Houghton: Tumor-infiltrating leukocytes from culture, side-by-side comparing flow vs. NanoString. CD8+ signal. P.02 or P=0.0015 #ASHG15
8:18am October 8th 2015 via Hootsuite
Houghton: 30 color flow is not practical to scale. Thus NanoString: 800K cells, easy to perform (even he did it), can expand panel #ASHG15
8:17am October 8th 2015 via Hootsuite
Houghton: Flow does accurate immune profiling; redundant immune supp factors always present, but vary. But - scale? sample amount? #ASHG15
8:16am October 8th 2015 via Hootsuite
Houghton: TCR-beta immune sequencing: Shows high clonality of CD8+. In adeno, reduced PDL1 in EGFR mutant AdenoCA #ASHG1510
8:14am October 8th 2015 via Hootsuite
Houghton: 75% of cells in tumor sample are immune cells (NSCLC). Shows somatic mutation profile from Alexandrov 2013 paper #ASHG15
8:12am October 8th 2015 via Hootsuite
Houghton: Reviews PDL1 and PD1 antibody therapy - why such low response in NSCLC? Explains flow immune profiling #ASHG15
8:09am October 8th 2015 via Hootsuite
Houghton: Points out NSCLC, 1/4 of pts, get OncoPlex assay at Fred Hutch; points out all actionable genes, and fusion detection #ASHG15
8:06am October 8th 2015 via Hootsuite
McGarry Houghton (Fred Hutch, WA) Profiling the Immune Response to Non-Small Cell Lung Cancer #ASHG15
8:04am October 8th 2015 via Hootsuite
Beecham: Has open-source R software for advanced analyses. #ASHG15
8:03am October 8th 2015 via Hootsuite
Beecham: Shows early immunotherapy clinical trial work (CITN network); Nov 15 Immunotherapy of Cancer mtg: http://t.co/cgGeXGm9VY #ASHG15
8:01am October 8th 2015 via Hootsuite
Beecham: Points out Gordon Mill's influence at MDA and on TCGA, and how quickly he recognized the capability of the platform. #ASHG15
8:00am October 8th 2015 via Hootsuite
Beecham: Ther '3D RNA:Protein Pan-cancer' product recently launched. 770 RNA, 30+ protein assays. Details: http://t.co/rJLbbNgPyf #ASHG15
7:59am October 8th 2015 via Hootsuite
Beecham: Measured BRAF, volcano plot of mRNA drivers +/- targeted melanoma Rx; and HLA-DRA and CD73 off-target effects #ASHG15
7:57am October 8th 2015 via Hootsuite
Beecham:Able to do SNV analysis - BRAF V600 from WT to V600E; showed data of WT, het and homozygous; both at DNA and mRNA levels #ASHG15
7:55am October 8th 2015 via Hootsuite
Beecham: Seeing 15 min, 2h, 24h response counts - and combined mRNA and protein data - impressive for ERK-P #ASHG15
7:54am October 8th 2015 via Hootsuite
Beecham: With protein, phosphorylation of EGF receptor. 15 minute respons, 24h reduced amount known. Internal signal? ERK-P #ASHG15
7:53am October 8th 2015 via Hootsuite
Beecham: Have a standard panel for pathway-based mRNA, key early protein and protein post-transl mod events. 'Pan-cancer' #ASHG15
7:52am October 8th 2015 via Hootsuite
Beecham: Where mRNA doesn't correlate to protein, mRNA to DNA. And sample input sampling - FISH, or MS or RNA-Seq req's #ASHG15
7:48am October 8th 2015 via Hootsuite
Beecham: Counts from 5k cells x 5k cells: r=0.98 across all three. Impressive - FISH, targeted RNA-Seq, MS: lost in translation prob #ASHG15
7:47am October 8th 2015 via Hootsuite
Beecham: Some samples were FNA for Rx monitoring, down to single-cell 88-plex. Now: 770 mRNAs, 15 proteins, 5 gene fusions simult. #ASHG15
7:46am October 8th 2015 via Hootsuite
Beecham: Has three different colors for each barcode type; represents DNA, RNA, protein. 2014 STM ref http://t.co/TkQq9E7sgf #ASHG15
7:44am October 8th 2015 via Hootsuite
Beecham: Thus direct detection of Ab - no secondary Ab labeling needed. Reminds us that nature has DNA, RNA, protein all present #ASHG15
7:41am October 8th 2015 via Hootsuite
Beecham: Tech enables direct measurement of nucl acid from cell, tissue or NA-labeled Ab, so protein molecules counted #ASHG15
7:39am October 8th 2015 via Hootsuite
Beecham: Intro to the technology - up to 800 analytes; single-molecule optical barcoding tech. Uses 50b target-spec probe, 50bp b/c ASHG15
7:37am October 8th 2015 via Hootsuite
Beecham: Unlock The Hidden Genome With 3D Biology- Simultaneous Measurement of DNA, RNA, & Protein. #ASHG15
7:35am October 8th 2015 via Hootsuite
Good morning #ASHG15 this AM @nanostring workshop Schedule http://t.co/iOxIHVgVGx First Joe Beecham (R&D lead, former CTO @LifeTechCorp
I think these @promega folks are great! Booth 611 Ask Eric for a cup of coffee! http://t.co/8TlXXxjk39
6:34pm October 7th 2015 via Hootsuite
Owen:Q:Extendable to other loci? A:May use for possible rearrangements in BRCA genes. Q:Time? A:Getting better, still takes time #ASHG15
4:24pm October 7th 2015 via Hootsuite
Owen: Of 189 cases, 72 (38%) clearly pathogenic; 55% clearly normal. Showed sample data from normal, potential FP via Southern #ASHG15
4:20pm October 7th 2015 via Hootsuite
Owen: Could determine relatedness between generation (mother/daughter) - very consistent #ASHG15
4:19pm October 7th 2015 via Hootsuite
Owen: Normal >12 repeats, abnormal <8. Cp Southern (contraction on the blot) vs 2-color combing; differentiate bands shown 4 alleles #
4:18pm October 7th 2015 via Hootsuite
Owen: Combing: High MW DNA, binds to silanized slide by exposed ends, and do a fiber-FISH. 2kb stretching / um. FSHD probes, 2 color #ASHG15
4:16pm October 7th 2015 via Hootsuite
Owen: D4Z4 repeats on Chr4 vs Chr10. A from B allele. 2012 ref: http://t.co/FuSL6ptHiY Gets convoluted quickly. #ASHG15
4:15pm October 7th 2015 via Hootsuite
Owen: FSHD 3rd most common muscular disorder; likely DUX4 gene that has double homeobox. TF that targets several genes. #ASHG15
4:14pm October 7th 2015 via Hootsuite
Renius Own (Quest Dx) DNA combing as a first-tier genetic testing for facioscapulohumeral dystrophy type 1: A cohort of 155 pts #ASHG15
4:12pm October 7th 2015 via Hootsuite
Sabatini:FPs concentrated in low coverage RPKM areas; prospectively, 426 clinical samples 3 TP, 8 FP (6 dup 2 del) 0 FN. #ASHG15
4:09pm October 7th 2015 via Hootsuite
Sabatini: Found 154bp duplicate in BRCA1 c.3363_3516dup154, missed in both NGS and MLPA, picked up by Sanger #ASHG15
4:07pm October 7th 2015 via Hootsuite
.@gsaldanha Hi Gabriela, would be happy to. Will come by in this evening's 4:30-7pm exhibit / poster session.
4:06pm October 7th 2015 via Hootsuite in reply to gsaldanha
Sabatini: Uses TruSight on NextSeq500; supplements with MLPA. Uses RPKM counting method for CNV. Overlapping tiles, focus on exons #ASHG15
4:05pm October 7th 2015 via Hootsuite
Peter Sabatini (North York Gen Hosp Toronto ONT) A method for detecting intragenic copy number changes of BRCA1 and BRCA2 using NGS #ASHG15
4:03pm October 7th 2015 via Hootsuite
Wu:Q:DNA quality differences? A:For LR-PCR, very sensitive to quality #ASHG15
Wu: Use LR-PCR and probe-capture (both), then MiSeq. Use of capture probes gets to struct var and introns. Dx rate: 75% #ASHG15
3:54pm October 7th 2015 via Hootsuite
Wu: Imptfor kidney donors, PGD, young individuals. Long-range PCR, Dx rate of 63-90%. NGS for reducing time, cost, etc. #ASHG15
3:53pm October 7th 2015 via Hootsuite
Wu: ADPKD is 1:400-1000; late on-set. 50% result in end-stage renal disease. PKD1/2 have 6 pseudogenes, 97% similarity #ASHG15
3:52pm October 7th 2015 via Hootsuite
Ping Chun Wu (Taiwan Univ) Next-generation sequencing-based genetic testing of autosomal dominant polycystic kidney disease #ASHG15
3:50pm October 7th 2015 via Hootsuite
Hyland:Q:How well with HLA targets? A:Not trying comprehensively, only 1 target present. #ASHG15
Hyland: Validation results on both PGM and new S5 system; >>97%, also nice Gentris data #ASHG15
3:49pm October 7th 2015 via Hootsuite
Hyland: Differently-sourced samples will behave differently. Within-chip normalization. Gaussian mixture model; can yield no-call #ASHG15
3:46pm October 7th 2015 via Hootsuite
Hyland: Explains why CYP2D6 important - effects from null to 1, 2 or 3 copies. Normalized - across all samples in 1 chip (run) #ASHG15
3:45pm October 7th 2015 via Hootsuite
Hyland: Now have Amplicon MapQV and strand-bias analysis optimization. Shows hard case of CYP2B6 / CYP2B7P1 #ASHG15
3:41pm October 7th 2015 via Hootsuite
