Jones: ... could be important in communicating transcription initiation. #ESHG14
3:43am June 2nd 2014 via Hootsuite
Jones: Histones, chromatin remodeller, Pol II accessibility can't access if a nucleosome occupies location. meC and Ac marks... #ESHG14
3:42am June 2nd 2014 via Hootsuite
Next: Peter Jones (Univ Southern Calif USA)Cancer genetics and epigenetics: Two Sides of the Same Coin? #ESHG14
3:40am June 2nd 2014 via Hootsuite
RT @LIFECorporation: Top contributors at #ESHG14 so far (in order): @DaleYuzuki, @DNADigest, @Ensemily, @SeqComplete, @OmicsOmicsBlog
3:39am June 2nd 2014 via Hootsuite
Anne Ferguson-Smith (U Cambridge): “Intergenerational epigenetic prog. in a mouse model of undernutrition” But unpubl; I won't tweet #ESHG14
3:10am June 2nd 2014 via Hootsuite
Feinberg: Q&A: Not knocking it, but the Illumina 450K is ‘way too low resolution for this kind of thing’ Wants single-molecule #ESHG14
3:01am June 2nd 2014 via Hootsuite
Feinberg: His model in a recent review - Nat Rev Cancer http://t.co/YB9NRzIDLl Platisticity a central driving force in cancer #ESHG14
2:57am June 2nd 2014 via Hootsuite
Feinberg: Pointed to this Genome Med: epigenetic var http://t.co/sxYZ3g1C3G Key feature of cancer: instability / randomness #ESHG14
2:55am June 2nd 2014 via Hootsuite
Feinberg: Believes a dynamic epigenetic landscape w/ stochasticity is deformable - regulated by nuclear structure. "Cancer hijacks" #ESHG14
2:53am June 2nd 2014 via Hootsuite
Feinberg: Photo of him and Vogelstein from 30y ago (!) - 1/3 of hypomethylation up to 30MB long. Highly variable. #ESHG14
2:52am June 2nd 2014 via Hootsuite
Feinberg: Can find Variable Methylated Regions (VMRs) in inbred mice. Can epigenetic var's can explain tumor het? #ESHG14
2:48am June 2nd 2014 via Hootsuite
Feinberg: An idea (while in Westminster Abbey): stochastic variation plays a role in development. A certain degree of randomness. #ESHG14
2:45am June 2nd 2014 via Hootsuite
Feinberg: Vogelstein Science 2012: http://t.co/RFBqrFQjwA looking at missing heritability, only 20% maximum could be accounted for #ESHG14
2:44am June 2nd 2014 via Hootsuite
Feinberg: Points to 2009 Nature Gen pub: http://t.co/veYJLcjEtl C-DMRs = t-DMRs, hypervariable regions yet have patterns to them #ESHG14
2:43am June 2nd 2014 via Hootsuite
First: Andy Feinberg, Johns Hopkins USA: “The epigenetic basis of common human disease” #ESHG14
2:38am June 2nd 2014 via Hootsuite
RT @SwedishCanary: Never argue with children... http://t.co/CHY04padGJ
2:25am June 2nd 2014 via Hootsuite in reply to
RT @Roche: Roche acquires Genia Technologies to strengthen next generation sequencing pipeline http://t.co/fUlHhw6OTt $RHHBY $ROG
1:31am June 2nd 2014 via Hootsuite in reply to
RT @AppliedBio: #ESHG14 Poster: Mapping SNP gt & CNV data patterns to PGx allele nomenclature http://t.co/IDe7QnRyRV http://t.co/RGT9s6u
11:25pm June 1st 2014 via Hootsuite in reply to
RT @palafo: Even if you don't "hate work," this is a good guide to a happier working life. http://t.co/bhYTuBp1bQ
4:10pm June 1st 2014 via Hootsuite
Korbel: GFI1/B - only expr. when SV nearby; could it be cancer driver? Neural stem cells + cMYC + CFI1 explants induced m'blastoma #ESHG14
12:49pm June 1st 2014 via Hootsuite
Korbel: Locus at 9q34 - a putative target gene adjacent GFI1B next to DDX31; 1:5, 1:6; 1:9; 1:21 Chr translocations 4 samples #ESHG14
12:48pm June 1st 2014 via Hootsuite
Korbel: 'Non-canonical' recurrent struct variation (SVs) in medulloblastoma. Patterns are irregular - tandem dup, del's, inversions #ESHG14
12:46pm June 1st 2014 via Hootsuite
Korbel: Diversity of cancers, mRNA-Seq, methylation, longitudinal sampling. Unifying data: ID new patterns, driver variants #ESHG14
12:40pm June 1st 2014 via Hootsuite
Korbel: Pan-Cancer Analysis of Whole Genomes (PAWG) 2K whole cancer genomes, reanalysis of existing data. #ESHG14
12:38pm June 1st 2014 via Hootsuite
Korbel: Expanding on standards: analytical pipelines that hamper data integration and interpretation. #ESHG14
Korbel: Issues: Ascertainment bias (only ORFs); analysis of somatic rearr's in intergenic regions w/large sample #'s; need for stds #ESHG14
12:37pm June 1st 2014 via Hootsuite
Korbel: Effect of PE, read depth, looking at somatic, german ICGC PedBrain medulla blastoma. Found chromothrypsis in these samples #ESHG14
12:35pm June 1st 2014 via Hootsuite
Korbel: Structural variation analysis - short read DNA technology is too short. SV's occur in repetitive regions. #ESHG14
Jan O. Korbel (EMBL Heidelberg): Medulloblastoma links chromothrypsis with TP53 mutations #ESHG14
12:34pm June 1st 2014 via Hootsuite
Nik-Zainal: Haven't been able to find kataegis in germline (yet), suspect in normal cells #ESHG14
12:29pm June 1st 2014 via Hootsuite
Nik-Zainal: Able to recapitulate Kataegis in Saccharomyces via APOBEC overexpression #ESHG14
12:16pm June 1st 2014 via Hootsuite
Nik-Zainal: Data suggest a sudden single event; "cytosine is a genomic 'wild card'" APOBEC gene is a de-aminase C to U and then to T #ESHG14
12:14pm June 1st 2014 via Hootsuite
Nik-Zainal: Kataegis microclusters demonstrate processivity; all along >one strand<. A TpC context 2012 Cell http://t.co/AnmGhI9Nwg #
12:12pm June 1st 2014 via Hootsuite
Nik-Zainal: Zooming in from 14MB to kb scale to bp scale: somatic mut's are in cis (!) #ESHG14
12:08pm June 1st 2014 via Hootsuite
Nik-Zainal: Chr6, many C to T mutations; 25 rearrangement breakpoints, 17 colocalizing in 14MB window #ESHG14
12:07pm June 1st 2014 via Hootsuite
Nik-Zainal: Localized hypermutation: BRCA2null; TNBC examples shown. BRCA1 has 800 subst in dense area called 'Kataegis' #ESHG14
12:06pm June 1st 2014 via Hootsuite
Nik-Zainal: Introduce the 'rainfall plot' with every somatic mut, with spacing according to reference. Most mut's are 1MB spacing #ESHG14
12:05pm June 1st 2014 via Hootsuite
Nik-Zainal: De-amination of methylated C's - depletes CpG's 'all the time' (catalyzed by H2O of all things!) #ESHG14
12:04pm June 1st 2014 via Hootsuite
Nik-Zainal: Laid out the record of mutagenesis and oncogenesis. Looked at 21 breast cancers; a high-quality catalog, over 212K mut's #ESHG14
Serena Nik-Zainal (Sanger Centre, UK) Kataegis: a mutation signature identified through whole-genome sequencing of human cancers. #ESHG14
12:01pm June 1st 2014 via Hootsuite
Cuppen: One line from electroporation of micronuclei found chromotrypsis - more clues #ESHG14
11:56am June 1st 2014 via Hootsuite
Cuppen: Inefficient technique, but need efficient system for study. Single chromosome transfer: make micronuclei / electroporate #ESHG14
11:54am June 1st 2014 via Hootsuite
Cuppen: mate-pair seq; plotted CNVs and showed higher aneuploidy and structural variation. aCGH on 50 lines; 1 looked like chromotr. #ESHG14
11:52am June 1st 2014 via Hootsuite
Cuppen: Back to chromotrypsis: Refers to Janssen et al Science 2011 pub http://t.co/KZoZoFDsC9 setup in-vitro system for anueploidy #ESHG14
Cuppen: Connection of replication timing; comparing all cancer genes and all de novo germline breakpoints, suggests mechanism #ESHG14
11:50am June 1st 2014 via Hootsuite
Cuppen: Congenital disorders and cancer intertwined? Two sides of the same coin? De novo germline & cancer SVs overlap #ESHG14
11:49am June 1st 2014 via Hootsuite
Cuppen: microRNA cluster (C19MC) upregulation in zebrafish, shows developmental defect. Found in MCA/ID, Thyroid adenoma #ESHG14
11:47am June 1st 2014 via Hootsuite
Cuppen: Another example: 425kb deletion, Cp RNA, H3K4me3 mark, small RNA upregulation. Proband vs parental ave #ESHG14
11:46am June 1st 2014 via Hootsuite
Cuppen: ETV1 driven by a fusion; turns out that it is an oncogenic fusion (2005 Science ref: http://t.co/iq6I1687BW ) #ESHG14
11:44am June 1st 2014 via Hootsuite
Cuppen: PBMCs - only source they had to start with. Chr7 del, some gene dosage across region observed; ETV1 upregulated in aff child #ESHG14
11:43am June 1st 2014 via Hootsuite
