Ran Blekhman (U Minn) Genomic landscape of colorectal tumors shapes the microbiome of the tumor microenvironment #ASHG15
3:31pm October 9th 2015 via Hootsuite
Cohen: Q:Genes that have lost function? A:Some TS genes, add'l work ongoing #ASHG15
3:30pm October 9th 2015 via Hootsuite
Cohen: Q:Has JQ1 been used for other cancers? A:Currently in PI trials for variety of cancers, incl CRC and heme #ASHG15
3:29pm October 9th 2015 via Hootsuite
Cohen: Q:Distance from VELs to transcipt start site? A: Have a predictive tool ("Prestige") ~100kb #ASHG15
3:28pm October 9th 2015 via Hootsuite
Cohen: 3D fig from this '07 ref http://t.co/lDF4kzBzFK and model of APC then KRAS then TP53 for CRC, overlay epigenetic disreg #ASHG15
3:27pm October 9th 2015 via Hootsuite
Cohen: GWAS ID' 75 CRC risk loci; 3/4 overlap enhancers; of these 1/2 cover recurrent gained VELs #ASHG15
3:23pm October 9th 2015 via Hootsuite
Cohen: Gained VELs are constituents of super-enhancers. H3K27ac signal. #ASHG15
Cohen: Have found recurrent VELs; gained ones 'target hallmarks of colon cancer' MYC, AXIN2, BMP4, TCF7 etc #ASHG15
3:22pm October 9th 2015 via Hootsuite
Cohen: VELs though do not correlate with tumor stage. Looking at MYC locus, Tumor/Normal comparison clear #ASHG15
3:20pm October 9th 2015 via Hootsuite
Cohen: Have signatures in H3K27ac, H3K4me1 and DHS. ID'd gain and loss of VELs (variant enhancer loci) #ASHG15
3:19pm October 9th 2015 via Hootsuite
Cohen:They look at aberrant histone methylation as a signature in colon cancer. 2012 paper http://t.co/0hRLT2J1Dl #ASHG15
3:17pm October 9th 2015 via Hootsuite
Cohen: Recurrent acquisition of super enhancer function drives druggable oncogenic expression programs in colorectal cancer #ASHG15
3:16pm October 9th 2015 via Hootsuite
Faucz: Found 50 TNS1 mutations in WT GIST pts w/o SDH mutations. Problem - unknown the connection between TNS1 to the mitochondria #ASHG15
2:54pm October 9th 2015 via Hootsuite
Faucz: TSN1 is a homologue of PTEN. Able to look at SDH enz activity in Drosophila, and mt defects in Blistery flies #ASHG15
2:53pm October 9th 2015 via Hootsuite
Faucz: TNS1 found by WES, model is melanogaster Blistery Tns1 KO. Looking for SDH expression #ASHG15
2:50pm October 9th 2015 via Hootsuite
Faucz: WT GIST is 10-15% and 95% of ped GIST, without KIT or PDGFRA. May have germline in SDH in 15% #ASHG15 ref: http://t.co/zX4Y1IyOJy
2:47pm October 9th 2015 via Hootsuite
Fabio Faucz (NIH NICHD) TNS1 mutations and GIST and defective mitochondria in the blistery (Tns1 KO) D. melanogaster #ASHG15
2:46pm October 9th 2015 via Hootsuite
Neidich: Q:Details on seq depth? A: 'Very deep' Even for their germline, they go several thousand #ASHG15
8:36am October 9th 2015 via Hootsuite
Neidich:QSens and spec? A:For borderline, re-sampled, and redrawn. #ASHG15
8:35am October 9th 2015 via Hootsuite
Neidich:Q:Enrichment method? A:Enrichment then NGS; assay captures mutation and removes WT; they know how much WT in 5mL plasma #ASHG15
Neidich: A2:Bianchi et al numbers for cancer - were a young female population. A bit of a caveat on the relative numbers #ASHG15
8:34am October 9th 2015 via Hootsuite
Neidich: Q:Does 4/100 sound too high? ALin JK 2014 had 4/47 w/low signals #ASHG15
8:31am October 9th 2015 via Hootsuite
Neidich: If <50 at known risk: (BRCA carriers, HNPCC or FAP families, long-time smokers, or strong family history) Healthy1K #ASHG15
8:27am October 9th 2015 via Hootsuite
Neidich: Report includes relevant literature summary. For Detect - only for high-risk individuals. Now onto Healthy 1000 (>50yo) #ASHG15
8:26am October 9th 2015 via Hootsuite
Neidich: As a screen, it won't be perfect. But it may indicate a previously undetected cancer. Not diagnostic, thus follow-up needed #ASHG15
8:23am October 9th 2015 via Hootsuite
Neidich: Borderline are 'two copies'. Detection rates will vary; only 96 hotspot mutations, dep on type, stage, rate of growth #ASHG15
8:22am October 9th 2015 via Hootsuite
Neidich: Their positive: undergoing add'l screening and whole-body scan. All 4 potential positives are >50yo #ASHG15
8:21am October 9th 2015 via Hootsuite
Neidich: Have IRB approved study, normal-risk. 'Healthy 100', unpubl prelim data. Of the 102, 1 positive, 2 mut's. 3 borderline #ASHG15
8:20am October 9th 2015 via Hootsuite
Neidich: Busy slide with 7 papers, early asymptomatic screens Gormally 2006 Cancer Res, includes Bianchi 2015 JAMA on NIPT #ASHG15
8:19am October 9th 2015 via Hootsuite
Neidich: Ovarian, 60% diagnosed after metastases, 5y is only 28.3%. All SEER study data.Shows figure from http://t.co/SyDnmaXcO0 #ASHG15
8:17am October 9th 2015 via Hootsuite
Neidich: Localized Lu ca - 16% of diag, 54.8% 5y survival. Pancreatic - 53% distant at diagnosis, 5y survival only 2.4% #ASHG15
8:15am October 9th 2015 via Hootsuite
Neidich: For CRC w/distant disease: 5y survival is only 13%. 20% diagnosed are in this group. Lu ca - 52% distant, with 4.2% 5y surv #ASHG15
8:14am October 9th 2015 via Hootsuite
Neidich: Br ca:61% localized, 98.5% survival at 5y. Sharp 5y survival reduction when metastasizes #ASHG15
8:12am October 9th 2015 via Hootsuite
Neidich: Early detection, prevent complications, natural history needs to be understood. Safe, effective trtmt shd be available #ASHG15
8:10am October 9th 2015 via Hootsuite
Julie Neidich (Pathway): Screening discussion - quotes Schiffman '15 ASCO education book. Screen for ave or higher prob of cancer #ASHG15
8:09am October 9th 2015 via Hootsuite
Braunstein: Collection stable at 7d at RT. Next: Julie Neidich, their Laboratory Director #ASHG15
8:08am October 9th 2015 via Hootsuite
Braunstein: Also clinical trial monitoring to make available if applicable. Must be done by Rx, need special collection #ASHG15
8:06am October 9th 2015 via Hootsuite
Braunstein: Reporting tailored to patient's clinical history; relevant literature; tailored comments from their Med Dir. #ASHG15
Braunstein: May be adjunct method when biopsies are difficult, or CUP, or limiting sample. For some may be prognostic #ASHG15
8:03am October 9th 2015 via Hootsuite
Braunstein: Other types where genes may overlap - prostate, gastric etc. Can monitor residual disease, progression, evolution #ASHG15
Braunstein: Shows data chart from COSMIC, for Lung, Br, Ov, Mel, CR, with genes and frequencies #ASHG15
8:01am October 9th 2015 via Hootsuite
Braunstein:Recovery, cost, hospital stay, all obviated by liquid biopsy. They have a 96-mutation panel, 9 driver genes. FOXL2, EGFR #ASHG15
8:00am October 9th 2015 via Hootsuite
Glenn Braunstein (Pathway): CancerIntercept in two flavors, one for monitoring, another for detection. Contrasts invasive vs. liquid #ASHG15
7:58am October 9th 2015 via Hootsuite
Showing this video http://t.co/eqajNJ1hf6 - detection before symptoms, monitor w/o biopsy. A 'cancer stethescope' #ASHG15
7:55am October 9th 2015 via Hootsuite
This AM checking out the Pathway Genomics talk https://t.co/fLpVKwXtmj they have 2 cancer tests, based on ctDNA #ASHG15
7:52am October 9th 2015 via Hootsuite
Creator of 5-hour Energy Wants to Power the World's Homes—With Bikes http://t.co/RQRmvoxXXs
6:20am October 9th 2015 via Hootsuite
Scharer: Showed CTCF peaks comparing fresh with frozen peaks, and data are comparable.#ASHG15
7:40pm October 8th 2015 via Hootsuite
Scharer: PBMC in their biobanked samples; either frozen after 1w or fresh; live cells compared well. ATAC-Seq correlation r=0.94 #ASHG15
7:37pm October 8th 2015 via Hootsuite
Scharer: Next: ATAC-Seq '13 Nature Methods http://t.co/XOa8b8j4R9 Transposase-tagging open chromatin. Can see nucleosomal peaks #ASHG15
7:35pm October 8th 2015 via Hootsuite
Scharer: Showed (major) loss of unique reads in 10pg samples. Rocket plot (log/log plot of read abundance) spreads wide at 10ng #ASHG15
7:32pm October 8th 2015 via Hootsuite
