August 2017

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

10:23am August 18th 2017 via Hootsuite

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

9:11am August 18th 2017 via Hootsuite

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

9:05am August 18th 2017 via Hootsuite

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

Vasmatzis: About $3K per pt. Expects to be so much better than the current non-targeted Rx approach. Mate-Pair, WES, GEX #NGDx17

8:55am August 18th 2017 via Hootsuite

Vasmatzis: Combined w/genomic info, sounds like her2+ cancer, pt treated w/afatinib. Pt responded but had a brain met #NGDx17

8:53am August 18th 2017 via Hootsuite

Vasmatzis: RNAseq shows genes as log2 looking at set of BrCa genes. Also CD274 cp for I-O Rx. 3D model: showed afatinib strong resp #NGDx17

8:52am August 18th 2017 via Hootsuite

Vasmatzis: Did FOne test, showed rearr using their WES CNV analysis, found ERBB2 ampl. FISH showed her2 neg. #NGDx17

8:51am August 18th 2017 via Hootsuite

Vasmatzis: Starting with GBM in 4 days get 10K cells. Example of BC liver metastatic pt, started Dec '16 Feb 17 lot of data #NGDx17

8:50am August 18th 2017 via Hootsuite

Vasmatzis: Hanging drop is not an organoid, he calls it microcancer model in 3D. Lists advantages over 2D culture and mouse avatars #NGDx17

8:49am August 18th 2017 via Hootsuite

Vasmatzis: CNVs via whole exome, RNAseq for GEX. Proteomics not done now b/c it's 'too expensive'. insphero tech - 3D culture #NGDx17

8:48am August 18th 2017 via Hootsuite

Vasmatzis: Doing a lot of sequencing (mate pair, RNA, exome) will go into 3D models, avatars, isolate ctDNA, generate hypotheses #NGDx17

8:47am August 18th 2017 via Hootsuite

Vasmatzis: Could design primers, and then find the cDNA to confirm. Shows ERBB2 amplification - cholangiocarcinoma #NGDx17

8:44am August 18th 2017 via Hootsuite

Vasmatzis: '16 ref https://t.co/xXlhEqHegA shows chromoplexy. Shows ALK rearranged twice. RNASeq fusion not detected (on the 5' end) #NGDx17

8:43am August 18th 2017 via Hootsuite

Vasmatzis: Another PrCa chr 21 del, 'completely different pattern', many different examples #NGDx17

8:40am August 18th 2017 via Hootsuite

Vasmatzis: In PrCa, shows event in chr6; another w/5 different deletions across four chromosomes. Another with a huge AR gene ampl #NGDx17

8:40am August 18th 2017 via Hootsuite

Vasmatzis: Linear plot, lines show a balanced transloc between chr2/8. Red show deletions across chromosomes. #NGDx17

8:38am August 18th 2017 via Hootsuite

Vasmatzis: Shows read pileup ALK gene; 100kb windows showing copy loss/gain. Linear 2D lines vs Circos (but circos not as helpful) #NGDx17

8:37am August 18th 2017 via Hootsuite

Vasmatzis: Fusions and DNA rearr's: points to Chinnaiyan's ERG-TMPRSS2 fusions in prostate. Now uses Ion Ampliseq method #NGDx17

8:35am August 18th 2017 via Hootsuite

Vasmatzis: Shows microarray gene expression plot; heatmaps clusters GEX by tissue of origin easily. PCA separated out #NGDx17

8:33am August 18th 2017 via Hootsuite

Vasmatzis: "Is a cancer where it came from, or where it evolved to?" Path slides - recognizable to a pathologist immediately #NGDx17

8:31am August 18th 2017 via Hootsuite

George Vasmatzis (Mayo Clinic MN) Predictive biomarkers for targeted therapy #NGDx17

8:30am August 18th 2017 via Hootsuite

Blood Biopsy Reveals Unique, Targetable Genetic Alterations in Patients with Rare Cancer | Newswise https://t.co/j7zRxJKXIH

6:30am August 18th 2017 via Hootsuite