Stratton: Kataegis always has TpCpN trinucleotides; hyperediting restricted to small area. APOBEC responsible (in yeast) #ESHG14
9:15am June 3rd 2014 via Hootsuite
Stratton: Never see kataegis in the same place twice; all unique #ESHG14
9:13am June 3rd 2014 via Hootsuite
Stratton: Localized hypermut: kataegis. Rainfall plot: 2012 Cell pub http://t.co/Fj5p1w4FXa Mutations <100bp spacing, Chr6 #ESHG14
Stratton: Illustrates: 4 signatures of mismatch repair; defective BRCA1/2 homologous recombination repair; others and 'unknown'. #ESHG14
9:11am June 3rd 2014 via Hootsuite
Stratton: APOBEC3A/3B can have a 30kb deletion forming a chimeric protein; increases risk of hypermut of Sig 2; inc risk for br ca #ESHG14
9:09am June 3rd 2014 via Hootsuite
Stratton: Switching on of APOBEC - is it amplification, overexpression, or response to a virus or retrotransposon? #ESHG14
9:05am June 3rd 2014 via Hootsuite
Stratton: AID cntral role in class switch recombination at Ig loci. APOBEC3A-H mutate HIV, HBV for defense #ESHG14
9:04am June 3rd 2014 via Hootsuite
Stratton: AID/APOBEC family of cytidine deaminases DNA editing machinery at an abasic site. C-T or C-G (like in Sig 2) #ESHG14
9:03am June 3rd 2014 via Hootsuite
Stratton: Sig 2 has about 12 mut/MB in 10% of breast cancers; C-T and C-G mutations, specific contexts. TpCpA etc. #ESHG14
9:01am June 3rd 2014 via Hootsuite
Stratton: From these processes - the desire to understand mechanism. Now onto signature 2, 50% of the cancer types. #ESHG14
9:00am June 3rd 2014 via Hootsuite
Stratton: Some signatures observed in almost every cancer type, others 50%, others only one. #ESHG14
8:58am June 3rd 2014 via Hootsuite
Stratton: Great diversity of patterns, some combinations that are somewhat similar. Across 30 types of cancers shown #ESHG14
8:57am June 3rd 2014 via Hootsuite
Stratton: Showing 26 (now 30) mutational signature. "More than we expected, more causes than we know of." #ESHG14
8:56am June 3rd 2014 via Hootsuite
Stratton: Of 7,042 samples of 30 cancer types; 4.9M mutations, now look cross the landscape #ESHG14
8:54am June 3rd 2014 via Hootsuite
Stratton: 6 types of C-T base substitutions (due to adjacent bases); move out from 6 to 96 due to 2 adjacent bases. #ESHG14
Stratton: A different math problem due to many unknowns. A blind source separation problem. 1999 Nature pub http://t.co/gK4cZxhQzW #ESHG14
8:52am June 3rd 2014 via Hootsuite
Stratton: The challenge is all three types are mixed together in the 'final cancer genome'. (Nicely laid out.) #ESHG14
8:51am June 3rd 2014 via Hootsuite
Stratton:From 1 fertilized egg to cancer cell: 3 models - constant, a burst in the middle, or steady later on through the end #ESHG14
8:50am June 3rd 2014 via Hootsuite
Stratton: Since 1980's, looking at TP53; of 686 skin cancers, 60% C->T mutations due to UV. Of 167 lung ca: C->A majority #ESHG14
8:47am June 3rd 2014 via Hootsuite
Stratton: Sources of mutatation: pollutants; mistakes in cell division; UV, cigarette smoke, aflatoxin, auto-repair mechanism damage #ESHG14
8:45am June 3rd 2014 via Hootsuite
Stratton: Detection / monitoring of circ. DNA impt finding. Today: mutational processes involved. 2013 Nature http://t.co/1WuC02X9QS #ESHG14
8:43am June 3rd 2014 via Hootsuite
Stratton: There are 5-600 mutated cancer genes, many insights from cancer genome sequencing; on the order of 10K now #ESHG14
8:41am June 3rd 2014 via Hootsuite
Final session: Sir Michael Stratton (Inst. of Cancer Research, UK): Signatures of Mutational Processes in Human Cancer #ESHG14
8:40am June 3rd 2014 via Hootsuite
RT @iontorrent: This video gives a first look at the PGM Dx #ESHG14 http://t.co/OPbWpMXfym
4:50am June 3rd 2014 via Hootsuite in reply to
RT @iontorrent: Andy Felton of Ion Torrent product management gives us a quick update on PII, Ion Chef from #ESHG14 http://t.co/IOQ4lAHtT4
4:35am June 3rd 2014 via Hootsuite in reply to
RT @LIFECorporation: Quick chat about #ESHG14 poster “Digital PCR for Quant. Chimerism in Leukemia Samples” http://t.co/6DevlCBTQK http://t…
4:16am June 3rd 2014 via Hootsuite
RT @LIFECorporation: Blog: Download copies of our posters presented at #ESHG14 http://t.co/fPySWz1Pvd
12:25pm June 2nd 2014 via Hootsuite in reply to
Soranzo: Suggests that WES you miss out on biologically important (albeit rare) variation in non-coding parts of the genome #ESHG14
11:56am June 2nd 2014 via Hootsuite
Soranzo: Exomes vs. Genomes? Did the comparison for SNPs within coding regions; low freq ass'n are found in non-coding domains #ESHG14
11:55am June 2nd 2014 via Hootsuite
Soranzo: Funded to make datasets freely available. Their URL to access data here http://t.co/3CvGiEbzKA #ESHG14
11:51am June 2nd 2014 via Hootsuite
Soranzo: Novel LDLR intronic variant ID via meta-analysis of 20K GWAS samples #ESHG14
11:50am June 2nd 2014 via Hootsuite
Soranzo: Inc. accuracy of imputation via combining UK10K and TGP data; r2 significantly higher #ESHG14
11:49am June 2nd 2014 via Hootsuite
Nicole Soranzo (Wellcome Trust UK) “WGS of 4K individuals provides insight into genetic architecture of complex traits” #ESHG14
11:44am June 2nd 2014 via Hootsuite
Tweeting on behalf of @LIFECorporation the digital PCR workshop (Amber 6 & 7) #ESHG14
9:38am June 2nd 2014 via Hootsuite
#ESHG14 @LIFECorporation Digital PCR workshop starting at 1530 in the Amber 7&8 rooms - several researchers looking at cell-free DNA
9:20am June 2nd 2014 via Hootsuite
Would you like to hear @iontorrent news from #ESHG14 ? We’ve got it on YouTube! http://t.co/VywAvgFsiY
5:37am June 2nd 2014 via Hootsuite
#ESHG14 Oops! Digital PCR session today is at 1530-1700 in Amber 7&8! @LIFECorporation All invited!
5:28am June 2nd 2014 via Hootsuite
#ESHG14 Today at 11:45-13:15 in Amber 7&8 hear about digital PCR applications from several invited speakers.
5:17am June 2nd 2014 via Hootsuite
.@robin_andersson You are most welcome - I'll be live-tweeting under @LIFECorporation at the digital PCR workshop at #ESHG14 in an hour...
5:07am June 2nd 2014 via Hootsuite in reply to
Jones: Using 450K chip, looking at 'DNA rebound methylation' after 5-Aza removed. Gene bodies are re-methylated. #ESHG14
4:03am June 2nd 2014 via Hootsuite
Jones: They work inhibiting methylation; incorporation into nascent DNA; remains in strand. Specificity is what is re-methylation #ESHG14
4:01am June 2nd 2014 via Hootsuite
Jones: Idea: in aging and infection, gene body methylation can induce mutations. Hypomethylating drugs - 5-Aza-CR in the 60's #ESHG14
4:00am June 2nd 2014 via Hootsuite
Jones: DNMT3A methylates itself, turning a base into a hotspot, inactivating the gene. 'Two sides of the same coin'. #ESHG14
3:59am June 2nd 2014 via Hootsuite
Jones: Interaction of epigenetics with genetics: mut promoter, or gene body; a genetic OR epigenetic mark causing oncogenic mutation #ESHG14
3:57am June 2nd 2014 via Hootsuite
Jones: TCGA observation “shocking” was that all cancers had aberrant methylation. ‘10K tumors' - had at least one. #ESHG14
3:53am June 2nd 2014 via Hootsuite
Jones: Genes actively expressed can have a lot of methylation (in the gene body), largely ignored to-date #ESHG14
3:52am June 2nd 2014 via Hootsuite
Jones: Epigenetic modifiers are often mutated in cancers; next cytosine modifications #ESHG14
3:49am June 2nd 2014 via Hootsuite
Jones: Showed data CpG island correlated with change in chromatin structure, along with nucleosome phasing #ESHG14
3:48am June 2nd 2014 via Hootsuite
Jones: De novo NDRs are enriched for distal regulatory regions including enhancers and xcription factor binding sites #ESHG14
3:46am June 2nd 2014 via Hootsuite
Jones: NOMe-Seq assay: nucleome occupancy and methylation assay. Methyl. and chromatin accessibility can be anticorrelated #ESHG14
3:45am June 2nd 2014 via Hootsuite
