Geldart: UBOs: universal blocking oligos: increasing on-target rate (75%). #AGBT18
9:11am February 15th 2018 via Hootsuite
Geldart: 2d workflow - frag, end-repair + A-tail, adapter ligation. Then Hypercap workflow. Dual indexing for higher mulitplex #AGBT18
9:10am February 15th 2018 via Hootsuite
Geldart: From 200 uL whole blook, elution in 100 uL; shows 3 samples on 24 and 96 instruments, sufficient for KAPA HyperCap #AGBT18
9:09am February 15th 2018 via Hootsuite
Geldart: They also have cfDNA blood collection tubes. Going downstream: MagNA Pure 24 through nasal swab, urine, stool purification #AGBT18
9:08am February 15th 2018 via Hootsuite
Geldart: AVENIO Millisect - laser-capture microdissection. Shows specificity of data compared to macrodissection. #AGBT18
9:07am February 15th 2018 via Hootsuite
Adriana Geldart (Roche) Leave no base behind: Unlock the potential in every sample #AGBT18
9:06am February 15th 2018 via Hootsuite
Worth a look RT @erlichya: The slides for my #AGBT18 talk on #dnastorage https://t.co/pFMtJL7vCX
11:53pm February 14th 2018 via Hootsuite
RT @mason_lab: Slides from my #AGBT18 talk "The genetic, physical, and molecular dynamics of long-term human spaceflight” Space is rough, b…
11:51pm February 14th 2018 via Hootsuite
Q: What fx is dsDNA molecule? Reichel: working on it, dep on sample and depth and mass of input #AGBT18
9:09pm February 14th 2018 via Hootsuite
Reichel: 9 endocrine-res br ca cfDNA: ESR1 Y537S at 69%, ESR1 D538G at 1%; across the pool, down to 0.23%. All validated via ddPCR #AGBT18
9:07pm February 14th 2018 via Hootsuite
Reichel: Took 9 cfDNA from lung ca pts; previously tested at ResolutionBio in WA state. both found EGFR T790M at 1.5%; now on osmer #AGBT18
9:06pm February 14th 2018 via Hootsuite
Reichel: Error supp via duplex UMIs. Can ID strand-specificity. Showed ability to reduce error 211-fold (cp to IMPACT) #AGBT18
9:05pm February 14th 2018 via Hootsuite
Reichel: Looked at 20K IMPACt cases - 30 muts/MB, OncoKB, all exons w/1 mut; hotspots, exons w/10 muts. #AGBT18
9:01pm February 14th 2018 via Hootsuite
Reichel: Had to trim panel down to 400K versus IMPACT 1.7 MB. 3,147 probes, 378kb, 60 genes for muts, 10 fusions, TERT #AGBT18
9:00pm February 14th 2018 via Hootsuite
Reichel: cfDNA gets only 10-30ng. 3,000 to 9,000 GE's. Updated adapters, dual index, duplex UMI's. 20k-50k fold. #AGBT18
8:59pm February 14th 2018 via Hootsuite
Reichel: Works on pan-cancer cfDNA: muts, indels, CNA, fusions, and MSI. Key feature: 0.1% to 0.03%. IMPACT: 2-5%. #AGBT18
Reichel: For MSKCC-IMPACT, Stg IV met pts: 50% could find nothing via biopsy. 62%: found sub-threshold muts (149/242) #AGBT18
8:58pm February 14th 2018 via Hootsuite
Reichel: examples of AKT inhibition '17 ref https://t.co/UiyfDJCQ2X #AGBT18
8:57pm February 14th 2018 via Hootsuite
Reichel: cfDNA reveals - one case, BRCA2, sens to olaparib. Serial cfDNA: monitoring tumor burden and evolution #AGBT18
8:55pm February 14th 2018 via Hootsuite
Reichel: Plasma seq several clinical appl's: pre-Rx; observe add'l heterogeneity cp to tissue. Longitudinally: surveill, quantify #AGBT18
8:53pm February 14th 2018 via Hootsuite
Reichel: Tumors are spatially and temporally heterogeneous. At t=0 vs. t=1 a mutaiton may appear that a biopsy may miss #AGBT18
8:52pm February 14th 2018 via Hootsuite
Jonathan Reichel (Memorial Sloan Kettering CC NY) Highly sensitive genomic surveillance via cell-free DNA NGS revea… https://t.co/f5thHWc53b
8:51pm February 14th 2018 via Hootsuite
Mason: Took plasma for examination of cfDNA. Found WBC ejecting mtDNA as a response to stress into the blood. Nucleosome depletion #AGBT18
8:50pm February 14th 2018 via Hootsuite
Mason: 30 more astronauts over the next several years. #AGBT18
8:47pm February 14th 2018 via Hootsuite
Mason: Could predict food they were eating (!) Still eating food, diversity stayed the same. Next: n=1, need to increase it. #AGBT18
8:46pm February 14th 2018 via Hootsuite
Mason: RNA methylation levels: difference observed pre- and post. Metagenomics: Buccal, saliva and fecal: separate out. #AGBT18
8:45pm February 14th 2018 via Hootsuite
Mason: In-flight mtRNA: enriched in the flight samples' blood. Validated via qPCR; from where - WBC and neutrophils #AGBT18
8:44pm February 14th 2018 via Hootsuite
Mason: Expression data indicates hypoxia; book 'Endurance' has sections of complaints about headaches. O2 fluctuations did occur #AGBT18
8:43pm February 14th 2018 via Hootsuite
Mason: Mars would be a 3y journey; DEGs over 1y? 7% did not, 1,703 that didn't return to normal after return. #AGBT18
8:42pm February 14th 2018 via Hootsuite
Mason: Looking at age via epigenetic shifts: plots w/predicted age, within range. #AGBT18
Mason: Showed 13% longer telomeres from spaceflight. Shortened again after return. Low-level xloc 'increase at linear scale' #AGBT18
8:37pm February 14th 2018 via Hootsuite
Mason: All measures: cytokines screaming. Post-flight cognition slightly impaired. 7.7% difference between identical twins. 5% GIAB #AGBT18
8:36pm February 14th 2018 via Hootsuite
Mason: Looking at everything. (Wow he can talk fast.) telomere length. Video - https://t.co/GRIpKzLpNa Skin weight painful - Kelly #AGBT18
8:34pm February 14th 2018 via Hootsuite
Mason: https://t.co/MLq7HzeGEF will map of where Musk's car is. 1-2B years? https://t.co/y4RZOFNLzt What about humans? #AGBT18
8:32pm February 14th 2018 via Hootsuite
Mason: The mission: (he notes that each subsection has about 50,000 slides) Journey to Mars: https://t.co/tTlOE0e6Af #AGBT18
8:31pm February 14th 2018 via Hootsuite
Chris Mason (Weill-Cornell NY) The genetic, physical, and molecular dynamics of long-term human spaceflight #AGBT18
8:29pm February 14th 2018 via Hootsuite
Q: bias due to extraction of 150K+ datasets? Dadlani: Hard-to-lyse perform differently. #AGBT18
8:24pm February 14th 2018 via Hootsuite
Dadlani: John Muir quote "When one tugs at a single thing in nature, one finds it is connected to everything in the universe" #AGBT18
8:23pm February 14th 2018 via Hootsuite
Dadlani: Shows PCA analysis from health stool from different countries; overlay Crohns, healthy now looks similar via PCA #AGBT18
8:22pm February 14th 2018 via Hootsuite
Dadlani: #AGBT18 Nota bene: Michael Porter in NEJM '10 https://t.co/6FeCrbBb9N
8:21pm February 14th 2018 via Hootsuite
Dadlani: Micheal Porter defines value = outcome / total cost of care. New diagnostics 'have to demo real value' #AGBT18
8:20pm February 14th 2018 via Hootsuite
Dadlani: NGS-based wound biofilme ID and AMR: 53 wound pts, directly seq and cultured. 98% sens to culture. #AGBT18
8:19pm February 14th 2018 via Hootsuite
Dadlani: Med Coll Wisc: UTI diagnostics and AMR. 20 urine samples. 95% sens entire sample, 96% sens on isolates; clin relevant org's #AGBT18
8:17pm February 14th 2018 via Hootsuite
Dadlani: Best-in-class performance. Show figure: https://t.co/eIYIYfv1gS #AGBT18
Dadlani: ID, char AMR, compare samples. Partnering with TMO, DNANexus; HIPAA and CLIA compliant. NIST, FDA contract for in-house svc #AGBT18
8:16pm February 14th 2018 via Hootsuite
Dadlani: Core is data; 150K+ bacteria, viruses, fungi. Databases the critical component. db as a phylogenetic tree #AGBT18
8:14pm February 14th 2018 via Hootsuite
Dadlani: Need remains: better Dx for inf disease. Using NGS for diagnostics applications: food safety, pathogen ID, environment #AGBT18
8:13pm February 14th 2018 via Hootsuite
Dadlani: Wellcome Trust predict: AMR deaths in 2050 is 10M. Today: about 700K deaths due to AMR. #AGBT18
8:11pm February 14th 2018 via Hootsuite
Dadlani: Cheese or wine. For E. coli - Vit K and B1, also protection against commensals. But also pathogenic #AGBT18
8:10pm February 14th 2018 via Hootsuite
Dadlani: From single isolates to parallel detection. Strain-level differentiation. Why inpt: lactobacillus can be used for... #AGBT18
