Seshagiri: PTPRK-RSPO3 fusion, rearrangement results in functional protein. #AGBT14
8:57pm February 13th 2014 via Hootsuite
Seshagiri:WES, WGS; RNA; SNP arrays from 72 tumor/normal pairs. Looking at RNA fusions, seeing a number of fusions in solid tumors #AGBT14
8:55pm February 13th 2014 via Hootsuite
Seshagiri: Colon cancer, 3rd most freq., 1.2M WW, 140K in US annually. 608K WW, 51k deaths in US annually. Drugs to treat few. #AGBT14
8:53pm February 13th 2014 via Hootsuite
Up next: Somasekar Seshagiri (Genentech) Exome Sequencing Identified Oncogenic ERBB3 Mutations #AGBT14
8:52pm February 13th 2014 via Hootsuite
Lipson: Q: (Plon) Any reporting of germline? A:If they suspect it they report it. #AGBT14
8:51pm February 13th 2014 via Hootsuite
Lipson: Q:Are fusions picked up in the routine pipeline? A:Defined capture of introns. Intron 19 of ALK will pull down other exon #AGBT14
Lipson: 2nd individual, KIF5B-RET fusion identified, completely novel. Looked for recurrence: of 600, 1% Cauc, 6.3% Asians #AGBT14
8:47pm February 13th 2014 via Hootsuite
Lipson: A complex ALK rearr. - 2012 Peled et al paper here http://t.co/A8yz0wnX7k #AGBT14
8:45pm February 13th 2014 via Hootsuite
Lipson: Gene fusions seen in 10% of NSCLC; a whole collection of them #AGBT14
8:44pm February 13th 2014 via Hootsuite
Lipson: 851/893 samples (95%) successfully seq.; 1,313 unique alterations, 181 genes; actionable targeted in >60 cases #AGBT14
Lipson: Base subst, indels, CNA, fusions with known cell line pools; hundreds of FFPE samples to compare to classical assays #AGBT14
8:42pm February 13th 2014 via Hootsuite
Lipson: Reporting their performance metrics from Nature Biotech paper Nov 2013 http://t.co/FxLKXl96qx #AGBT14
8:41pm February 13th 2014 via Hootsuite
Lipson: Turnaround time is 14 d. >99.5% of exons at >100x; 236 known relevant cancer genes, all coding regions & select introns #A
8:39pm February 13th 2014 via Hootsuite
Lipson: Data from their Nature Biotech paper - 46% had mut freq <20%. Their test has specialized sample prep, hybrid capture, HiSeq #AGBT
8:37pm February 13th 2014 via Hootsuite
Lipson: Many NSCLC are fine needle aspirates, fixed small needle biopsies, and low tumor purity. Little control over amt of tumor #AGBT14
8:36pm February 13th 2014 via Hootsuite
Lipson: Listed many relevant genes for NSCLC - yet just a handful of gene-specific tests. And all the different types - not only SNV #AGBT14
8:35pm February 13th 2014 via Hootsuite
Lipson: Foundation Med. accepting samples now for 3y; lung ca aggressive; 27% of all cancer deaths in US annually #AGBT14
8:33pm February 13th 2014 via Hootsuite
Up next: Doron Lipson (Foundation Medicine): Clinical NGS of Advanced NSCLC Reveals a High Frequency of Genomic Alterations #AGBT14
8:31pm February 13th 2014 via Hootsuite
Hadfield: Using Broad's Connectivity Map, found a candidate compound. Using now never-smoker cell lines http://t.co/i7Xzg1LYAT #AGBT14
8:26pm February 13th 2014 via Hootsuite
Hadfield: Interesting network plot. Organized around ncRNAs with particular function. "Science is just organized curiosity." #AGBT14
8:24pm February 13th 2014 via Hootsuite
Hadfield: Found miR-424 (poster, Teresa Wang #21?) using miR ConnX tool. Then built a ncRNA network via corr. betw ncRNAs and mRNA #AGBT14
8:23pm February 13th 2014 via Hootsuite
Kusko: Detected 120 genes that fit; 50% ncRNA; looked at miRNAs to regulate the mRNAs. Mirconnx tool NAR http://t.co/Zxjbl216pg #AGBT14
8:20pm February 13th 2014 via Hootsuite
Kusko: Looking for oncogenes up-regulated in only never smokers; or tumor supp. down-reg in only never smokers #AGBT14
8:18pm February 13th 2014 via Hootsuite
Kusko: Goal - ID therapeutic targets, and ID approved treatments to address these targets. 22 samples, RNA-Seq (whole transcriptome) #AGBT14
8:17pm February 13th 2014 via Hootsuite
Kusko: Ever smokers and Never smokers: lung adenocarcinomas common to both. #AGBT14
8:15pm February 13th 2014 via Hootsuite
Up next: Rebecca Kusko (Boston Univ), SEQing the shared and distinct transcriptional events underlying lung adenocarcinoma... #AGBT14
Hadfield: Q:Cancer types and shed ctDNA? A:Mechanism not completely understood... #AGBT14
8:12pm February 13th 2014 via Hootsuite
Hadfield: Q: Regulatory concerns? A: This is research, everyone struggles with these questions. Not insurmountable challenges #AGBT14
Hadfield: Q: How soon to implement widely? A: "Right around the corner, not sure how far the corner is though" #AGBT14
8:10pm February 13th 2014 via Hootsuite
Hadfield: Detection of a TP53 mut in the ctDNA of a normally healthy person is not a good thing #AGBT14
8:09pm February 13th 2014 via Hootsuite
Hadfield: Concl: ctDNA 'liquid biopsy' allows unbiased detection and monitoring. Emph. of not 'which tool' but application #AGBT14
8:06pm February 13th 2014 via Hootsuite
Hadfield: They haven't pushed it down further, "looks promising" #AGBT14
8:02pm February 13th 2014 via Hootsuite
Hadfield: And then TruSeq Exome, couldn't have done it without Rubicon tech. Hairpin adapter, cleavable, extend, cleave, amplify #AGBT14
8:01pm February 13th 2014 via Hootsuite
Hadfield: cdDNA is only 150bp, 1000's of copies/mL; normal DNA 'overload', only 2mL draws every 3w. Uses ThruPLEX-FD (Rubicon) #AGBT14
8:00pm February 13th 2014 via Hootsuite
Hadfield: Looking at Darwinian evolution, looking at branched evolution. Refers to 2013 Nature http://t.co/UBa3aW1ZeR #AGBT14
7:59pm February 13th 2014 via Hootsuite
Hadfield: Able to track individual genes over time. Looking at ctDNA correlate to survival Dawson NEJM 2013 http://t.co/W1L2xUrnH1 #AGBT14
7:57pm February 13th 2014 via Hootsuite
Hadfield: Able to monitor tumor dynamics during progress of treatment; see tumor DNA coming back. Measuring ctDNA in copies/mL #AGBT14
7:56pm February 13th 2014 via Hootsuite
Hadfield: Amplicon seq via FLDM access array, seeing TP53 in ovaran, PIK3CA and TP53 in bowel. A relapse of the same muts #AGBT14
7:55pm February 13th 2014 via Hootsuite
Hadfield: Circulating tumor DNA (ctDNA) - diagram with different methods of detection - BEAMing, real-time PCR, Access Array #AGBT14
7:53pm February 13th 2014 via Hootsuite
Up next on cancer track: James Hadfield (CRUK), Monitoring cancer genome evol. with circulating tumor DNA exome sequencing #AGBT14
7:52pm February 13th 2014 via Hootsuite
Kim: Conclude: P53 pathway alterations in drving high rate of subclonal muts in GBM #AGBT14
7:48pm February 13th 2014 via Hootsuite
I'm told by @illumina that there's a Tweetup at the Marriott "Lounge" 9:30pm after the sessions tonight. Hope to meet you there! #AGBT14
7:47pm February 13th 2014 via Hootsuite
Kim: Recurrent GBM tumors didn't have many shared mutations #AGBT2014
7:46pm February 13th 2014 via Hootsuite
I'm told by @illumina that there's a Tweetup at the Marriott "Lounge" 9:30pm after the sessions tonight. Hope to meet you there! #AGBT2014
7:44pm February 13th 2014 via Hootsuite
Kim: Looking at primary and recurrent GBM of 23 individuals, using PyClone tool described Nature 2012 http://t.co/cDRnbGcQOv #AGBT2014
7:43pm February 13th 2014 via Hootsuite
Kim: Mutation spectrum - CpG to T in clonal mutations; TP53 sig ass'd with fx of subclonal mutations #AGBT2014
7:39pm February 13th 2014 via Hootsuite
Kim: Over age groups - clonal muts increased but not among subclonal. 40y over decades to >70y #AGBT2014
7:38pm February 13th 2014 via Hootsuite
Kim: TCGA data on GBM, have 252 primary, 23 recurrent GBM (post-treated); classified somatic muts into clonal & subclonal #AGBT14
7:36pm February 13th 2014 via Hootsuite
Concurrent Cancer track Up next: Hoon Kim (UT MDA): Intratumoral hetergeneity of Glioblastoma (&) role for clonal evolution #AGBT14
7:35pm February 13th 2014 via Hootsuite
Good crowd at the Software Demo - here is Ion Reporter http://t.co/NWUf3puKhn #agbt14
5:44pm February 13th 2014 via Hootsuite
