Iwin De Vlaminck (Cornell NY) "Diagnostic applications of cell-free DNA in solid organ and bone marrow transplantation" #NGDx15
9:02am August 20th 2015 via Hootsuite
Speicher: One of several Plasma-Seq papers 2014 http://t.co/3UY61vLQGr #NGDx15 Turnaround time is ~2d. Close collaborator with Klaus Pantel
9:01am August 20th 2015 via Hootsuite
Speicher: And yet no CNV observed. Work published 2014: http://t.co/trZOIpJubq #NGDx15
8:59am August 20th 2015 via Hootsuite
Speicher: Seq of 500 CTCs (singly or in pools) established a lineage between CTCs and lymph node cells. Non-responder, progressive .#NGDx15
8:58am August 20th 2015 via Hootsuite
Speicher: Looking now at CTCs, case with >100K CTCs from three different draws. (Mentioned yesterday.) DDR2, MLL3 high VAF #NGDx15
8:56am August 20th 2015 via Hootsuite
Speicher: Tyr Kinases 2009 GRAIL paper: http://t.co/FM5TJ0mO0n Loking at translocations. Showed example of prostate ca changing type NGDx15
8:54am August 20th 2015 via Hootsuite
Speicher: Prostate ca - much higher in ctDNA. Not reported in literature in pr ca - 'probably due to not looking at advanced cases' #NGDx15
8:51am August 20th 2015 via Hootsuite
Speicher: Cp to ctDNA (88 br ca smpls) very similar types of focal events. For4 prostate, large increase in 108 ctDNA vs 492 #TCGA #NGDx15
8:49am August 20th 2015 via Hootsuite
Speicher:Focal somatic CNVs in prostate, breast and other cancers. Looking at #TCGA data, 1058 smpls focal events by stage increases #NGDx15
8:47am August 20th 2015 via Hootsuite
Michael Speicher (Medical Univ Graz) "Whole genome sequencing of plasma DNA in patients with cancer" #NGDx15
8:45am August 20th 2015 via Hootsuite
.howitts_done Thanks for the kind word! Late to this AM's cfDNA talk and figuring out how I can manage at #NGDx with a broken laptop...
8:40am August 20th 2015 via Hootsuite
Business cards may not be going away soon. | WaPo http://t.co/kdjCI6Onw5
8:05am August 20th 2015 via Hootsuite
RT @MishaAngrist: The $100 Million App Store for Your DNA http://t.co/jc2aLJg4cy >@TechReview
7:00am August 20th 2015 via Hootsuite
What we can learn from sequencing our genome | Tech Insider http://t.co/CVQsiaek08
5:30am August 20th 2015 via Hootsuite
RT @EBNAdvertising: Infographic puts $1000 genome into perspective via @Clin_Chem_AACC http://t.co/usOa0ARj0P http://t.co/q8lJrO7AgV
4:35am August 20th 2015 via Hootsuite
RT @AACR: NCI-MATCH to treat cancer based on actionable mutations—Dr. Barbara Conley explains: http://t.co/OdwG9xykLp http://t.co/95fsTNgAno
10:05pm August 19th 2015 via Hootsuite
RT @gatk_dev: Q: How similar is an unmapped BAM (uBAM) to a BAM? A: Close, but no CIGAR.
9:50pm August 19th 2015 via Hootsuite
RT @AACR: Many cancers are preventable. You can take steps to reduce your risk: http://t.co/sMAJVPQZZj http://t.co/PpzbCgkwDV
8:50pm August 19th 2015 via Hootsuite
RT @moorejh: I thought #Microsoft wasn’t relevant anymore. Then I installed #Windows10 http://t.co/XP3EAqkto0
7:10pm August 19th 2015 via Hootsuite
Genovese: Work published here in NEJM http://t.co/g6ZJPZ5POC #NGDx15
6:10pm August 19th 2015 via Hootsuite
Genovese: Found that clonal expansion 13x-fold increased risk, but low absolute risk (~1%/year); most will not develop in lifetime #NGDx15
6:06pm August 19th 2015 via Hootsuite
Genovese: Their selection - one in a key leukemia gene, or three across the whole exome. Graphed vs. age: marked inc >45y old #NGDx15
6:03pm August 19th 2015 via Hootsuite
Genovese: Most common AML (FLT3 NPM1) never observed in mutated healthy subjects. #NGDx15
6:01pm August 19th 2015 via Hootsuite
Genovese: Four genes enriched: DNMT3A, ASXL1, TET2, PPM1D; first 3 often found in AML. Likely initiating lesions - find 1 or 2 per #NGDx15
Genovese: Very low allelic fraction, could distinguish somatic from inh mutations. >3K somatic mutations ID'd from 12.3K indivds #NGDx15
6:00pm August 19th 2015 via Hootsuite
Genovese: 12K blood samples from Sweden, looked into somatic mutations from blood-derived DNA. Devised novel analytical approach #NGDx15
5:58pm August 19th 2015 via Hootsuite
Genovese: There must be a long history of pre-cancer mutations (and clonal expansions) that goes undetected. #NGDx15
5:56pm August 19th 2015 via Hootsuite
Genovese: AML, CLL genes Lawrence Nature 2014 http://t.co/MLZfJX0Wti AML often w/coding mutations in several genes #NGDx15
5:54pm August 19th 2015 via Hootsuite
Genovese: Leukemia is 1.5% overall lifetime incidence; 52K new cases/y in US. 58.5% of dx will survive after 5y #NGDx15
5:52pm August 19th 2015 via Hootsuite
Guilio Genovese (Broad Inst MA) "Clonal hematopoiesis and blood-cancer risk inferred from exome sequencing of blood-derived DNA" #NGDx15
5:51pm August 19th 2015 via Hootsuite
Khush: Q:Can this technology be used in-tandem with cancer det? A:Transplant pts have high rates - 2x-14x-fold. Yes, potential there #NGDx15
5:49pm August 19th 2015 via Hootsuite
Khush: Q:What about discordant cases? A:Evidence of graft disfunction, or biopsy-neg rejection #NGDx15
5:48pm August 19th 2015 via Hootsuite
Khush: Q:Lung vs heart, could it be cell turnover? Or infection? A:Data to be presented tomorrow #NGDx15
5:47pm August 19th 2015 via Hootsuite
Khush: Liver transplantation, SRY gene monitoring for male liver organ donation to female recipients 2013 ref http://t.co/JJg1qq93pE #NGDx15
5:45pm August 19th 2015 via Hootsuite
Khush: Onto kidney, cfDNA can be detected in urine. #NGDx15 2013 ref http://t.co/EqK85OaehZ
5:43pm August 19th 2015 via Hootsuite
Khush: Evidence for ongoing tissue damage post-transplant. But acute rejection showed similar rise in cfDNA levels #NGDx15
5:41pm August 19th 2015 via Hootsuite
Khush: Unlike heart, lung has a much slower decline in cfDNA, perhaps reflecting higher mass, and single (ischemic) blood supply #NGDx15
5:40pm August 19th 2015 via Hootsuite
Khush: Shows dd-cfDNA levels decreasing following rejection treatment. For lung transplant - survival 4-7 years #NGDx15
5:39pm August 19th 2015 via Hootsuite
Khush: CareDx using retrospective dd-cfDNA in acute heart transplant rejection. CARGO-II study. Rejection in 2-6% range. #NGDx15
5:37pm August 19th 2015 via Hootsuite
Khush: Shotgun NGS is used by them, others use targeted. Both req recipient and donor genotypes. CareDx is using SNPs (266) not req #NGDx15
5:36pm August 19th 2015 via Hootsuite
Khush: AUC results reported 2014 Sci Trans Med http://t.co/rZZBcSz1Qo #NGDx15
5:35pm August 19th 2015 via Hootsuite
Khush: One loss of a graft, received a second transplant. Spike, then loss. AUC is 0.83 for cfDNA; Allomap (gene exp) 0.72 (CareDx) #NGDx15
5:33pm August 19th 2015 via Hootsuite
Khush: High signal immed post-transplant, with a 2-4d steep decay. For acute rejection: 5mos post-transplant elevated to 5% cfDNA #NGDx15
5:32pm August 19th 2015 via Hootsuite
Khush: Results: 2011 PNAS http://t.co/JybssnuQ3X Did prospective study then - N=161, serial blood over 2y post-transplant #NGDx15
5:30pm August 19th 2015 via Hootsuite
Khush: Hypothesis - in rejection, donor DNA cfDNA will rise with damaged tissue. ID'd SNPs that differed between donor/recipient #NGDx15
5:29pm August 19th 2015 via Hootsuite
Khush: But subjective - 71% agreement between pathologists. About 30K heart transplants/year. For heart - small amt from donor organ #NGDx15
5:28pm August 19th 2015 via Hootsuite
Khush: For cardiac transplant - biopsy is >$4K, catheterization to detect acute rejection. But 'gold std' for rejection surveillance #NGD
5:27pm August 19th 2015 via Hootsuite
Khush: Type of cfDNA in kidney transplant - SRY gene, donor-derived cfDNa #NGDx15 2005 demonstrated http://t.co/5K5OTmgIom
5:26pm August 19th 2015 via Hootsuite
Khush: 14/17 recipients in 1999 had male donor organs and female recipients, detected Y-chr DNA in urine #NGDx15
5:24pm August 19th 2015 via Hootsuite
Khush: Detect non-invasive marker for acute rejection post-transplantation. #NGDx15
5:23pm August 19th 2015 via Hootsuite
