November 2017

Koboldt: Ideally: precise, few FPs: establish 'ground truth' w/orthogonal valdatoin, manual review, or in silico datasets #AMP2017

3:55pm November 16th 2017 via Hootsuite

Koboldt: Shows signal-to-noise ratio - 'not entirely random, not entirely uniform'. Accurate est of VAF requires deep NGS coverage. #AMP2017

3:53pm November 16th 2017 via Hootsuite

Koboldt: Makes point that tumor/normal pairs should be used, under same protocol, similar conditions. #AMP2017

3:47pm November 16th 2017 via Hootsuite

Koboldt: And transcriptome: may not be the best for somatic discovery. Powerful to use as complement #AMP2017

3:47pm November 16th 2017 via Hootsuite

Daniel Koboldt (Nationwide Children's Hosp Columbus OH) Strategies and challenges for somatic mutation detection by NGS #AMP2017

3:44pm November 16th 2017 via Hootsuite

Mullighan: Looking at secondary lesions: IKZF1 '15 ref https://t.co/rIWTcT1JZs find de-repression of cellular programs: adhesion #AMP2017

12:40pm November 16th 2017 via Hootsuite

Mullighan: Data suggests 'transformation of early progenitor' driving phenotype. #AMP2017

12:38pm November 16th 2017 via Hootsuite

Mullighan: Shows gene expression from ZNF384-rearr in B/myeloid mixed. Lymphoid and myeloid lineage splits. #AMP2017

12:38pm November 16th 2017 via Hootsuite

Mullighan: New subtypes - MEF2D-rearr B-ALL, RNA-seq of 560 B-ALL cases, multiple recurring targets MEF2D, ZNF384, NUTM1, IGH. #AMP2017

12:34pm November 16th 2017 via Hootsuite

Mullighan: #AMP2017 '17 review of Ph+like ALL https://t.co/NMqUwbGwKe

12:33pm November 16th 2017 via Hootsuite

Mullighan: Shows mouse data showing feasibility for TKI with std therapy. COG AALL1131, COG AALL1521 clinical trials. #AMP2017

12:32pm November 16th 2017 via Hootsuite

Mullighan: Druggability work: Over-expression and truncation of EPOR - several tyr residues, thus negative regulation of receptor #AMP2017

12:31pm November 16th 2017 via Hootsuite

Mullighan: 'As we sequence more we find more kinases and rearrangements'.... '12 ref https://t.co/e2OltwkhTG #AMP2017

12:30pm November 16th 2017 via Hootsuite

Mullighan: Classes - JAK-STAT, ABL, other signaling including STAT MAPK. Pathways raise possibility of multiple drugging #AMP2017

12:28pm November 16th 2017 via Hootsuite

Mullighan: Ph-Like ALL: similar transcriptome to Ph+ ALL. Then looked at prevalence. '17 JCO https://t.co/H1m6HN7kFW Most diverse #AMP2017

12:27pm November 16th 2017 via Hootsuite

Mullighan: #AMP2017 Shows summary of >2500 ALL and type of lesions '14 NEJM https://t.co/jfmluLA0Zs

12:25pm November 16th 2017 via Hootsuite

Charles Mullighan (St Jude Memphis TN) Precursor B-cell Neoplasms (ALL) #AMP2017 In '00, used cytogenetics.

12:22pm November 16th 2017 via Hootsuite

Q: Methyl-Seq on cfDNA? Tissue of origin from cfDNA? Feinberg: Haven't looked at cell-free (yet). #AMP2017

12:22pm November 16th 2017 via Hootsuite

Feinberg: Now onto EWAS: epigenome-wide assoc study. Combining with GWAS for rheumatoid arthritis '13 ref https://t.co/C4Tuqp3ggz #AMP2017

11:07am November 16th 2017 via Hootsuite

Feinberg: Genetic vars increase epigenetic plasticity. Shows a VMR, variably methylated region, in inbred mice. #AMP2017

10:49am November 16th 2017 via Hootsuite

Feinberg: What if some signal for stochastic var related to common SNPs? And why in the context of evolution? #AMP2017

10:47am November 16th 2017 via Hootsuite

Feinberg: Like quantum mechanics where stochastic variation plays a fundamental role. '10 PNAS https://t.co/9xViWAMn9Q #AMP2017

10:46am November 16th 2017 via Hootsuite

Feinberg: While visiting Big Ben in London, '09: shows difference between Newton's grave (elaborate) and Darwin's grave (simple). #AMP2017

10:44am November 16th 2017 via Hootsuite

Feinberg: Meeting 'missing heritability in common disease' NIH conference, he had only 7 minutes! Battle over comment in publ. #AMP2017

10:39am November 16th 2017 via Hootsuite

Feinberg: Clustering from '09 ref: stochastic var in DNAm in isogenic mice: is there a conserved driver for epigenetic var? #AMP2017

10:38am November 16th 2017 via Hootsuite

Sabath (Univ WA) '09 from Feinberg's group Nature Gen https://t.co/Xm2qd92XCw that looked at 4.6M CpG's genomewide via method CHARM #AMP2017

10:36am November 16th 2017 via Hootsuite

What an interesting way to look at tissue-specific developmental changes. Daniel Sabath #AMP2017 https://t.co/Jd4JkNdUzv

10:30am November 16th 2017 via Hootsuite

Harris con't:Sarcomas likely have oncogenic fusion. In 9pts, had enough smaple to send for RNA seq to look for fusions #AMP2017

9:58am November 16th 2017 via Hootsuite

Q: Comment on employing other genomic technology (i.e. RNA) Harris: If enough sample, aCGH. If CNA led to inc expression, then IHC #AMP2017

9:57am November 16th 2017 via Hootsuite

Q: What was TAT for iCat? Harris: On the order of months. Realistically: 4 weeks. Sending samples, review, sending out... #AMP2017

9:54am November 16th 2017 via Hootsuite

Harris: Unanswered Q's: impact of receiving matched Rx on outcome; factors influencing receipt of matched Rx #AMP2017

9:52am November 16th 2017 via Hootsuite

Harris: Also ID'd 11 pts with potential germline variants for cancer risk, even though germline samples were not provided. #AMP2017

9:51am November 16th 2017 via Hootsuite

Harris: Showed all the tissue types from this '16 JAMA Oncol paper https://t.co/td4Vmu6kIb #AMP2017

9:42am November 16th 2017 via Hootsuite

Harris: Called iCat, samples sent to Dana Farber, molecular testing, expert panel review, letter of treatment back to host inst. #AMP2017

9:40am November 16th 2017 via Hootsuite

Harris: Looked at feasibility of Precision Med for pediatric recurrent, refractory, or high risk solid tumors #AMP2017

9:39am November 16th 2017 via Hootsuite

Harris: Rare, few sequence alterations, small biopsies (from small people), few trials and drugs #AMP2017

9:37am November 16th 2017 via Hootsuite