November 2017

Li: Def'n of biomarkers: all vars are biomarkers, but not the other way around. Pred sens, resist. or toxicity to spec Rx #AMP2017

12:57pm November 18th 2017 via Hootsuite

Li: In '14 - Assembled multidisciplinary group Feb '15; May finished technical survey; June '16 std guidelines pub end of '16 #AMP2017

12:56pm November 18th 2017 via Hootsuite

Marilyn Li (Childrens Hosp Philadelphia PA) AMP/ASCO/CAP Stds and Guidelines of Somatic Variant Interpretation and Reporting #AMP2017

12:54pm November 18th 2017 via Hootsuite

Curious what @Pillar_Bio is up to for clinical oncology at #AMP2017 ? Here’s an interview for you. https://t.co/pnH6pQuY9F

12:50pm November 18th 2017 via Hootsuite

Hey #AMP2017 - Fran de Abreu (L) presenting @Pillar_Bio data at ST131 in the poster session happening now. https://t.co/EeCH760jsk

12:05pm November 18th 2017 via Hootsuite

Tadimety: Shows capture from 20-150 ng/mL mut and wt DNA binding, and peak wavelength. #AMP2017

9:45am November 18th 2017 via Hootsuite

Tadimety: Peak shifts from 900 empty, shows difference in peak from wt to mutKRAS bound. #AMP2017

9:44am November 18th 2017 via Hootsuite

Tadimety: Have gold nanorods with PNA that bind, and surface plasmon can detect on surface. Showed nanorod conj w/PNA w/mut G12V #AMP2017

9:43am November 18th 2017 via Hootsuite

Tadimety: Small scale is better sens / spec due to surface to volume, and conserving sample. Also can multiplex #AMP2017

9:41am November 18th 2017 via Hootsuite

Tadimety: Also Cellsearch CTC is used. Use of microchip biosensors: a recognition element; a transduction element; readout #AMP2017

9:39am November 18th 2017 via Hootsuite

Tadimety: PDAC - poor prognosis, difficult to diag, most Dx at adv stage, absence of spec symptoms. CT imaging, Pathway Genomics #AMP2017

9:39am November 18th 2017 via Hootsuite

Tadimety: Shows intro slides on liquid biopsies' usage, and focus on G12V in KRAK for PDAC (common mutation) #AMP2017

9:38am November 18th 2017 via Hootsuite

Amogha Tadimety (Dartmouth NH) TT24 Screening circ nucleic acids of pancreatic ductal adenocarcinoma using a plasmonic nanosensor #AMP2017

9:36am November 18th 2017 via Hootsuite

Q: At higher input (50ng) could 3 droplets be detected? Wood-Bouwens: Recommend increase replicates. >10ng, noisy data #AMP2017

9:34am November 18th 2017 via Hootsuite

Wood-Bouwens: Simple to perform, customizable; TAT from draw to data in <1d. Sens down to 0.1%. #AMP2017

9:32am November 18th 2017 via Hootsuite

Wood-Bouwens: 5 courses of treatment overlay - lower ctDNA counts; higher counts when off-Rx. #AMP2017

9:30am November 18th 2017 via Hootsuite

Wood-Bouwens: At day 154 - spike in ccfDNA but TP53 steady at 20 ctDNA per mL. Spike may be normal cell death due to chemo #AMP2017

9:29am November 18th 2017 via Hootsuite

Wood-Bouwens: Shows 182 d Rx course; and wt ccfDNA molecules/mL from 6K downt to 2K and day 154 spike. ctDNA/mL from 0 to 50. #AMP2017

9:28am November 18th 2017 via Hootsuite

Wood-Bouwens: Gemcitabine and cisplatin, monitoring TP53 E285K, and RPP30 (general ccfDNA quant to det tumor burden) #AMP2017

9:27am November 18th 2017 via Hootsuite

Wood-Bouwens: Better sens is from more DNA input. Now they have their first longitudinal pt - Pt has bile-duct ca TP53 p.E285K #AMP2017

9:26am November 18th 2017 via Hootsuite

Wood-Bouwens: Shows 1ng, 300 haploid equiv, only 3 KRAS G12D mutant molecules called. Shows expected and meas at 0.1% 10ng input #AMP2017

9:25am November 18th 2017 via Hootsuite

Wood-Bouwens: Basically a training set with a confidence interval. '17 ref called 'data gridding' https://t.co/c4yF1iP2QH #AMP2017

9:24am November 18th 2017 via Hootsuite

Wood-Bouwens: High density droplets - clustering is clear. Low conc, hard to cluster. Uses a mixed ca cell line, with 50% mutants. #AMP2017

9:23am November 18th 2017 via Hootsuite

Wood-Bouwens: The longer amplicon can then be differentiated between empty, wild type, and mutant products. #AMP2017

9:22am November 18th 2017 via Hootsuite

Wood-Bouwens: Looking for dual allele - with reverse primers. Each droplet has all 3 primers; mutant allele primer has AAAT repeats #AMP2017

9:21am November 18th 2017 via Hootsuite

Wood-Bouwens: Single-color: forward primer is matches; genotyping reverse is perfect match or mutant. +/- amplicons #AMP2017

9:21am November 18th 2017 via Hootsuite

Wood-Bouwens: ctDNA's low abundance, fragmented, different between time points and pts. Need high sens and short TAT #AMP2017

9:19am November 18th 2017 via Hootsuite

Wood-Bouwens: Imaging is used but promise of liquid biospies to longitudinally monitor genetic features over time #AMP2017

9:18am November 18th 2017 via Hootsuite

Wood-Bouwens: Overall goal to 'reach every pt at every visit'. Illustrates time from original tissue biopsy to relapse, metastasis #AMP2017

9:17am November 18th 2017 via Hootsuite

Christina Wood-Bouwens (Stanford CA) TT82 High performance detection of cancer mutations from circ DNA using single-color dPCR #AMP2017

9:15am November 18th 2017 via Hootsuite

Restrepo: Cp to FISH and karyotype, 24/24 TP; 2/24 were neg on FISH and kayrotype, pos on NGS. 16/16 both neg #AMP2017

9:10am November 18th 2017 via Hootsuite

Restrepo: Yield correlated with age; used 50-200ng; used ArcherDx FusionPlex HemeV2. 42/43 Ct<30 (threshold for quality) #AMP2017

9:09am November 18th 2017 via Hootsuite

Restrepo: Also Promega Blood DNA kit, w/o RNAse step for total NA. Succeeded in every case - 0.1 to 11.3ug; av 4.9ug #AMP2017

9:07am November 18th 2017 via Hootsuite

Restrepo: 43 cases w/smears: from 1mo to 2y of RT storage. Hydrated w/lysis buffer, scrapted, heated 56C; Maxwell RSC #AMP2017

9:05am November 18th 2017 via Hootsuite

Restrepo: Imptc of fusion RNA; they use it for heme malignancies; retrospective and prospective tissue is scarce. #AMP2017

9:04am November 18th 2017 via Hootsuite

Tamara Restrepo (Boston Childrens MA) TT92 Extraction of RNA from archived bone marrow aspirate smears for targeted RNA seq #AMP2017

9:02am November 18th 2017 via Hootsuite

RT @gizbab: @gtsonga Greg Tsongalis receives the Jeffrey A Kant Leadership Award #AMP2017 #AMPlifier @AMPath https://t.co/IV0TVTWcLt

5:57am November 18th 2017 via Hootsuite

Hi #AMP2017 - take a look at Dr. Greg Tsongalis’ Poster ST131 “Evaluation of the Pillar NGS SLIMamp Cancer Hotspot Panel” at the break.

3:45pm November 17th 2017 via Hootsuite

Iafrate: Pathogenesis of Fusion+ tumors: bad luck, env exposure to radiation (other sources of DSBs) #AMP2017

3:44pm November 17th 2017 via Hootsuite

Iafrate: Eng cell lines or spiked artificial templates 'are a good start'. #AMP2017

3:43pm November 17th 2017 via Hootsuite

Iafrate: Normal tissues have 2 copies of DNA, and wide variation in RNA. Dilute into 'normal RNA' can be problem #AMP2017

3:43pm November 17th 2017 via Hootsuite

Iafrate: Orthogonal approaches can be time consuming; need for new FISH probes for ex. LOD is also challenge #AMP2017

3:42pm November 17th 2017 via Hootsuite

Iafrate: Validation challenges: fusions are rare, RNA not routinely extracted (archives don't exist) #AMP2017

3:42pm November 17th 2017 via Hootsuite

Iafrate: 39yo F left foot melanoma, MLPH-ALK, no other muts, expressed in melanocytes, coil-coil domain #AMP2017

3:41pm November 17th 2017 via Hootsuite

Iafrate: 73yo m Lung ACA, LPCAT1-TERT, surfactant metab promoter driving TERT, 'promoter hijacking' #AMP2017

3:40pm November 17th 2017 via Hootsuite

Iafrate: 3 cool cases: 63yo M Sigmoid Colon ACA, TCF7L2 = TCF4 binding domain, activates Wnt pathway EWSR1-TCF7L2 #AMP2017

3:40pm November 17th 2017 via Hootsuite

Iafrate: Shows criteria they use: in-frame, canonical breakpoint, prevalent, supporting reads >100, known anchor #AMP2017

3:38pm November 17th 2017 via Hootsuite

Iafrate: May be seen as normal alt splicing. Learned: 2K pts, 20% have >0 Met ex14 skip reads #AMP2017

3:36pm November 17th 2017 via Hootsuite

Iafrate: #AMP2017 MET ex14-skipping '15 ref https://t.co/YqMG5onMy2 more common than ALK, intronic splice-site muts

3:35pm November 17th 2017 via Hootsuite