Mueller: Security requirements, limited IT and bioinf. resources are limited. #Tricon
11:19am February 22nd 2017 via Hootsuite
Mueller: New methods, workflows of a mix of tech and vendors, software a mixture, reference data from many palces, PHI and HIPAA #Tricon
Mueller: Gives example of data intensive science: from specimen receipt to sample prep, seq, mapping, analysis, reporting #Tricon
11:18am February 22nd 2017 via Hootsuite
Chris Mueller (Founder Lab7 TX) Working on integrating data intensive applications into the clinic #Tricon
11:17am February 22nd 2017 via Hootsuite
Applications in future: Immunotherapy and applying Microbiome #Tricon
11:16am February 22nd 2017 via Hootsuite
Moderator's headlines: HTP screening, genomic sequencing; biobanking has had its struggles. Tech in future? CRISPR, Cloud compute #Tricon
11:15am February 22nd 2017 via Hootsuite
Panel is called 'Emerging technologies and industry perspective',, panelists have 7 min to present at #Tricon about problems, tech & sol
11:11am February 22nd 2017 via Hootsuite
#Tricon - poster winner described fast 30min POC antibiotic resistance detection method.
11:09am February 22nd 2017 via Hootsuite
Diagnostics World (publ of BioIT World) have five finalists for 'Early Innovators' 2, 98, 17; winner is Travis Schlappi of CalTech #Tricon
11:08am February 22nd 2017 via Hootsuite
Great to meet @DCGenomics IRL here at #Tricon!
11:03am February 22nd 2017 via Hootsuite
#Tricon Panel of Leaders from Lab7, iSpecimen, Accell Biotech, Boston Healthcare, BioCartis, SeraCare, NanoString, Silicon Biosystems
RT @pickover: This is a joke that could appeal to mathematicians. https://t.co/EDX9vc5kQL
9:40pm February 21st 2017 via Hootsuite
Garlick: Software available for tracking metrics, and easily report out metrics #Tricon
7:11pm February 21st 2017 via Hootsuite
Garlick: Showes results from @archerdxinc assay, as well as @ThermoFisher Oncomine detection (all except for one not assayed) #Tricon
7:09pm February 21st 2017 via Hootsuite
Garlick: Shows results with @QIAGEN RNAscan assay; all are detected. #Tricon
7:08pm February 21st 2017 via Hootsuite
Garlick: Shows dCPR results across partners: NTRK1/3, ROS1, RET, ALK etc. Done for each lot; 'think about 2y from now' testing again #Tricon
7:07pm February 21st 2017 via Hootsuite
Garlick: 10um FFPE curls or purified version. Each curl obains at least 100ng, typically 200 or 300ng #Tricon
7:06pm February 21st 2017 via Hootsuite
Garlick: Every fusion transcript is digital PCR quantitated, 400bp on each side of the breakpoint. Mfg under 13485 #Tricon
7:05pm February 21st 2017 via Hootsuite
Garlick: 15 Fusion RNAs, @SeraCare announced today a second version @httpseracare https://t.co/Za55wTsGh7 #Tricon
7:04pm February 21st 2017 via Hootsuite
Garlick: Clinical labs need reference samples; you need as much info as possible for highly multiplexed test in 1 run. #Tricon
7:02pm February 21st 2017 via Hootsuite
Garlick: Unique challenges, NGS is much more complex than cyto; Fusion RNAs more complex than most DNA muts; RT also source of var #Tricon
7:01pm February 21st 2017 via Hootsuite
Garlick: There are many QC checkpoints - he counts 12. Requires 'Truth Set', and a continuous monitoring of performance w/software #Tricon
7:00pm February 21st 2017 via Hootsuite
Garlick: NGS can detect unknown fusion pairs, superior to classical FISH. Hernandes showed difficulty on preanalytic, bioinf steps #Tricon
6:59pm February 21st 2017 via Hootsuite
Garlick: Tropomyosine receptor kinase is a Rx target - known as OncD, NTRK1/2/3 now known, leads to oncogenesis #Tricon
6:58pm February 21st 2017 via Hootsuite
Garlick: Darah Aisner from Univ CO with scant amt of sample, kept looking at the data, and EGFR mutation was underlying below cutoff #Tricon
6:57pm February 21st 2017 via Hootsuite
Garlick: SeraCare has used over 50K liters of plasma in the past year for different IVD manufacturers #Tricon
6:56pm February 21st 2017 via Hootsuite
Russell Garlick (SeraCare MA) NGS-based solid tumor iagnostics: the next fronter, RNA Fusions #Tricon
6:55pm February 21st 2017 via Hootsuite
Sebra: Did deep WES (116x, 229x, 323x); all 4 germline confirmed; 16 somatic vars in met confirmed '16 ref https://t.co/SvdlksS7NR #Tricon
6:35pm February 21st 2017 via Hootsuite
Sebra: Orthogonal somatic variant detection from bulk tissue: DNA from blood normal; primary FFPE colon (50% pure); met liver (10%) #Tricon
6:33pm February 21st 2017 via Hootsuite
Sebra: But in 3 high-risk pt samples, >100 novel mutations seen of all types. Only 3 samples, but still significantly large number #Tric
6:32pm February 21st 2017 via Hootsuite
Sebra: Whole-gene BRCA 1/2: still find a 'ton of novel information'. 70 targets 3-5kb each; dbSNP is biased toward exons #Tricon
6:30pm February 21st 2017 via Hootsuite
Sebra: Proved functionally in zebrafish (OTX2, mandible of fish model for human). 'Why we should be pushing these technologies' #Tricon
6:29pm February 21st 2017 via Hootsuite
Sebra: Large SVs related to disease: Goldenhar syndrome, craniofacial disorders. Very rare; 1.3Mb chr 14 duplication in proband #Tricon
6:28pm February 21st 2017 via Hootsuite
Sebra: Now doing extreme cases where there are hundreds of repeats for Fragile X. #Tricon
6:27pm February 21st 2017 via Hootsuite
Sebra: Up to 10kb long, very G-C rich. FMR1 for Fragile X: WT 30 repeats vs 120 repeats for affected data shown #Tricon
6:26pm February 21st 2017 via Hootsuite
Sebra: C9orf72 G4C2 repeat discovered in ALS, complex structure https://t.co/6kLkkOypaQ Also want to get to methylation #Tricon
6:25pm February 21st 2017 via Hootsuite
Sebra: Looking now at trinucleotide repeats w/ a PCR-free target enrichment via SMRTbell and capture adapter #Tricon
6:23pm February 21st 2017 via Hootsuite
Sebra: CYP2D6 is hard to phase with heterozygotes. On Sequel: can multiplex 384 samples; also covered GBA, full-length gene #Tricon
6:22pm February 21st 2017 via Hootsuite
Sebra: Each of us have about 1K SVs that are >2500bp in length. These have yet to be characterized #Tricon
6:21pm February 21st 2017 via Hootsuite
Robert Sebra (Mt Sinai SoM NY) Leveraging long read technologies for developing niche assay with diagnostic potential #Tricon
6:18pm February 21st 2017 via Hootsuite
Qiu: Data interoperability on WES '16 ref https://t.co/fTTWUOjoi3 #Tricon
Qiu: Now onto bioinformatics: '13 ref comparing different WES pipelines https://t.co/oQm0WheAgK #Tricon
6:09pm February 21st 2017 via Hootsuite
Qiu: Did tumor purity mixes, from 40% to 100%; showed sensitivity drop from 98% down to 74% the lower % #Tricon
6:08pm February 21st 2017 via Hootsuite
Qiu: Only 326 called by both; lots of false positives in panels w/o matched normals. #Tricon
6:06pm February 21st 2017 via Hootsuite
Qiu: WES requires matched normals; for targeted not req'd. Same samples, tumor burden almost 4x/MB. Same samples! #Tricon
Qiu: Calculation of mutations per MB - shows a input dependency (200ng has 40% higher mutations cp to 50ng input) #Tricon
6:04pm February 21st 2017 via Hootsuite
Qiu: Showed distribution of failures by input, w/dPCR of input: 10ng - 20ng of amplifiable able to get successful Agilent WES #Tricon
6:03pm February 21st 2017 via Hootsuite
Qiu: Theoretically 1 ng = 33o copies; using FF cell ines, WES from 10ng https://t.co/pvZ5g57EKI #Tricon
6:02pm February 21st 2017 via Hootsuite
Qiu: Measured Ct via qPCR for RNA. Showed chart of 'higher DNA input can compensate for low DNA quality'. Used QFI adjustments #Tricon
5:59pm February 21st 2017 via Hootsuite
Qiu: Also wide variation; also some assay-spec differences. RNA peforms comparably, less variability than DNA #Tricon
5:58pm February 21st 2017 via Hootsuite
