KR:Chromosomal instability is a hallmark of HGSC - CNA analysis shows strong cis-effects between RNA & protein #AACR15
11:08am April 22nd 2015 via Hootsuite
KR: The 5: differentiated, immunoreactive, mesenchymal, proliferative, unknown. New 'innate' and 'stromal' emerge from re-analysis #AACR15
11:07am April 22nd 2015 via Hootsuite
KR: 5 proteomic subtypes: did not map well to 5 mRNA subtypes from initial #TCGA analysis. #AACR15
11:05am April 22nd 2015 via Hootsuite
KR: Poorly correlating: ribosomes, mRNA splicing, ox-phosphorylation. Biological regulation of RNA -> protein. 'this is real' #AACR15
11:04am April 22nd 2015 via Hootsuite
KR: No normal tissues; but could segregate on HRD or overall survival. mRNA to protein: across 3 centers, 3 sites: 2/3rd correlation #AACR15
11:03am April 22nd 2015 via Hootsuite
KR: Defined protocol collection (60m limitation on warm ischemia); deep sequencing (CNV, methylation, transcription, RPPA, miRNA) #AACR15
11:02am April 22nd 2015 via Hootsuite
KR: Ovarian ca: high-grade serous (HGSC) severely lethal; a pathway approach needed. #AACR15
11:01am April 22nd 2015 via Hootsuite
Karin Rodland (Pac NW Nat Lab WA) “Proteogenomic and phosphoproteomic analysis of ovarian cancer: analysis of TCGA tumor samples” KR #AACR15
10:59am April 22nd 2015 via Hootsuite
PM:Q:Potential kinases to target? A:Some found on basal-like, but stratification may not be possible from their dataset. #AACR15
10:58am April 22nd 2015 via Hootsuite
PM: Found PI3K and TP53 signaling events observed in mutant tumors can be validated. #AACR15
10:50am April 22nd 2015 via Hootsuite
.@TCGAupdates Do you know if that chart has been published already?
10:49am April 22nd 2015 via Hootsuite in reply to TCGAupdates
PM: PIK3CA and TP53 commonly mutated in br ca: looked at isogenic cellines to compare spec phosphorylation events #AACR15
10:48am April 22nd 2015 via Hootsuite
PM: Knock-down SKP1+CETN3 increases EFFR, YES1 and DAPK3 expression. #AACR15
10:46am April 22nd 2015 via Hootsuite
PM: Leverage LINCS http://t.co/BqOERxk6qf an extension of Broad's Connectivity Map. SKP1 + CETN3 new cand. causal genes 5q CNA #AACR15
10:45am April 22nd 2015 via Hootsuite
PM: CNA pos correlated to both mRNA and protein exp; 46% CNAxRNA; 11% CNAxProtein; 5.2% CNAxPhosphorylation #AACR15
10:43am April 22nd 2015 via Hootsuite
PM: Busy chart across 4 types of br ca, x 6 genes, and 5 types of data ea (Mut, CNV, RNAseq, MS Proteome, MS pS162, RPPA protein) #AACR15
10:39am April 22nd 2015 via Hootsuite
PM: Major br ca genes can be accurately quantified at protein/phosph level 'thanks to advances in MS technology' @servingscience #AACR15
10:37am April 22nd 2015 via Hootsuite
RT @TCGAupdates: PM goes over details from #TCGA breast cancer paper http://t.co/6HTwPylGhW #AACR15
10:36am April 22nd 2015 via Twitter Web Client
RT @TCGAupdates: PM: Personalized proteome analysis pipeline for deep proteome phosphoproteome data sets by QUILTS http://t.co/FFT8dgMSQw #…
PM: 2/3 of all proteins correlate well w/RNA; but particular pathways (E3 ligases, proteases) do not correlate well. #AACR15
10:36am April 22nd 2015 via Hootsuite
PM: Subset of genetic alterations obs at protein lvl 0.2%-3.8% of frameshift, alt splice & single aa var's observable via proteomics #AA
10:34am April 22nd 2015 via Hootsuite
PM: 105 tumors and MS/MS data, along w/WES/RNA-Seq; 11.3K proteins, 63.8K phosphorylation sites #AACR15
10:33am April 22nd 2015 via Hootsuite
PM: #TCGA generated 30,626 somatic mut's across 507 tumors; but which br ca subtypes represented at the protein level? #AACR15
10:32am April 22nd 2015 via Hootsuite
Phillipp Mertins (Broad Inst MIT MA) “Proteogenomic and phosphoproteomic analysis of breast cancer” PM #AACR15 CPTAC Br Ca Analysis Grp
10:30am April 22nd 2015 via Hootsuite
RT @TCGAupdates: DL: Top take home - Proteome is an integrator of multiple genomic characteristics; allows knowledge integration #AACR15
10:29am April 22nd 2015 via Hootsuite
RT @TCGAupdates: Daniel Liebler presenting “Proteogenomic analysis of human colon and rectal cancer” #AACR15 #TCGA @VUMChealth
10:28am April 22nd 2015 via Hootsuite
RT @TCGAupdates: DL: Our first project was the #TCGA colorectal cancer paper http://t.co/CLpDNPh7vO #AACR15
RT @TCGAupdates: DL is reviewing the solid data generated from #TCGA CRC project #AACR15
10:27am April 22nd 2015 via Hootsuite
RT @TCGAupdates: DL: mRNA does not reliably predict protein abundance across tumor collection; differential based on fn'l categories #AACR15
SP:Q:Tumor-only seq? A: @hail_CSER has spec recommendations for tumor-only seq in upcoming paper; have to anticipate conversations #AACR15
8:05am April 22nd 2015 via Hootsuite
SP:Q:Multiple, small centers? A:A small % will have findings, spec pathway for that group, perh tele-medicine, videos, need support #AACR15
8:02am April 22nd 2015 via Hootsuite
SP:Q:Why different consents for parents/child? A:Part of IRB requirement in US; parents also research subjects #AACR15
7:59am April 22nd 2015 via Hootsuite
SP:Q:Evidence has changed after reporting? A:Re-analysis, re-eval for publication. They will put out addendum. #AACR15
7:58am April 22nd 2015 via Hootsuite
SP: In acknowledgements, BASIC3 BCM Advancing Sequencing Into Childhood Cancer Care #AACR15
7:56am April 22nd 2015 via Hootsuite
RT @iontorrent: #AACR15 | cfDNA & CTC by the New LiquidBiopsy Platform: Vidya is giving us a first look http://t.co/ObciUzrilA
7:55am April 22nd 2015 via Hootsuite
SP: For the lab - who will do followup testing (confirmation)? Who are the genetics specialists available? #AACR15
7:54am April 22nd 2015 via Hootsuite
SP: Summarizing, plan for which family members will be involved. For adults - 'who gets results if you cannot come back' #AACR15
7:53am April 22nd 2015 via Hootsuite
SP: One cardiologist: "a genotype w/o phenotype" "we have little experience w/this new type of genetic medicine" "re-eval in 5y" #AACR15
7:50am April 22nd 2015 via Hootsuite
SP: (Discusses individ ped cases: Li Fraumeni, MSH2 in GBM, multiple germline findings) #AACR15
7:47am April 22nd 2015 via Hootsuite
SP: Delays in result disclosure: freq of return visits, other treatment institutions, declining health. #AACR15
7:44am April 22nd 2015 via Hootsuite
SP:A hard copy of WES report given; long history in genetic counseling. "Looked at 5 years later". 'there is still value in paper' #AACR15
7:43am April 22nd 2015 via Hootsuite
SP:Parents of a child enrolled: sometimes parents won't agree (and veto'ed). Sometimes other parent will say 'I was told I have to' #AACR15
7:38am April 22nd 2015 via Hootsuite
SP: Many common questions: kinds of results, impact on family, threats to privacy: 'You may need to guide pt' about these Q's #AACR15
7:36am April 22nd 2015 via Hootsuite
SP: Spanish-speaking families (they have 15%); everything translated; trained interpreters on-hand; no diffs. in willingness #AACR15
7:34am April 22nd 2015 via Hootsuite
SP: Also found high willingness 90% to deposit data into NIH databases. #AACR15
7:32am April 22nd 2015 via Hootsuite
SP: For cancer, results for consent was different. 83% agreed; 10% overwhelmed w/their own care. http://t.co/vmqZLZNuQ0 #AACR15
7:31am April 22nd 2015 via Hootsuite
SP: Front-end: consent and disclosure.'We're quite deliberative'; introduction to idea by oncologist, study team coordinator #AACR15
7:30am April 22nd 2015 via Hootsuite
SP: ACMG56 for cardiovascular - think carefully who will look at it (expertise needed in reporting out), ~30 cancer suscept genes #AACR15
7:26am April 22nd 2015 via Hootsuite
SP: Current ver: recommends to allow subjects to op-out (but not the lab); ACMG56 gene list has ~20 cardiovas genes 'not easy' #AACR15
7:25am April 22nd 2015 via Hootsuite
SP: No other guideline; they voiced concerns about cancer '14 ref http://t.co/FBvqycWRsN Req for reporting 'pathogenic muts only!' #AACR15
7:24am April 22nd 2015 via Hootsuite
