normal and tumor resected sample. Able to predict amt of tumor cellularity #NGDx17
11:12am August 18th 2017 via Hootsuite
Murphy: lots of Q's about bias, FP's and ampl errors. Onto in-situ WGA - a touchpad, a smear on a slide. Appears like nothing at all #NGDx17
11:09am August 18th 2017 via Hootsuite
Murphy: Doing LCM, then taking it across to WGS and multiplex PCR. Many publications - from '13 Cancer Res through '17 #NGDx17
11:08am August 18th 2017 via Hootsuite
Stephen Murphy (Mayo MN) Clinical utility of cytology touch-preparation specimens for genomic testing #NGDx17
11:06am August 18th 2017 via Hootsuite
Netto: May need to look at longitudinally. #NGDx17
10:23am August 18th 2017 via Hootsuite
Q: 3D culture from few cells reflects heterogeneity? Vasmatzis: The cells get dissociated first, if the sample is small. Best early #NGDx17
Panel discussion: Q: I-O induced toxicity biomarkers? Vasmatzis: Could be simple or complex analyses, no one will stop the Rx #NGDx17
10:21am August 18th 2017 via Hootsuite
Farhad Kosary (Mayo MN) EGFR mediates activation of Neurendocrine differentiation cells (NED) in AD NSCLC and ASCL1 expression #NGDx17
9:35am August 18th 2017 via Hootsuite
Netto: Hypermutated - resp better (TMB). Checkmate-032 no relation to PD1 '16 ref https://t.co/uzqHiZtur2 and deaths, side-effects #NGDx17
9:26am August 18th 2017 via Hootsuite
Netto: What Ab? SP142 (Ventana) What population? A hot topic. Subtypes by cluster of TCGA, differences in PDL1 expression #NGDx17
9:24am August 18th 2017 via Hootsuite
Netto: Feb '17 Nivolumab approved for 2nd line use. Showed K-M curve from '16 Lancet https://t.co/aOBDY5qnKF #NGDx17
9:23am August 18th 2017 via Hootsuite
Netto: BladderCa and immune checkpoint inhibitors: atezolizumab approved for 2nd line use, Ph2 trial. (IMvigor 210) #NGDx17
9:22am August 18th 2017 via Hootsuite
Netto: Showed '16 data https://t.co/MhyZFGqlPE and class shift, additional MI-BC pathway, looking at both RNA and DNA #NGDx17
9:20am August 18th 2017 via Hootsuite
Netto: '14 ref https://t.co/zkRDbsCvNq used mRNA, ID'd the 3 types, showed resistance to chemo for p53-like type #NGDx17
9:18am August 18th 2017 via Hootsuite
Netto: 3 types - mRNA/miRNA from TCGA and protein analysis. Showed targets for MI-BC - ERBB2 Breast, Gastic, Bladder by ampl or mut #NGDx17
9:15am August 18th 2017 via Hootsuite
Netto: Integrated GEX subtypes from TCGA: papillary-like, basal/squamous-like (chemo responders), luminal/breast-like #NGDx17
9:13am August 18th 2017 via Hootsuite
Netto: Confirm 32 genes in cell-cycle, RTK signalling, chr regulation. Rx targets in 69% in MI-BC (!) #NGDx17
9:12am August 18th 2017 via Hootsuite
Netto: TCGA show ave 302 mut, 204 segmental CNA 22 rearr. TCGA is now being expanded to 400 smpls #NGDx17
9:11am August 18th 2017 via Hootsuite
Netto: He finds huge resistance for bladder cancer for biomarkers from biopsy. Shows fig 6 of K-M curve w/a new 'keratinized' type #NGDx17
Netto: Historical context '06 ref https://t.co/isHdfGGyLl histology. Pre-TCGA '12 ref https://t.co/2AazW88uAZ ID 2 distinct circuits #NGDx17
9:08am August 18th 2017 via Hootsuite
Netto: Two distinct pathways: NMI-BC is HRAS/FGFR3/mTOR; MI is P53/RB/E2F3. can you ID the 20% of the MI? #NGDx17
9:05am August 18th 2017 via Hootsuite
Netto: Chr rearr reflect NMI (superficial) and MI. Cell-cycle markers much higher too. #NGDx17
Netto: NMI-BC (non-muscle invasive 60-70%) also MI-BC (muscle invasive 30-40%) MI-BC is much higher mortality. Different Rx #NGDx17
9:04am August 18th 2017 via Hootsuite
Netto: Highest cost/pt than any type of cancer. Great source of biomarkers in urine. #NGDx17
9:03am August 18th 2017 via Hootsuite
Netto: (Show off some Alabama pride - beautiful building!) Bladder ca - two cancers. Major health care burden $3B in US #NGDx17
9:02am August 18th 2017 via Hootsuite
George Netto (Univ AL Birmingham) Genomic advances in urinary bladder cancer - taxonomy, therapeutic targets #NGDx17
9:01am August 18th 2017 via Hootsuite
Q: Protein approach? Vasmatzis: Use sequencing for biomarker ID, and then zero-in on particular peptide or proteins via IHC etc #NGDx17
8:59am August 18th 2017 via Hootsuite
Q: Input req for Mate-Pair library? Vasmatzis: Have developed a method (expanded on later) with only 500ng input that works well #NGDx17
8:58am August 18th 2017 via Hootsuite
