Sanders: For ALL, CLL, MM, and NHL use clonoSeq assay, to monitor relapse and MRD monitoring #AMP2015
3:22pm November 4th 2015 via Hootsuite
Sanders: Have an ImmunoSeq assay for research, and a clonoSeq assay for diagnostics for MRD in lymphoid. tilSeq is in development #AMP2015
3:20pm November 4th 2015 via Hootsuite
Sanders:They have flexible input - PBMC, sorted cells, gDNA; cDNA, FFPE feasible but not part of kit yet #AMP2015
3:17pm November 4th 2015 via Hootsuite
Sanders:Able to get r=0.97 correlations of mouse kit they now offer between labs. 4-5h hands-on, 8-10h from sample to seq #AMP2015
3:16pm November 4th 2015 via Hootsuite
Sanders: They use synthetic sequences as in-process controls. Can back-calc how many original cells were present #AMP2015
3:13pm November 4th 2015 via Hootsuite
RT @AdaptiveBiotech: Dr. Sanders kicks off @AdaptiveBiotech workshop on immunosequencing in MRD and TILs at #AMP2015 https://t.co/QkjzpA5V3H
3:11pm November 4th 2015 via Hootsuite
Sanders: Challenge was ampl bias - optimized primer concentration; synthesized 1100 synthetic targets ref: https://t.co/hI8OSGQe7l #AMP2015
3:10pm November 4th 2015 via Hootsuite
Sanders: Before: 30K unique TCRs took 20y to generate. Showed assay design, first round V/J regions; 2nd round w/barcodes, fusion #AMP2015
3:09pm November 4th 2015 via Hootsuite
Sanders: 75B sequences, of which 1.7B unique. Their core tech: CDR3 region of TCR, det Ag specificity. 54 V / 2 D / 13 J regions #AMP2015
3:06pm November 4th 2015 via Hootsuite
Sanders: Raised $400M, 1.5B T-cell sequences. 4 core areas - research, diagnostics, therapeutics, and data generation. #AMP2015
3:05pm November 4th 2015 via Hootsuite
Catherine Sanders (Adaptive) Measuring MRD in lymphoid malignancies and profiling TILs in solid tumors using immunosequencing #AMP2015
3:04pm November 4th 2015 via Hootsuite
Patterson: (TIL that sterile PBS is Pedialyte.) Oral rinse, incellRinse and obtain 4x10^6 cells/mL #AMP2015
2:47pm November 4th 2015 via Hootsuite
Patterson: Shows predictors of anal squamous dysplasia; a 'field effect' of HPV virus to different sites #AMP2015 https://t.co/ctg0NTGWNs
2:46pm November 4th 2015 via Hootsuite
Patterson: Showed individual cells' morphology. Other disease states - different cell collection ('squamous is squamous') #AMP2015
2:43pm November 4th 2015 via Hootsuite
Patterson: Their 2nd gen test, uses DNA plus mRNA, called OncoTect 3Dx. Can also do morphology in add'n to cell cycle, E6/E7 #AMP2015
2:41pm November 4th 2015 via Hootsuite
Patterson: #AMP2015 Published HPV OncoTect compared to Roche assay 2012 PLOS https://t.co/alkBgeWo98
2:40pm November 4th 2015 via Hootsuite
Patterson: Can do cell cycle plus E6/E7 in 4h; not only up-regulation but proliferation (involvement of cell cycle genes) #AMP2015
2:38pm November 4th 2015 via Hootsuite
Patterson: Shows figure from this '14 PLOS One article https://t.co/nL6JRCp7M3 comparing HPV assays #AMP2015
2:37pm November 4th 2015 via Hootsuite
Patterson: Moves onto HPV and CIN1-2-3 and E6/E7 mRNA a genotype independent biomarker #AMP2015
2:35pm November 4th 2015 via Hootsuite
Patterson: Conclude - more than enough for multiparameter flow cytometry; assay takes 4h. Can detect heterogeneous tumor clones #AMP2015
2:32pm November 4th 2015 via Hootsuite
Patterson: Shows several examples and chart of PD1 and PDL1 status of both tumor and immune cell populations #AMP2015
2:30pm November 4th 2015 via Hootsuite
Patterson: Showed AE1/AE3 epithelial marker, also DAPI. Showed data of PD1 and PDL1 expression from FNA, also incellPrep #AMP2015
2:27pm November 4th 2015 via Hootsuite
Patterson: IncellFP is a proprietary cell stabilization reagent. Took 12 samples for NSCLC, FNAs, fresh cell suspensions, and FFPE #AMP2015
2:26pm November 4th 2015 via Hootsuite
Patterson: They can look at mRNA via flow, including cell cycle genes. Showed their protocol: 20 FNA, placed into IncellFP reagent #AMP2015
2:24pm November 4th 2015 via Hootsuite
Patterson: They start with either fresh or FFPE blocks, and go into cell suspension without enzymes that destroy IHC #AMP2015
2:23pm November 4th 2015 via Hootsuite
Patterson: ImmunoOncology needs a single-cell assay technology to differentiate tumor from immune cells. Standardization of IHC... #AMP2015
2:22pm November 4th 2015 via Hootsuite
Next Bruce Patterson (IncellDx) "OncoTect Lung CxDx using IncellPrep on fresh lung tissue" #AMP2015
2:21pm November 4th 2015 via Hootsuite
Brown: Table of their microHomogenizer compared to other devices - % of single cells, % bare nuclei. And viability, enzyme-free #AMP2015
2:18pm November 4th 2015 via Hootsuite
Brown: Showed increassed yield (2x-4x compared to RNeasy) and no impact on performance. Working on HTP automation #AMP2015
2:17pm November 4th 2015 via Hootsuite
Brown: For RNA, showed BioAnalyzer traces w/RQI of 9.1-9.5 and are working with NASA to do RNA sample prep on the ISS #AMP2015
2:15pm November 4th 2015 via Hootsuite
Brown: Their microHomogenator - low voltage, 200-600 uL, 2-3 min Tested many tissues, including FFPE. Impact on DNA: 200kb #AMP2015
2:14pm November 4th 2015 via Hootsuite
Brown: 1-8 samples, used stool, sputum, soil samples tested. Methods for homogenization - mortar, grinder, rotor stator, beads #AMP2015
2:12pm November 4th 2015 via Hootsuite
Brown: 5' nucleic acid prep, lyse, wash and elute 'for even hard to lyse organisms'. 6 min automated device #AMP2015
2:11pm November 4th 2015 via Hootsuite
Brown: Energy imparted into fluid, single-cell suspension, '14 BMC ref https://t.co/NAdTM6BneL comparing 11 methods #AMP2015
2:10pm November 4th 2015 via Hootsuite
Brown: Made a single-cell disaggregator; compatible for DNA, RNA and/or protein. Their core technology: micromotor, added impeller #AMP2015
2:08pm November 4th 2015 via Hootsuite
IncellPrep at #AMP2015 'Quantitative cellular multiplex'. Founded in '09, has an HPV OncoTect Cervical. First: Mark Brown (ClairemontBio)
2:07pm November 4th 2015 via Hootsuite
RT @QIAGEN: Don’t miss Dr. Steelman @broadinstitute about clinical insights enabled by our #GeneReader #NGS System in Grand Ballroom E at 3…
1:54pm November 4th 2015 via Hootsuite
Arcila: Q:Turnaround time? A:About 5-7 days. #AMP2015
12:46pm November 4th 2015 via Hootsuite
.@archerdxinc Really enjoyed Dr. Arcila's #AMP2015 workshop - the case studies are eye-opening.
12:46pm November 4th 2015 via Hootsuite in reply to archerdxinc
Arcila: Concludes 'vastly improves workflow in laboratory'. #AMP2015
12:45pm November 4th 2015 via Hootsuite
Arcila: Rapid, easy to use; replaces RT-PCR and FISH; known and novel gene fusions. They use 50ng; if degraded need 250ng. #AMP2015
Arcila: Found NAB2-STAT6, 2013 Nature Genet 2013 ref http:/ow.ly/UfmIJ #AMP2015
12:44pm November 4th 2015 via Hootsuite
Arcila: Case 2 - highly unusual neoplasm, 'variant of solitary firous tumor with osteogenic metaplasia' #AMP2015
12:42pm November 4th 2015 via Hootsuite
Arcila: After 9w treatment after reclassification - dramatic results, scans show hardly any tumor left. #AMP2015
12:41pm November 4th 2015 via Hootsuite
Arcila: Used MSK IMPACT assay and Archer; reclassified disease. ETV6-NTRK3 fusion; mammary analogue secretory carcinoma of salivary #AMP2015
12:40pm November 4th 2015 via Hootsuite
Arcila: Case presented w/left parotid mass '06 initial Dx. 2012-14 progressive disease. 2 resections, 3 lines of chemo #AMP2015
12:39pm November 4th 2015 via Hootsuite
Arcila: BRC-ABL, PML-RARA, RUNX1 in a heme - rare. n=22. Accuracy 100% (22/22), sensitivity of ~2%; but pts have blasts #AMP2015
Arcila: Did dilutions and reprod; able to go down to 3% in 3 cell line fusions; low end with 22-34 split reads, 11-29 start sites #AMP2015
12:37pm November 4th 2015 via Hootsuite
Arcila: Accuracy was 57/58 between FISH and NGS; due to low tumor content (and completely expected) #AMP2015
12:36pm November 4th 2015 via Hootsuite
Arcila: Shows screenshot - reconstructed xcript, annotation tracks, coverage plot, read support underneath (paired ends indicated) #AMP2015
12:35pm November 4th 2015 via Hootsuite
