ICYMI: Pillar Biosciences at Association for Molecular Pathology #AMP2017 https://t.co/CS1fFbP4kz
7:39am November 19th 2017 via Hootsuite
New post: Pillar Biosciences at Association for Molecular Pathology #AMP2017 https://t.co/CS1fFbP4kz
7:05pm November 18th 2017 via WP to TWTR on Yuzuki.org
Q: Same coverage depth for WGS, WES? Jennings: "No." The allele burden is different. Binomials illus - how to sep FP from TP #AMP2017
1:54pm November 18th 2017 via Hootsuite
Q: 250x min read count; but base and map quality? Jennings: FP/FN was statistical model on 1% error. #AMP2017
1:50pm November 18th 2017 via Hootsuite
Jennings: New guideline rec'd an 'error-based approach'. #AMP2017
1:49pm November 18th 2017 via Hootsuite
Jennings: Rec'd appropriate design mods or controls when potential errors remain high. FLT3-ITD - will you have 59 samples? #AMP2017
1:48pm November 18th 2017 via Hootsuite
Jennings: CI useful but for that next sample, tolerance interval impt. Population distribution may be different shapes #AMP2017
1:43pm November 18th 2017 via Hootsuite
Jennings: 20 samples is good for est of mean; ave read depth 95% CI 253 to 301x read depth. Tolerance interval introduced #AMP2017
Jennings: '17 J Mol Diag paper https://t.co/Nl9RcmfiqI AMP/CAP guidelines for validation of oncology panels #AMP2017
1:41pm November 18th 2017 via Hootsuite
Lawrence Jennings (Childrens Hosp Chicago IL) AMP/Cap guidelines for validation of NGS-based oncology panels #AMP2017
1:37pm November 18th 2017 via Hootsuite
Li: Went through three detailed case studies in Dx. Last was a novel EWSR1-CREB3L3 fusion, ended up w/radical mandible resection #AMP2017
1:35pm November 18th 2017 via Hootsuite
Li: change of gears: CHOP NGS Panel description: large for solid, heme, fusion and hereditary. All coding flanking 10bp#AMP2017
1:27pm November 18th 2017 via Hootsuite
Li: Other rec's: clear desc of clin sig; clear desc of confirmation methods. Ref J Mol Diagn '17 https://t.co/Noyq5Y9Fzv #AMP2017
1:26pm November 18th 2017 via Hootsuite
Li: Var nomenclature: Gene name; Transcript ID accession and ver number; nucleotide change; aa change; VAF; coord's… https://t.co/hbf4qTb76H
1:24pm November 18th 2017 via Hootsuite
Li: Shows a few examples of older / newer classification. Recommend 4-tier reporting, only 1-3 to physician. #AMP2017
1:22pm November 18th 2017 via Hootsuite
Li: Germline in tumor testing: Consider gene char - tumor supp or oncogene; pt information, family history etc #AMP2017
1:20pm November 18th 2017 via Hootsuite
Li: Tier IV benign / likely benign. Find germline vars in tumor testing: var freq usu 50% for germline. But CNVs mu… https://t.co/F8t8Spm5U1
1:19pm November 18th 2017 via Hootsuite
Li: Ex of Tier III, vars of unk sig, showed on dbSNP entry, low freq, controversial via SIFT and other tools #AMP2017
1:16pm November 18th 2017 via Hootsuite
Li: Tier II: fusion in Ph-like ALL, GENEA1-JAK2. No drug, in pediatric case, no guidelines at present. db's don't apply. #AMP2017
1:15pm November 18th 2017 via Hootsuite
Li: (Tier III/IV have insufficient evidence, a matter of degree.) Tier I examples: EGFR exon 14 18bp inframe del, shows chart #AMP2017
1:13pm November 18th 2017 via Hootsuite
Li: Tier II evidence is var's of potential clin significance. Level C/D. #AMP2017
1:11pm November 18th 2017 via Hootsuite
Li: Evidence-based char: Tier I vars have strong clinical significance, includes Level A and Level B evidence. #AMP2017
1:10pm November 18th 2017 via Hootsuite
Li: Dx/Prog for Lvl D: TP53 common muts, deletion of CDKN2A also. #AMP2017
1:09pm November 18th 2017 via Hootsuite
Li: Lvl D: Rx plausible preclin data derived from cell lines (in vitro) and animal models. Early Ph1 for safety. #AMP2017
1:08pm November 18th 2017 via Hootsuite
Li: Lvl C MDS-RS + SF3B1 mut good prognosis. #AMP2017
1:07pm November 18th 2017 via Hootsuite
Li: Lvl C Rx: Ph-like ALL: P2RY8-CRLF2 activates JAK-STAT, clin trial using JAKi. Lvl C Dx: spliceosome mutations #AMP2017
Li: Pilocytic Astrocytoma - KIAA1549-BRAF -> good prognosis, level B evidence for prongnosis #AMP2017
1:05pm November 18th 2017 via Hootsuite
Li: Lvl B Dx: Cutaneous mastocytosis, others types ruled out. KIT D816V found in bone marrow of ~100% CM pts. #AMP2017
1:04pm November 18th 2017 via Hootsuite
Li: Level B vars: for Rx, very strong evidence, not FDA-approved. Hairy Cell Leuk: BRAF V600E ~100% response to vemurafenib #AMP2017
1:03pm November 18th 2017 via Hootsuite
Li: Leval A Dx: prof guidelines. Level A prognosis: also prof guidelines. In AML, FLT3-ITD -> poor prognosis #AMP2017
1:01pm November 18th 2017 via Hootsuite
Li: Level A Rx: FDA-approved biomarker for spec Rx; or predict response. Ex ALK mut predicts resistance #AMP2017
12:59pm November 18th 2017 via Hootsuite
Li: Grouped evidence to 4 levels: A-D, clinical and/or expt'l evidence. Therapeutics, diagnosis, prognosis. #AMP2017
12:58pm November 18th 2017 via Hootsuite
Li: Biomarker can alter fn of gene, can serve to include to trials, influence prognosis, est Dx, may warrant surveillance #AMP2017
12:57pm November 18th 2017 via Hootsuite
Li: Def'n of biomarkers: all vars are biomarkers, but not the other way around. Pred sens, resist. or toxicity to spec Rx #AMP2017
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
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
