Qiu: Normalized per mm2 of tissue slices. Wide variation between yields/mm2. Amplifiability: QFI (Asuragen), RNAseP #Tricon
5:57pm February 21st 2017 via Hootsuite
Qiu: 5 labs send same samples from blocks; they extracted RNA/DNA, 5um slides; 2-5 slides sent. Either QIAamp or cobas for DNA #Tricon
5:56pm February 21st 2017 via Hootsuite
Qiu: FFPE suffers from C->T artifacts. Many different kits with pro's and con's. Objective was to ID CRO capability #Tricon
5:55pm February 21st 2017 via Hootsuite
Qiu: DNA input quant and quality. Library prep etc. FFPE challenges: WES has high failures, due to yield and quality. #Tricon
5:53pm February 21st 2017 via Hootsuite
Qiu: Mutational load assoc' wtih response to immunotherapy; gave a lot of references by cancer type. But detection affected... #Tricon
5:52pm February 21st 2017 via Hootsuite
Qiu: Two impt areas- pre-analytical and bioinformatics. Mendelian disorders, NIPT, infectious disease; complex disorders, oncology #Tricon
5:51pm February 21st 2017 via Hootsuite
Ping Qiu (Merck NJ) Implementing NGS as a clinical assay: FFPE pre-analytical optimization in WES commercial lab selection #Tricon
5:50pm February 21st 2017 via Hootsuite
Great work being done @DanaFarber and @VanAllenLab @cityofhopereported at #Tricon https://t.co/IIETLl9goT
5:46pm February 21st 2017 via Hootsuite
Fernandes: Need to be reported in HGVS nomenclature; proficiency testing (CAP) surveys, one for solid tumors #Tricon
5:44pm February 21st 2017 via Hootsuite
Fernandes: Interpretation and reporting results '17 JMD https://t.co/eeuY8saRII Four tiers of reporting; III=VUS; IV=benign #Tricon
5:43pm February 21st 2017 via Hootsuite
Fernandes: Shows sorted graph of list of amplicons by depth; with threshold cutoff for coverage; makes into final report #Tricon
5:41pm February 21st 2017 via Hootsuite
Fernandes: Analytical sensitivity for SNVs and indels: using diluted cell lines, est. LoD of 1.5% #Tricon
5:39pm February 21st 2017 via Hootsuite
Fernandes: For precision (repeatability) 3x's may not be enough. Repro: 3 different days, 3 diff operators #Tricon
5:37pm February 21st 2017 via Hootsuite
Fernandes: Accuracy for gene fusions: select TMPRSS2-ERG; EML4-ALK; MET exon 14 skipped. #Tricon
5:36pm February 21st 2017 via Hootsuite
Fernandes: VAF by percent, run1 vs run2. ERBB2 ampl can be tested by FISH, WES, CNV, need to provide details on algorithm for calls #Tricon
5:32pm February 21st 2017 via Hootsuite
Fernandes: Resistance var's: EGFR T790M; ALK L1196M, G1202R; PDGFRA D842V #Tricon
5:30pm February 21st 2017 via Hootsuite
Fernandes: EGFR in lung ca: two most common are ex19 del (15bp), also exon 21 L858R. About 80% of mutated lung #Tricon
5:29pm February 21st 2017 via Hootsuite
Fernandes: Analytical validation for SNVs - correlate to results from previously validated assay #Tricon
5:28pm February 21st 2017 via Hootsuite
Fernandes: For 100 gene panel - 10 vars per gene? 'Validate what you can, others are 'rolling - as you run and test'. #Tricon
Fernandes: Also each sample type (FFPE, FF, core biopsies etc). SNVs: 20 target areas. Indels: same. CNVs: 10. 3 for Translocations #Tricon
5:27pm February 21st 2017 via Hootsuite
Fernandes: Validation guidelines for NYS: have to be est 'for each type of variant'; SNVs, indels, CNVs, structural variants. #Tricon
5:26pm February 21st 2017 via Hootsuite
Fernandes: Can do tumor geome, transcriptome, exome. Nice figure from '16 review https://t.co/x5Pl4GSwMW #Tricon
5:25pm February 21st 2017 via Hootsuite
Fernandes: Bioinformatics processes have no standardization. Interpretation - same. Points out that Oncology is the fastest growth #Tricon
5:24pm February 21st 2017 via Hootsuite
Fernandes: Review of NGS process: specimen prep; analytical NGS for those having done it for a while, 'it's pretty good') #Tricon
5:23pm February 21st 2017 via Hootsuite
Fernandes: Nov '16, FDA annc a delay finalizing. Jan '17 discussed releasing paper again. #Tricon
5:22pm February 21st 2017 via Hootsuite
Fernandes: During PMI, FDA to create regulatory guidance. '16 June - draft guidance. @SeraCare blog: https://t.co/QfnhielNze #Tricon
5:20pm February 21st 2017 via Hootsuite
Fernandes: Going back to FDA and LTDs: Oct '14 framework for regulatory oversight; Reporting. Jan '15 Public meeting, comments #Tricon
5:19pm February 21st 2017 via Hootsuite
Helen Fernandes (Columbia Univ NY): Choosing an effective validation plan for NGS assays in oncology #Tricon
5:17pm February 21st 2017 via Hootsuite
Armstrong: Describes Paragon test for immuno-oncology. Escape - expresion arrays; activation via flow cytometry. #Tricon
3:09pm February 21st 2017 via Hootsuite
Armstrong: Reporting: all sample metadata provided; key genes highlighted; visual representation of flagged genes #Tricon
3:03pm February 21st 2017 via Hootsuite
Armstrong: Cofactor Pinnacle cp aberrant gene expression to other cancers of the same type. Report is 379 oncology-relevant genes #Tricon
3:02pm February 21st 2017 via Hootsuite
Armstrong: Goes through biology of ALK fusion. Shows 12 FFPE FISH as gold std; 8/12 by DNA; 8/12 by RNA; IHC was 10/12. #Tricon
2:57pm February 21st 2017 via Hootsuite
Armstrong: Illustrates challenge of finding breakpoints, and how much more sequence needs to be done; whereas RNA straitforward #Tricon
2:53pm February 21st 2017 via Hootsuite
Armstrong: DNA doesn't look at expression, large rearr detection limitations; but RNA has its own weakness: FFPE, variation in fix #Tricon
2:51pm February 21st 2017 via Hootsuite
Armstrong: Via sequencing-based Dx - majority DNA-based; most are tumor-only; #Tricon
2:49pm February 21st 2017 via Hootsuite
Armstrong: Molecular Dx - goal is to char difficult-to-understand biology on a molecula level. #Tricon
2:47pm February 21st 2017 via Hootsuite
Jon Armstrong (Cofactor MO) Reaching the Pinnacle: a unique cancer diagnostic tool that harnessess the power of RNA #Tricon
2:46pm February 21st 2017 via Hootsuite
Kuo: Have a two-tier classification: pathogenic or VUS. 30% are from BMT's, sometimes 2x or 3x. Thus germline SNPs w/varying AF #Tricon
2:34pm February 21st 2017 via Hootsuite
Kuo: Reviews complex calling pipeline. ClinVar, dbSNP, ESP100, ExAc, COSMIC, TCGA all involved. Links Mut Assessor, KEGG, GeneCard #Tricon
2:30pm February 21st 2017 via Hootsuite
Kuo: Run 30 samples/run; use 250ng; 1.8m reads at 1500x. No matched pairs, 2-3 runs/week. #Tricon
2:24pm February 21st 2017 via Hootsuite
Kuo: Decided to build custom TruSeq, 95 genes, 1330 amplicons, 175K. SNVs, indels to 55bp, CNV, FLT3-ITD. No translocations #Tricon
2:22pm February 21st 2017 via Hootsuite
Kuo: 1y costs of single-genes '14 on the order of $343K. Rapid heme panel goals: TAT of a few days, detecte low AF, cost-effective #Tricon
2:21pm February 21st 2017 via Hootsuite
Kuo: Shows very large menu of Non-NGS tests for solid and heme tumers;for NGS; Snapshot and Oncopanel #Tricon
2:19pm February 21st 2017 via Hootsuite
Kuo: Starts with JAMA editorial https://t.co/CfBP1lUY2f that TCGA was $675M, 10K samples. #Tricon
Frank Kuo (Brigham and Women's Hosp MA) NGS-based panel testing for hematologic malignancies #Tricon
2:16pm February 21st 2017 via Hootsuite
.@kennamshaw Wonderful talk Kenna! I really enjoyed it (unlike the, um, plenary <cough cough> session)
2:16pm February 21st 2017 via Hootsuite in reply to kennamshaw
MT @SeraCare: #TRICON We're launching new fusion #RNA reference materials developed in collaboration with @QIAGEN https://t.co/u1Sp4ByzHk
2:14pm February 21st 2017 via Hootsuite
Shaw: These were pts who had exhausted all treatment options. #Tricon
2:04pm February 21st 2017 via Hootsuite
Shaw: 7% of their pts with VUS enrolled. Showed unpublished K-M curve for OS afte doubling participation: clearly better #Tricon
2:03pm February 21st 2017 via Hootsuite
Shaw: They've now been able to get 25% of pts with mutations in actionable genes enrolled in clin trials #Tricon
2:02pm February 21st 2017 via Hootsuite
