Connelly:PowerPlex Forensic ID runtime reduced from 75m to 22m Six color detection. #TRICON
7:40pm March 7th 2016 via Hootsuite
Connelly: 4x 8-well modules, special plasticware that's deformable, optical bottom. Very fast and accurate thermal control #TRICON
7:35pm March 7th 2016 via Hootsuite
Connelly: Core tech is cell stabilization, now stabilization for NIPT. Moved into real-timePCR, called Philisa. #TRICON
7:30pm March 7th 2016 via Hootsuite
Chris Connelly (Streck) Utility of a rapid real-time PCR using a novel random-access 20 minute system #TRICON
7:29pm March 7th 2016 via Hootsuite
Quinones:Q:How to account of geographical regions? A:Primer design, some are degenerate #TRICON
7:27pm March 7th 2016 via Hootsuite
Quinones: Multiplex to 96/run, TAT 5-15 d, low cost, stringent QC is required #TRICON
Quinones: Put all the primary HIV-1 drug resistance mutations, in mixtures. 1%, 5%, 10%, 20%, 100%: consistent detection across muts #TRICON
7:26pm March 7th 2016 via Hootsuite
Quinones: Using 3 internal controls - WT, 2 mutant. Better one: SeraCare partner, used AccuPlex sinbis virus, to use like HIV #TRICON
7:25pm March 7th 2016 via Hootsuite
Quinones: Illustrates sample failed detection via Sanger, but picked up with NGS. Able to detect down to 1% #TRICON
7:23pm March 7th 2016 via Hootsuite
Quinones: Have tested >1K samples from N Ohio, agreement with ARUP, now samples from Uganda #TRICON
7:22pm March 7th 2016 via Hootsuite
Quinones: Results of several years '14 ref https://t.co/kCMTv5bJZw Multiple databases (Stanford, Germany, their own) #TRICON
Quinones: Detection via Sanger, about 20% LOD; 2y ago developed on Ion PGM. #TRICON 4 platforms '12 PLoS One https://t.co/crNqlrocRF
7:19pm March 7th 2016 via Hootsuite
Quinones: Shows very bsuy list of current retrovirals - some 29 of them - triple drug cocktails. '90s: phenotypic assays #TRICON
7:17pm March 7th 2016 via Hootsuite
Quinones: HIV infection and CD4 cel counts, against HIV-1 RNA: acute infection, clinical laterncy, HIV drug resistance #TRICON
7:16pm March 7th 2016 via Hootsuite
Miguel Quinones (Case Western) Clinical testing using an NGS-based HIV-I genotyping assay (DEEPGEN HIV): the need for stringent QC #TRICON
7:15pm March 7th 2016 via Hootsuite
David Rimm (Yale) Quant comparison of IHG and mRNA by nearly point-of-care biomarker platform #TRICON
6:12pm March 7th 2016 via Hootsuite
Fernandes: FNA cytologic smears for lung adeno. Cell block, Diff-Quik, Pap: library quant of DQ low. Good concordance but Pap better #TRICON
6:11pm March 7th 2016 via Hootsuite
Fernandes: IGV inspection can help - looking for C>T, G>A artifacts. They look at strand bias - <0.65; VAF 5%, 400X; VAF 3%, 1000X
6:07pm March 7th 2016 via Hootsuite
Fernandes: Using Ion AmpliSeq, 10ng was inconsistent. Did experiments - #TRICON Effect of dilution '15 ref https://t.co/Kr8xUPZFCP
6:01pm March 7th 2016 via Hootsuite
Fernandes: QC: Qubit, NanoDrop, Bioanalyzer, fragment analysis;13 PLoS One https://t.co/v0oj3NmvF2 #TRICON
6:00pm March 7th 2016 via Hootsuite
Fernandes: But side-by-side VAF has r2=0.92; coverage of automated generally better too. They have 50-70 smpls/week #TRICON
5:59pm March 7th 2016 via Hootsuite
Fernandes: Onto comparing extraction: Manual QIAamp DNA FFPE vs Maxwell 16 FFPE (Promega) Chart shows improved yield w/Promega #TRICON
5:58pm March 7th 2016 via Hootsuite
Fernandes: FF, FFPE, New (PAXgene); Cp same sample w/3 mutations; one drops out w/FFPE, new comparable to fresh frozne (FF) #TRICON
5:55pm March 7th 2016 via Hootsuite
Fernandes: Some report addition of EDTA helps. #TRICON '15 paper evaluates tissue fixatives; H&E stains in PAXgene https://t.co/vEm1Ed6y
5:54pm March 7th 2016 via Hootsuite
Fernandes:Factors: Time to fixation in formalin. pH, conc., temp, purity of formalin all affect. <24h; temp of paraffin (low melt) #TRICO
5:52pm March 7th 2016 via Hootsuite
Fernandes: Sequencing artifacts: C>T or G>A may be reduced by pre-treatment with UDG (via degradation of Uracil) #TRICON
5:51pm March 7th 2016 via Hootsuite
Fernandes: For resection - lots of necrosis, DNA quality varies. #TRICON
5:47pm March 7th 2016 via Hootsuite
Fernandes:;Failure rates for FNAs on the order of 20%; yield mean 3.6 ng. Failure due to lack of material. #TRICON
5:46pm March 7th 2016 via Hootsuite
Fernandes: Tumor heterogeneity: best results are >10% cellularity. Sample quality (i.e. melanin in melanomas are PCR inhibitors) #TRICON
5:43pm March 7th 2016 via Hootsuite
Fernandes: 5ng is 400-600 cells; 1ng is only 80-100 cells. #TRICON
5:42pm March 7th 2016 via Hootsuite
Fernandes: Shows slides of a surgical biopsy, a core biopsy, cytology smears. 'If you need 5ng of DNA, how many cells are req'd?" #TRICON
5:41pm March 7th 2016 via Hootsuite
Helen Fernandes (Weill Cornell) Assessment of FFPE samples for success in NGS #TRICON
5:39pm March 7th 2016 via Hootsuite
RT @SeraCare: SeraCare Launches #ctDNA Reference Materials for #NGS and #DigitalPCR #Oncology Assays https://t.co/i9YtLBatuL #TRICON
5:01pm March 7th 2016 via Hootsuite
Holt: Lists product req's: Sample type, colleciton, transport, volume, dilution, ext/int controls, calibrators.. a long list #TRICON
4:54pm March 7th 2016 via Hootsuite
Holt: Lays out complex diagram: Y-axis: Assay/HW/SW/Mfg/OTS/OTS Eng/Materials/Facilities/QE/QC/Clinical/Reg #TRICON
4:49pm March 7th 2016 via Hootsuite
Holt: Time for LDT: 1-6 mos; CE marking: 8-12 mos; 510(k) 1-2 y; PMA is 2+ years. #TRICON
4:48pm March 7th 2016 via Hootsuite
.@Erika_Check @antonioregalado So the rumors swirling around for the past several months were true...
4:46pm March 7th 2016 via Hootsuite in reply to antonioregalado
RT @antonioregalado: New DNA: Jay Flatley to hand over Illumina CEO job to @fdesouza . Flatley becomes executive chairman of the board.$ILMN
4:46pm March 7th 2016 via Hootsuite
Holt: 700 biomarkers were used in clinical trials in 2015. Vast majority are false discovery. #TRICON
Holt: Tepnel is the CRO arm of Hologic (parent has $2.8B revenue, 5.5K employees). "There are 1500 biomarker publ/week" 750K total #TRICON
4:43pm March 7th 2016 via Hootsuite
Bob Holt (Hologic) How to turn a biomarker into a clinical test #TRICON
4:42pm March 7th 2016 via Hootsuite
Buckingham: Emphasizes speed from discovery gene signature to clinical trial; reiterates need for pre-selecting statistical test #TRICON
4:37pm March 7th 2016 via Hootsuite
Buckingham: Det cell of origin for diffuse large b-cell lymphoma, a PIII clinical trial, called ROBUST. #TRICON
4:36pm March 7th 2016 via Hootsuite
Buckingham: Lists 5 prospective evaluations - UK Optima (4.5K HR+/N+), ECOG EA1131; NeoPAL; PRECISION; EXPERT #TRICON
4:32pm March 7th 2016 via Hootsuite
Buckingham: 2014 validation study of the PAM50 in BMC Cancer https://t.co/xh3Ng95zyw #TRICON
4:30pm March 7th 2016 via Hootsuite
Buckingham: Their SD for prosigna score 2.9. Showed 5 pooled RNA samples cross-site: very low variance #TRICON
4:29pm March 7th 2016 via Hootsuite
Buckingham: Most impt for decentralized testing: reprod from 43 FFPE tissues; 3 diff labs, 3 different pathologiest, 3 tech's. #TRICON
4:28pm March 7th 2016 via Hootsuite
Buckingham: For br ca subtypes: LumB, LumA, Basal-like, HER2-enriched. Do corelation to centroids, risk of recurrance score (ROR) #TRICON
4:27pm March 7th 2016 via Hootsuite
Buckingham: '13: marketed in EU, Israel, US after CE and 510(k) clearance. #TRICON
4:26pm March 7th 2016 via Hootsuite
Buckingham:3407 FFPE samples for development: 514 for sig training; 256 for testing training; 1017 for study 1; 1620 for study 2 #TRICON
4:25pm March 7th 2016 via Hootsuite
