Greenleaf: Recent work in Nature Gen https://t.co/ZrYEqu5wdJ in mouse eSCs #AGBT17
6:53pm February 13th 2017 via Hootsuite
Greenleaf: Regions of accessibility; positioning nucleosomes; can infer transcription factor presence; can call chromatin state #AGBT17
6:52pm February 13th 2017 via Hootsuite
Greenleaf: The regulome: if 'on', accessible; if 'off', inaccess. Assay of Transposase Accessible Chromatin https://t.co/GciDyUUwnS #AGBT17
6:51pm February 13th 2017 via Hootsuite
Greenleaf: Shows Waddington's 1957 image https://t.co/AY1u4nHuYE of development. 3m into 5um via folding. #AGBT17
6:49pm February 13th 2017 via Hootsuite
William Greenleaf (Stanford Univ CA) ATAC-in single-cell regulatory variation #AGBT17
6:47pm February 13th 2017 via Hootsuite
Churchman: Yeast ribo profiling work '09 Science ref https://t.co/jN3MIlGuTA Sees rapid and dynamic regulation of xlation in mito #AGBT17
6:41pm February 13th 2017 via Hootsuite
Churchman: Nucl, mito have orthogonal mechanisms, orthogonal machinery. In yeast: looking at ribosome profiling cross-compartments #AGBT17
6:40pm February 13th 2017 via Hootsuite
Churchman: Onto nuclear and mitochondrial genomes: 10 genes vs ~10K genes that are transcribed. #AGBT17
6:35pm February 13th 2017 via Hootsuite
Churchman: BRD4 is a 'master regulation of transcription', showed effect of the two compounds. #AGBT17
Churchman: One cmpd targeting BRD4 is JQ1, '10 Nature ref https://t.co/EFcaJPdzbC also '15 Science https://t.co/6EikMCBjva #AGBT17
6:32pm February 13th 2017 via Hootsuite
Churchman: Looking at dysregulated transcription, and Rx targets such as BRD4 common in many cancers #AGBT17
6:30pm February 13th 2017 via Hootsuite
RT @healthhashtags: New Health Hashtag
6:29pm February 13th 2017 via Hootsuite
Churchman: In HeLa S3: a 50b promoter-proximal pause, and not at a single nucleotide but at several specific sites. #AGBT17
6:28pm February 13th 2017 via Hootsuite
Churchman: Isolate nuclei, ID 3' end of nascent RNA, ligate hexamer to 3' end. Can map Pol II density genome-wide #AGBT17
6:26pm February 13th 2017 via Hootsuite
Churchman: nt resolution, maps across yeast, drosophila, mammalian cells '15 Cell ref https://t.co/nDJj6AzzX1 #AGBT17
6:25pm February 13th 2017 via Hootsuite
Churchman: Describes her Net-Seq method '11 Nature ref https://t.co/HKbfxaHcf0 #AGBT17
6:24pm February 13th 2017 via Hootsuite
Churchman: Many intermediate stages, and impt roles. From DNA/chromatin, NET-seq looking at xcription. RNApol not a wind-up car #AGBT17
6:23pm February 13th 2017 via Hootsuite
Churchman: Starts off with the Central Dogma and where genes are regulated; transcripts are degraded; RNA processed is degraded #AGBT17
6:21pm February 13th 2017 via Hootsuite
Stirling Churchman (Harvard MA) Gene expression at high resolution, from the nuclear and mitochondrial genomes #AGBT17
6:20pm February 13th 2017 via Hootsuite
J. Hadfield: @coregenomics perhaps use CRSPR to fix? Kung: A daunting task for cancer, to fix 100% of cells. Maybe T-cells for ca #AGBT17
6:19pm February 13th 2017 via Hootsuite
Q: 1/1M sens? Kung: Done with Adaptive Biotechnologies (ha, I was right!) About 10-20ug of DNA, getting into the noise of the assay #AGBT17
6:18pm February 13th 2017 via Hootsuite
Q:Can you get blinded data? Kung: Hard Q - proving the value of these kinds of tests. #AGBT17
6:16pm February 13th 2017 via Hootsuite
Kung: From GWAS to genome-wide causation studies (a prospective approach), potential to benefit individual pts. #AGBT17
6:14pm February 13th 2017 via Hootsuite
Kung: 'We moved the experiment to the pt'. compassionate use, AKT-inh. 1mo - all active disease disappeared (!) #AGBT17
6:13pm February 13th 2017 via Hootsuite
Kung: Precision Medicine - emphasis now on the medicine. 3yo girl - 8y of chemo, surgery. Found LAMTOR1-AKT1 fusion, TERT promoter #AGBT17
6:12pm February 13th 2017 via Hootsuite
Kung: PIPseq impacted 65-70% of all cases (surprising). 40% by RNA, 7% CNV, 45% cWES, 8% CNV+RNASeq #AGBT17
6:10pm February 13th 2017 via Hootsuite
Kung: With this data - modulate immunsupressives, allow immune system to eliminate rare recurrent cells. Looking deeply by NGS#AGBT17
6:09pm February 13th 2017 via Hootsuite
Kung: Describes an Adaptive Biotech-like barcoding of B-cells to monitor tags that indicates relapse after BMT. 1/1M cells to 5/1M #AGBT17
6:08pm February 13th 2017 via Hootsuite
Kung: Went from 80% to 0.04% in bone marrow, could then go to BMT after chemo plus dasatinib #AGBT17
6:06pm February 13th 2017 via Hootsuite
Kung: Via RNA-Seq, 175 samples x 112 genes, most like BCR-ABL1. A BCR-ABL-like disease, found NUP214-ABL1 for B-cell ALL Treatable. #AGBT17
6:05pm February 13th 2017 via Hootsuite
Kung: 30% novel discovery to guide clinical decision making. Moving beyond genetically-encoded vulnerabilities #AGBT17
6:04pm February 13th 2017 via Hootsuite
Kung: Large mass on 15mo old child forearm; looked like infantile fibrosarcoma. But neg for ETV6-NTRK3 fusion. Via RNAseq EML4-NTRK3 #AGBT17
6:01pm February 13th 2017 via Hootsuite
Kung: Thus they avoided ineffective Rx; 13% underlying cancer predisposition in all pts they treat. 'We need to look broadly' #AGBT17
6:00pm February 13th 2017 via Hootsuite
Kung: ID of germline ca risk: young female w/AML, referred for BMT; sister perfect HLA. Found RNX1 splice var, sister had it too #AGBT17
5:59pm February 13th 2017 via Hootsuite
Kung: 3% 'compelled inaction' with 'significant clinical impact'. #AGBT17
5:56pm February 13th 2017 via Hootsuite
Kung: Inactionable - MLL2 mut and, mild immune impairment. Ruled out BMT for hereditary HLH, large clinical impact (no BMT needed) #AGBT17
Kung: VUS in databases, but GOOG search picked it up in a letter to the editor! Imatinib, leukemia spread to 80% of blood #AGBT17
5:52pm February 13th 2017 via Hootsuite
Kung: Case: 5yo boy, relapsed, salvage chemo + BMT; relapsed again, no options. Seq showed cKit mut; a VUS Asn655Lys #AGBT17
5:51pm February 13th 2017 via Hootsuite
Kung: Could assign tiers - actionable, 2 assoc'd with other tumor types etc. Can ID actionable alterations. #AGBT17
5:50pm February 13th 2017 via Hootsuite
Kung: Decided to do PIPseq (Precision in Pediatric Sequencing), results w/in 3-4 weeks. Used WES of tissue/normal/RNASeq #AGBT17
5:49pm February 13th 2017 via Hootsuite
Kung: Cancer is the leading cause of disease-related death in children. 2/3rds of survivors have long-term consequences to chemo #AGBT17
5:48pm February 13th 2017 via Hootsuite
Andrew Kung (Memorial Sloan Kettering, NY) Clinical impact of NGS in pediatric oncology #AGBT17
A2 Kenny: Info is contained in family history; ethnicity, race is part of a continuum. #AGBT17
5:44pm February 13th 2017 via Hootsuite
Green: How often is self-reporting conflict w/genetic data? Kenny: Self-reporting is a social construct; genetics is biological... #AGBT17
5:43pm February 13th 2017 via Hootsuite
Kenny: Can use EHR to alert Drs. to detect this disorder, alert to get genetic testing. PM is individualized, ancestry w/shared risk #AGBT17
5:41pm February 13th 2017 via Hootsuite
Kenny: Found common freq in Caribbean, 2% of spine and joint degradation in Puerto Rico. Now working to implement clinically #AGBT17
5:40pm February 13th 2017 via Hootsuite
Kenny: Looking at protein fn - should be recessive, other evidence of dominance; looking for heterozygous, reviewed >50 hets... #AGBT17
5:39pm February 13th 2017 via Hootsuite
Kenny: Found evidence of Steel Syndrome (COL27A1 mutation) in EHR, can also find other non-documented features of disease #AGBT17
5:36pm February 13th 2017 via Hootsuite
Kenny: Describes mutation in COL27A1 '15 ref https://t.co/2iZaJYaKDQ homozygotes = extreme short stature in BioMe #AGBT17
Kenny: Showed Puerto Rico and geography (Southern Bronx, El Barrio in E Harlem). Genetic clusters / geographies overlaid #AGBT17
5:29pm February 13th 2017 via Hootsuite
