Nolte: #AMP2017 Det assays '17 rev https://t.co/Uh8QUISjb4 80% was the best; 77% for Infl B. For NAAT Infl A 97%; B 95%
10:21am November 17th 2017 via Hootsuite
Nolte: 80% sens for NA, 90% sens for culture. Issued Jan '17. Enforcement Jan '18. Expect fewer but better, choices #AMP2017
10:19am November 17th 2017 via Hootsuite
Nolte: HTN1 in '09: prompted focus, '13 changed from Class I to Class II for rapid antigen test for influenza. #AMP2017
10:18am November 17th 2017 via Hootsuite
Nolte: Case of rapid influenza tests - CDC table https://t.co/oUrV4j09OI RADT - good spec but poor sens. #AMP2017
10:17am November 17th 2017 via Hootsuite
Nolte: #AMP2017 Shows nice review table of POCT from '17 J Clin Micro https://t.co/OYIdd5ToCR
10:14am November 17th 2017 via Hootsuite
Nolte: #AMP2017 Chose figures from this '17 CLP online pub https://t.co/KMkHfVAIHr
10:13am November 17th 2017 via Hootsuite
Nolte: Challenges: dozens of sites, greater than hundreds of instruments, thousands of operators. Connectivity too #AMP2017
10:12am November 17th 2017 via Hootsuite
Nolte: WHO ASSURED: Affordable, Sens, Spec, User-friendly, Rapid, Robust, Equipment-Free, Deliverable #AMP2017
10:11am November 17th 2017 via Hootsuite
Nolte: Shd result 'in clear and actionable mgmt decisions... e.g. when to start trtmt or req confirmation w/in same clin encounter' #AMP2017
10:10am November 17th 2017 via Hootsuite
Nolte: "but I smile b/c people will find a way to do it wrong" Milestone: 2015 of first CLIA-waived NAAT Alere i Influenza A&B Test #AMP
10:09am November 17th 2017 via Hootsuite
Nolte: Def'n of waived: simple to do, little chance that test will provide wrong info or cause harm. #AMP2017
10:08am November 17th 2017 via Hootsuite
Nolte: Near-pt can be at home; POC is CLIA-waived tests. But some know POC are moderately complex, not nec CLIA-waived #AMP2017
Nolte: POC is near-patient, outside the lab, by non-lab personnel. <20 min analysis time. Def'ns vary. #AMP2017
10:07am November 17th 2017 via Hootsuite
Nolte: Will start with general concepts; describe how NA-based detection are disruptive; use infl. and gr A strep as examples #AMP2017
Special Molecular Infectious Disease Session: Frederick Nolte (Med Univ SC) Point of Care: Opportunities and Challenges #AMP2017
10:06am November 17th 2017 via Hootsuite
A2: Druley: MeDIP, other methods are possible but aren't sens enough. Haven't looked at other mods for same reasons #AMP2017
9:47am November 17th 2017 via Hootsuite
Q: Can you look at epigenetics, MSI with MRD? Druley: Problem with harsh bisulfite treatment. Libraries haven't suf… https://t.co/xjuIUlv5XD
9:46am November 17th 2017 via Hootsuite
A4 Druley: Multiplexed ddPCR isn't cheap nor easy; orthogonal platform with same LOD #AMP2017
9:45am November 17th 2017 via Hootsuite
A3 Druley: Tries to start with 500K template molecules / sample. 1:10K you need to have enough molecules to start with #AMP2017
A2 Druley: 8-oxo-guanine due to oxidative damage in extraction, G to T. '15 paper was 1:300 to 1:500 for G to T change #AMP2017
9:44am November 17th 2017 via Hootsuite
Q: For MRD, how consistent over time? Validation for new var's? Druley: The answer is no; expected C to T b/c of deamination #AMP2017
9:43am November 17th 2017 via Hootsuite
A2: Druley: Also rules around read families to ensure fidelity of UMI identifier #AMP2017
9:42am November 17th 2017 via Hootsuite
Q: Errors in the UMI? Druley: Looking at redundancy - errors in the index. Only need 3-7 reads/index. An early 'new… https://t.co/Fy19o4uCij
Druley: Ped AML - 'we've made progress but at a cost - delayed learning and growth'. Credits Illumina, Archer. Inde… https://t.co/4NAeOXrFjk
9:40am November 17th 2017 via Hootsuite
Druley: Goal - build comprehensive 'sequencing toolbox to improve MRD detection and precision drug selection for ped AML' #AMP2017
9:39am November 17th 2017 via Hootsuite
Druley: custom Archer 40 genes, 28kb, also Archer Heme v2. Also w/CHOP - proteomics. Cp against MRD via flow #AMP2017
9:38am November 17th 2017 via Hootsuite
Druley: Earlier finished largest AAML 1531, 870 dx, 870 EOI1, 170 relapse 1,900 samples. 80 genes, 200kb custom ILM myeloid. #AMP2017
9:37am November 17th 2017 via Hootsuite
Druley: DNA, RNA, imaging, cyto, age, gender... use machine learning to use PCA and stratify #AMP2017
9:36am November 17th 2017 via Hootsuite
Druley: Fish plots: tracking clonal expansion. Circos: if you can squint... you'll 'go nutty if you look at them too much' #AMP2017
9:35am November 17th 2017 via Hootsuite
Druley: Shows interesting visual data rep - reactome, fish plot, circos. Ph+-like ALL: how can this be best shown? #AMP2017
Druley: TARGET initiative ('TCGA for ped ca'): EOI2 AML samples, only 1 known fusion via 'COG'. Able to detect fusi… https://t.co/3l0XoWTnEd
9:32am November 17th 2017 via Hootsuite
Druley: Unk whether RUNX1 abnormal transcript is clin significant, but interesting biology that couldn't be detected previously. #AMP2017
9:31am November 17th 2017 via Hootsuite
Druley: Looking at structural diff in RNA - back to ArcherDx HemeV2, looked at splice muts in RUNX1. #AMP2017
9:30am November 17th 2017 via Hootsuite
Druley: Have applied UMIs to RNA, collab with QIAGEN. All genes <100 count transcripts. Able to get counts to 3.5 c… https://t.co/zoZ5nHH
9:29am November 17th 2017 via Hootsuite
Druley: 47 clonal types pre-Rx. But post-chemo they disappear. Post-chemo 30 new ones appear #AMP2017
9:28am November 17th 2017 via Hootsuite
Druley: Using de novo assembly, 'LOD 0.001' or 0.1%. #AMP2017
9:25am November 17th 2017 via Hootsuite
Druley: Looking at FLT3-ITD, working with ArcherDx explains single-primer method for multiple different size amplicons #AMP2017
9:24am November 17th 2017 via Hootsuite
Druley: From close analysis: found four mutations (DNMT3A 2x), ASXL1, JAK2 with p-values <0.01, up to 15y in advanc… https://t.co/kF5oV8X
9:22am November 17th 2017 via Hootsuite
Druley: no difference in overall mutation burden between healthy and those who develop disease. Showed plot of DNMT3A muts #AMP2017
9:19am November 17th 2017 via Hootsuite
Druley: Were these just quiescent cells? 40y old blood examined via flow: data suggest normal hematopoetic aging #AMP2017
9:17am November 17th 2017 via Hootsuite
Druley: Showing rise of mutations over time across 5 samples, 10y: appear to be self-renewing (!). 2nd and 3rd hits… https://t.co/4krJhA4UcI
9:16am November 17th 2017 via Hootsuite
Druley: Demonstrated 95% of samples had clonal mutations, in contrast to prior work. 40% in DNMT3A and TET2. #AMP2017
9:15am November 17th 2017 via Hootsuite
Druley: Using 20 samples from healthy elderly nurses (Nurses' Health cohort) https://t.co/megBpCj4GK validated to 0.1% #AMP2017
9:14am November 17th 2017 via Hootsuite
Druley: In order to expand (up to date only known mutations), used TruSight Myeloid panel, and added UMI's #AMP2017
9:12am November 17th 2017 via Hootsuite
Druley: Published their error-corrected method in '15 https://t.co/dzhVj02BOH #AMP2017
9:11am November 17th 2017 via Hootsuite
Druley: 20y of samples of AML pts at WashU; track TP53 mutations as pre-existing and selected for via chemo #AMP2017
9:10am November 17th 2017 via Hootsuite
Druley:GATA1 for ped cancer in Trisomy 21 is common, showed 5bp ins downt to 1:10,000 #AMP2017
9:09am November 17th 2017 via Hootsuite
Druley: Points out limitations of regular NGS (0.5% to 2% limit of detection), and have developed a 16bp UMI method #AMP2017
Good morning! Todd Druley (WashU) Single Molecule Quantification of Rare DNA and RNA Variants in Heterogeneous Samples #AMP2017
9:08am November 17th 2017 via Hootsuite
Koboldt: 'Database-driven methods (eg COSMIC for TPs and dbSNP for FPs) are increasingly unreliable' #AMP2017
3:55pm November 16th 2017 via Hootsuite
