Asaf Rotem (Dana Farber Cancer Inst) Immunotherapy resistant sates revealed by single-cell characterization of melanoma tumors #AGBT18
8:52pm February 13th 2018 via Hootsuite
Q: Would it scale? Piskorz: Concentrating on FFPE for clinical samples; idea to cover entire TP53 coding region. #AGBT18
8:50pm February 13th 2018 via Hootsuite
Piskorz: Now working on more samples; 'exciting future for developing an assay for test sens to Pt Rx; PARPi, Wee inh Rx' #AGBT18
8:48pm February 13th 2018 via Hootsuite
Piskorz: H&S vs nCounter, R2=0.96 across 2 HGSOC samples. 4 samples cross-platform: MYC CNA very close (2.7x vs 3x) TP53 3.1x vs 3x #AGB
8:46pm February 13th 2018 via Hootsuite
Piskorz: For CNAs: MYC, CCNE1 and normal TP53 for HL60 line; for HGSOC, shows two examples of NGS data where CNA is stable (diploid) #AGBT18
8:44pm February 13th 2018 via Hootsuite
Piskorz: Shows how the sequencing is done; 4 mutations, H&S error 0.11% to 0.59%; MiSeq, .49% to 0.95%. #AGBT18
8:42pm February 13th 2018 via Hootsuite
Piskorz: Shows Hyb&Seq workflow; 35 min protocol, 5min hands-on. No library prep. Showed automated prototype, and imaging. #AGBT18
8:38pm February 13th 2018 via Hootsuite
Piskorz: Mutation against anti-sense strangs for coding regions in TP53; for CNA, antisense in non-coding; GEx to splicing site #AGBT18
8:37pm February 13th 2018 via Hootsuite
Piskorz: Idea - combine diagnostic, prognostic and predictive assays. TP53 mutations; CNA for CCNE1, MYC, TP53; and GEx six genes #AGBT18
Piskorz: Dx: TP53 can help; high-grade vs low-grade: metrics '16 ref https://t.co/77O9h7cKbI #AGBT18
8:35pm February 13th 2018 via Hootsuite
Piskorz: 99% have TP53, excess CNA. Many could be drugged - MET ampl. Survival has not changed in 20y. #AGBT18
8:34pm February 13th 2018 via Hootsuite
Piskorz: 4 types of ovariant ca - mucinous, endometroic, clear cell, high-grade serous. Main problem: 70% relapse in 12 mo #AGBT18
8:33pm February 13th 2018 via Hootsuite
Piskorz: SOAC=high grade serous ovarian cancer #AGBT18
8:32pm February 13th 2018 via Hootsuite
Anna Piskorz (Cancer Res UK) Simultaneous mutation detection, copy number, and digital gene expression profing SOAC FFPE w/Hyb & Seq #AG
8:31pm February 13th 2018 via Hootsuite
Schatz: Assembling a 'perfect' personalized diploid genome, as a simple example. Shows ex of improved RNA-seq mapping. #AGBT18
8:26pm February 13th 2018 via Hootsuite
Schatz: In human disease, SVs publ '17 by Ashley https://t.co/ExdQUeSd7U #AGBT18
8:24pm February 13th 2018 via Hootsuite
Schatz: NGMLR - convex gap penalty. Looking at xloc's in IGV but missing pairs. Same w/PACB or ONT: a short insertion #AGBT18
8:23pm February 13th 2018 via Hootsuite
Schatz: 10X + Hi-C: 145Mb N50 phase blocks. For SVs: long-read data but noisy. bioRxiv: https://t.co/nygLSa8tys #AGBT18
8:21pm February 13th 2018 via Hootsuite
Schatz: Long reads to phase, NA12878 - 1kb blocks by short reads; ONT has 500kb phase blocks; linked reads to 10Mbp Hi-C 100Mb #AGBT18
8:20pm February 13th 2018 via Hootsuite
Schatz: #AGBT18 Dev CrossStitch on Github https://t.co/mrKD9vuvU0 SNPs + Indels, and then SVs. Phasing with blocks unphased hard to solve
8:19pm February 13th 2018 via Hootsuite
Schatz: Phasing need 10X and/or HiC, or trios. Data requirements similar to de novo but less demanding. #AGBT18
8:16pm February 13th 2018 via Hootsuite
Schatz: Need sample-specific data (SNPs and Indels, SVs, Phasing); need multiple datatypes. SNPs via ILMN; SVs via PB or ONT... #AGBT18
Schatz: Propose: Reference Guided Assembly. First was '04 ref https://t.co/TI6gN8AYby Need ref genome to be sufficiently similar #AGBT18
8:14pm February 13th 2018 via Hootsuite
Schatz: Could we de novo assemble everyone? Is still slow, demanding at the bench, and unpredictable. #AGBT18
8:13pm February 13th 2018 via Hootsuite
Schatz: The reference: "doesn't represent *any* human"; the reference can limit analysis how genome variatns impact regulation #AGBT18
8:12pm February 13th 2018 via Hootsuite
Micheal Schatz (Hopkins) In pursuit of perfect whole genomes (alt "Whole genome haplotype resolution of small and structural var") #AGBT18
8:11pm February 13th 2018 via Hootsuite
Navin: Data consistent of punctuated copy number evolution; early CNA and mutational events may be preprogrammed in the duct. #AGBT18
8:06pm February 13th 2018 via Hootsuite
Navin: Shows clonal evolution of subclones, and localization in relation to the ducts. Of 12 pts: shows distribution of clones (1-5) #AGBT18
7:59pm February 13th 2018 via Hootsuite
Navin: Looked for synchronous DCIS-IDC regions in same tissues. Shows single-cell CN aberrations. Collapsed data - MYC, ALK, FOXA1 #AGBT18
7:56pm February 13th 2018 via Hootsuite
Navin: Shows a movie of H&E stain, highlighting, 1um laser cutting. 96 cells in 1-2h. Shows CN profiles; sometimes UV laser damages #AGB
7:54pm February 13th 2018 via Hootsuite
Navin: Call it topographic sc Sequencing TSCS - laser-catapulting, onto a 96-well stage, using WGS calling DOP-PCR. Then map back #AGBT18
7:53pm February 13th 2018 via Hootsuite
Navin: Reviews stages and classification. SCS technologies require suspensions, so cannot preserve spatial info. Can't image either #AGBT18
7:52pm February 13th 2018 via Hootsuite
Navin: DCIS is ductal carcinoma in-situ: most common form of early stage br ca. 10% of low-grade, 30% high-grade progress #AGBT18
7:50pm February 13th 2018 via Hootsuite
Nicholas Navin (MD Anderson CC) Multiclonal evolution during invasion in DCIS breast cancer #AGBT18
7:49pm February 13th 2018 via Hootsuite
Mungall: Lokking at RFTN1 somatic variants and assoc'n with increased mRNA; showed signif difference w/mutations causing increase #AGBT18
7:45pm February 13th 2018 via Hootsuite
Mungall: Shows their lymphoma pts, and shows RFTN1::PVT1 in patient data in Hodgkins #AGBT18
7:41pm February 13th 2018 via Hootsuite
Mungall: 10y ago at AGBT, did 2.9M fingerprints from 24 follicular lymphoma pts. '07 ref https://t.co/Cjlewb5N70 #AGBT18
7:38pm February 13th 2018 via Hootsuite
Mungall: 3mos, dramatic and sustained response. Mining data: a novel Raftlin (RFTN1) rearrangement. Forming B-cell recept signalling #AGBT18
7:36pm February 13th 2018 via Hootsuite
Mungall: There was a local inversion at 3' ISH probe site. ALK exp - very high (99th %'ile), also ROS1 (94%'ile). TKI crizotinib Rx #AGBT18
7:35pm February 13th 2018 via Hootsuite
Mungall: DELLY, deStruct, Manta alignment. All part of Peronalized OncoGenomics (POG) project. Cryptic EML4-ALK only 3% by FISH #AGBT18
7:34pm February 13th 2018 via Hootsuite
Mungall: 80x WGS of tumor, 40x WGS of normal, 100M RNA-seq read-pairs. Does de novo assembly using Trans-ABySS, Alignment #AGBT18
7:32pm February 13th 2018 via Hootsuite
Andrew Munger (BC Cancer CAN) Recurrent raftlin gene fusions in cancer #AGBT18
7:30pm February 13th 2018 via Hootsuite
Schnell-Levin: Points to poster 1115 for more info at #AGBT18
5:07pm February 13th 2018 via Hootsuite
Schnell-Levin: Shows a 5% spike-in, and data with 7% with a q-arm duplication. Cell lines are heterogeneous. Recovered 5% #AGBT18
5:03pm February 13th 2018 via Hootsuite
Schnell-Levin: Thus one cell to one gel bead co-encapsulated via microfluidics. #AGBT18
5:01pm February 13th 2018 via Hootsuite
Schnell-Levin: Cell beads trap single-cells. Then you can digest protein, alkalai denature. Then form CBGBs (cell beads gel beads) #AGBT18
5:00pm February 13th 2018 via Hootsuite
Schnell-Levin: 3rd annc: scCNVs. Shows video explaining process. Needs cell-beads/gel-beads. Multiple steps rather than all at-once #AGBT18
4:59pm February 13th 2018 via Hootsuite
Schnell-Levin: From1000 PBMC's: able to separate monocytes, dendritic, B, CD4 T, CD8 T... #AGBT18
4:56pm February 13th 2018 via Hootsuite
Schnell-Levin: 2nd annc: scATAC-seq Scalable from 100 to 10K cells. Captures open chromatin; insert-lengths- nucleosomes periodicity #AGBT18
4:55pm February 13th 2018 via Hootsuite
Schnell-Levin: Perturb-Seq https://t.co/wGahvKcYyp for CRISPR perturbations. Will offer both Ab and CRISPR products #AGBT18
4:50pm February 13th 2018 via Hootsuite
