Fabrizio: Accuracy 90%; precision 96%; LoD 20% tumor purity for analytical validation for TMB (Cp against WES TMB calling) #NGDx17
9:13am August 17th 2017 via Hootsuite
Fabrizio: Then count somatic mutations/megabase. Same test workflow; ranking of hi/med/lo, shows I-O OS via K-M curve in Melanoma #NGDx17
9:11am August 17th 2017 via Hootsuite
Fabrizio: TMB algorithm, built a db of rare germline events; somatic-germline zygosity modeling (copy number) are specialty filters #NGDx17
9:10am August 17th 2017 via Hootsuite
Fabrizio: FMI looked at TCGA data, and downsampled '17 Genome Med https://t.co/EU6oCnzxyM #NGDx17
9:08am August 17th 2017 via Hootsuite
Fabrizio: FMI was 315 genes, 203, 160, 76 genes with assoc'd Kaplan-Meier curves show effect of downsample #NGDx17
9:05am August 17th 2017 via Hootsuite
Fabrizio: '15 Oncotarget ref https://t.co/BwNpKlrl8S downsampled WES to predict clinical utility to a FMI 315 panel #NGDx17
9:04am August 17th 2017 via Hootsuite
Fabrizio: Can a panel be equivalent to WES for TMB? Faster TAT (FMI is 10d TAT), cheaper, no matched normal needed #NGDx17
9:03am August 17th 2017 via Hootsuite
For those following #NGDx17 at home, check out @Pillar_Bio updated website next week; my take is at https://t.co/aeiuCtplgb
9:02am August 17th 2017 via Hootsuite
Fabrizio: Pieces of the puzzle over time include MSI, TCR, TMB, GEX, (unk). Shows Chen/Mellman figure from '13 Cancer Immunity Cycle #NGDx17
9:00am August 17th 2017 via Hootsuite
Fabrizio: Show Larkin NEJM 2015 of durable benefit on Ipi or Nivo either 20% or 40% in melanoma https://t.co/GKpERVWbPu #NGDx17
8:58am August 17th 2017 via Hootsuite
Fabrizio: Need to think of patient's cancer not as organ-specific but driver mutation-specific. 'Everyone is a snowflake'. #NGDx17
8:56am August 17th 2017 via Hootsuite
Fabrizio: 300 gene panel test gives also MSI and TMB; ability for comp. profiling 'has opened the door for personalized medicine' #NGDx17
David Fabrizio (Foundation Medicine MA) Tumor mutational burden as a biomarker for cancer immunotherapy #NGDx17
8:54am August 17th 2017 via Hootsuite
RT @FoundationATCG: Join us at #NGDx17 for a 9AM presentation on TMB as a biomarker for immunotherapy based on clinical evidence from CGP t…
Brohawn: And conversely, increased difference in VAF meant shorter PFS probability #NGDx17
8:48am August 17th 2017 via Hootsuite
Brohawn: Shows data from AACR Abstract 582 CP1108 NSCLC: ctDNA mutations over time. Mutations shown that decreasing VAF w/inc PFS % #NGDx17
Brohawn: Two FDA PMA approvals - Foundation Focus and Oncomine Dx. Guardant 360 panel also illustrating broad coverage of drivers #NGDx17
8:45am August 17th 2017 via Hootsuite
Brohawn: Rizvi '15 TMB https://t.co/rwa2cxqwCu 'expanding evidence' for its role in I-O #NGDx17
8:43am August 17th 2017 via Hootsuite
Brohawn: Feels targeted RNAseq 'overlooked'. Able to go at low-levels - '15 ref https://t.co/C8rfXh4E80 #NGDx17
8:42am August 17th 2017 via Hootsuite
Brohawn: scRNASeq - may find Treg and other cell types. May help unlock best Rx strategy, 'still evolving, interesting application' #NGDx17
8:41am August 17th 2017 via Hootsuite
Brohawn: Starts with review of some of their RNASeq work, shared at ASCO17. 'Potential for exciting application: scRNAseq' #NGDx17
8:40am August 17th 2017 via Hootsuite
Phillip Brohawn (MedImmune) Application of NGS to Drug Development #NGSDx17
8:39am August 17th 2017 via Hootsuite
Great AM session roundtable on biomarker technology for I-O and CDx w/Michael Montalto (BMS) David Rimm (Yale) and others! #NGDx17
Annular Eclipse of the Sun by Phobos, as Seen by Curiosity | NASA https://t.co/7bgeUXijYc
5:30am August 17th 2017 via Hootsuite
Sequencing of Circulating Tumor DNA Detects Early Cancers | GenomeWeb https://t.co/DwwHduNTGK
8:20pm August 16th 2017 via Hootsuite
RT @biorxivpreprint: Detection and removal of barcode swapping in single-cell RNA-seq data https://t.co/stMf1yURdn #bioRxiv
7:50pm August 16th 2017 via Hootsuite
RImm: All but two complementary - b/c 'they didn't work'. "I'm not doing a complementary test, no reimbursement, pt will get anyway' #NGDx17
6:11pm August 16th 2017 via Hootsuite
RImm: Shows many papers of PD-L1 by IHC in NSCLC. "There is signal there" Shows approval timelines '11-'17 of I-O 'it's amazing' #NGDx17
6:09pm August 16th 2017 via Hootsuite
RImm: 'Quite a good test' but also 'can we get this lame test to work?' #NGDx17
6:08pm August 16th 2017 via Hootsuite
RImm: Has a lot of disclosures - 'I need partners'. Outline - talking about PD-L1, IHC, standardization of PD-L1 today's test #NGDx17
6:07pm August 16th 2017 via Hootsuite
David Rimm (Yale CT) Companion diagnostics for immunotherapy: Challenge of picking the responders #NGDx17
6:05pm August 16th 2017 via Hootsuite
Li: Had prospective study with ResolutionBio of Seattle, how it could impact pt care #NGDx17
5:48pm August 16th 2017 via Hootsuite
Li: Shows figure of all the liquid biopsy assay providers - ILMN, Q, Genomic Helath, Guardant, Myriad, exosomeDx, PGDx, Pathway, FMI #NGDx17
5:47pm August 16th 2017 via Hootsuite
Li: Found instances where ddPCR missed where NGS picked up. Collab w/GRAIL, 'clonal muts more likely to be detected in plasma' #NGDx17
5:43pm August 16th 2017 via Hootsuite
Li: Showed EGFR and ERBB2 ampl in plasma ctDNA, results presented at AACR '16. Cp to ddPCR and NGS, 'sensitivity as good' #NGDx17
5:42pm August 16th 2017 via Hootsuite
Li: Showed several cases from this '17 ref https://t.co/PmS2lAzHHG #NGDx17
Li: Describes MSK-IMPACT, and limitations of scaling number of samples. But still did 10K samples '17 ref https://t.co/Z2m3cjRt6H #NGDx17
5:39pm August 16th 2017 via Hootsuite
Li: T790M by ddPCR is now 'std of care' for MSK pts with metastatic EGFR who progress. #NGDx17
5:36pm August 16th 2017 via Hootsuite
Bob Li (MSKCC) Utility of ctDNA for patients at MSKCC #NGDx17
5:35pm August 16th 2017 via Hootsuite
Bijwaard: FDA-AACR workshop Liquid Biopsies in Oncology Drug and Device Development Part II Oct 10 2017 https://t.co/a2OgudvlgL #NGDx17
5:29pm August 16th 2017 via Hootsuite
Bijwaard: Poorer result - PPA 58.7%. PPV 89%. OOR rate by plasma result status among enrolled patients w/confirmed responses #NGDx17
5:24pm August 16th 2017 via Hootsuite
Bijwaard: 2nd indication was for Tagrisso (T790M resistance). Clinical bridging study AURA2. #NGDx17
5:23pm August 16th 2017 via Hootsuite
Bijwaard: PFS benefits to pts who are tissue whether plasma pos or neg. Approval - reflex to routine biopsy for EGFR status #NGDx17
5:22pm August 16th 2017 via Hootsuite
Bijwaard: Shows 22/212 had 1.5-1.9mL; 17/212 had 0.4-1.4mL. Had PPA across n=431 of 76.7%. High NPA 98.2% #NGDx17
5:21pm August 16th 2017 via Hootsuite
Bijwaard: Reviews cobas EGFR Mut Test v2 - ENSURE study. An issue was 2.0mL plasma not available for all 212 pts. #NGDx17
5:20pm August 16th 2017 via Hootsuite
RT @DXWorldNews: Always a treat to hear from @DaleYuzuki His insights are spot on. Congrats on the new gig at Pillar Biosciences! #NGDx17 h…
5:15pm August 16th 2017 via Hootsuite
Bijwaard: Specimen collection and processing should follow same protocol; clinical trial assay used for pt enrollment #NGDx17
Bijwaard: DNA input and MAF 'down to the lowest levels' #NGDx17
5:12pm August 16th 2017 via Hootsuite
Bijwaard: Roche's SSED needed to be renamed. same vars, same conc, 5 dil levels from est LoD down to est LoB. #NGDx17
Bijwaard: Need to demonstrate similar fragment sizes, background. Functional char formerly referred to commutability study #NGDx17
5:11pm August 16th 2017 via Hootsuite
