Wong: LFS-related early onset, number of germline TP53 hotspot mutations (133 and 175), among top 8. #ASHG2013
9:18am October 25th 2013 via TweetDeck
Cancer genomics: J. Wong (Krahe lab MDAnderson): Comparative WGS for Li Fraumeni Syndrome (LFS) sarcomagenesis #ASHG2013
9:17am October 25th 2013 via TweetDeck
Ongen: For more information about SYSCOL (EU colorectal cancer project) http://t.co/mNyrFiKnpf #ASHG2013
9:14am October 25th 2013 via TweetDeck
Ongen: Tumor-spec eQTLs are enriched for somatic muts, likely germline regulatory drivers. #ASHG2013
9:12am October 25th 2013 via TweetDeck
Ongen: Looking at shared eQTLs - direction is conserved in tumorigenesis #ASHG2013
9:11am October 25th 2013 via TweetDeck
Ongen: 32 (25 novel) genes significantly mutated in CRC (by calling genotypes from RNA-seq data). #ASHG2013
9:10am October 25th 2013 via TweetDeck
Ongen: Significant rise of ASE in tumors compared to normal (P<10^-16) #ASHG2013
9:07am October 25th 2013 via TweetDeck
Ongen: Looking at ASE - of 6889 het sites, 10% exhibit ASE (P<0.001, FDR of 1%) #ASHG2013
9:06am October 25th 2013 via TweetDeck
Ongen: 213 diff. spliced genes. Chr20 tumor/normal increased correlation of regulatory blocks. #ASHG2013
9:05am October 25th 2013 via TweetDeck
Ongen: SYSCOL project in EU, diff. exp showed 5321 up or down-reg genes. #ASHG2013
9:03am October 25th 2013 via TweetDeck
Cancer genomics: H. Ongen: Transcripome sequence analysis of human colorectal cancer #ASHG2013
9:02am October 25th 2013 via TweetDeck
Cromer: Conclude: 33% of insulomas have YY1, not in any other tumor, able to regulate novel genes, ACDY1 / CACNA2D2. #ASHG2013
8:45am October 25th 2013 via TweetDeck
Cromer: Mouse model for overexp of 2 ID genes, looked at insulin secretion in the model. Explained GLP-1, YY1 pathway mechanism #ASHG2013
8:44am October 25th 2013 via TweetDeck
Cromer: PCA of microarray data shows exp. profile. Combining exp + ChIP: ID 24 genes, narrow to 2 ADCy1 91x up CACNA2D2 13x up #ASHG2013
8:41am October 25th 2013 via TweetDeck
Cromer: Expect novel binding of TF across the genome, affecting many aberrant genes. Via ChIP, confirmed. #ASHG2013
8:39am October 25th 2013 via TweetDeck
Cromer: Altered binding - examined by ChIP. Cp wt and mut T372R. Loss of upstream specificity of DNA motif. #ASHG2013
8:38am October 25th 2013 via TweetDeck
Cromer: YY1 = 'Yin Yang 1' transc. factor, believe it is gain of fn. 1996 crystal structure solved; mut w/in Zn finger binding dom #ASHG2013
8:37am October 25th 2013 via TweetDeck
Cromer: 26 protein altering muts, validated by Sanger, YY1, T372R only recurrent one. YY1 transc. factor, binds DNA, protein, RNA #ASHG2013
8:36am October 25th 2013 via TweetDeck
Cromer: Late onset, no family history. ID somatic tumors via tumor/normal pairs. ID of drivers: recurrent across pts. #ASHG2013
8:35am October 25th 2013 via TweetDeck
Cromer: Looking at pancreatic beta-cell tumors - hypersecreting insulin #ASHG2013
8:34am October 25th 2013 via TweetDeck
Cancer genomics: M.K. Cromer (Yale, Lifton Lab): Recurrent somatic mut. altering DNA-binding motif of transc. factor YY1 #ASHG2013
8:33am October 25th 2013 via TweetDeck
Van Loo: Conclude: 2137 primary tumors, discovered 12 tumor suppressors, 11 sites of telomeric instabl. 24 candidate tumor supp's #ASHG2013
8:28am October 25th 2013 via TweetDeck
Van Loo: The 2010 PNAS publication using SNP arrays for allele-specific CNV analysis in cancer. #ASHG2013 http://t.co/ziRnNsePlr
Van Loo: CPEB3 identified via SNP arrays, repressor of EGFR in lung Ca. #ASHG2013
8:26am October 25th 2013 via TweetDeck
Van Loo: Tumor suppressors - focus on homozyg. deletions. Strong negative selection pressure. #ASHG2013
8:20am October 25th 2013 via TweetDeck
Cancer Genomics: Van Loo: The landscape of tumor suppressors in primary tumors. #ASHG2013
8:18am October 25th 2013 via TweetDeck
Leiserson: Referenced this Nature pan-cancer paper for the Multi-Dentrix tool #ASHG2013 http://t.co/dpqvrJDKqP
8:16am October 25th 2013 via TweetDeck
Leiserson: Also looks at mutually exclusive genes 'Multi-Dendrix' applied to GB. Only picked up by patterns of mutations. #ASHG2013
8:15am October 25th 2013 via TweetDeck
Leiserson: Reference noted for discussion on BAP1 Nature Rev Cancer http://t.co/5JS4fX9AlU #ASHG2013
8:14am October 25th 2013 via TweetDeck
Leiserson: Identified 121 genes in 21 subnetworks in 'HotNet2' Illustrates several examples incl. TP53, BAP1 #ASHG2013
8:12am October 25th 2013 via TweetDeck
Leiserson:4 different mutation scores, 3 different interaction networks, pooling 12 consensus subnetworks #ASHG2013
8:08am October 25th 2013 via TweetDeck
Leiserson: Goal is to find subnetworks mutated more than expected by chance. HotNet tool (2011) used in TCGA pubs. #ASHG2013
8:05am October 25th 2013 via TweetDeck
#ASHG2013 Session on Cancer Genomics: Leiserson: Network analysis of mutations across cancer types
8:04am October 25th 2013 via TweetDeck
MT @OmicsOmicsBlog: Souvenir from this evening's demo. Yup, @nanopore... let a clumsy bioinformaticist run a MinION http://t.co/mW2dWDZv2c
7:21am October 25th 2013 via TweetDeck
RT @dgmacarthur: #ASHG2013 Me running a @nanopore MinION: http://t.co/JCJGHcOxYQ
6:21am October 25th 2013 via TweetDeck
Wow! MT @olinhyde: Fascinating analysis of American communication patterns http://t.co/nYpPaZYxzx
5:21am October 25th 2013 via TweetDeck
RT @kbradnam: For every bioinformatician! PLoS Comp. Biol. 10 Simple Rules for Reproducible Computational Research http://t.co/31LbmZkZht
4:21am October 25th 2013 via TweetDeck
RT @mmarchin: The joy of data analysis http://t.co/1at351tN1y
8:52pm October 24th 2013 via TweetDeck
Wow. RT @HistoryInPics: Sitting in the ruins of Hiroshima, Dec 1945 http://t.co/v4SD09x1OE
7:35pm October 24th 2013 via TweetDeck
Bale: Commenter: "An incredibly important project" (ClinVar) "A perfect way to fix mistakes in the past" (i.e. OMIM, HGMD) #ASHG2013
6:03pm October 24th 2013 via TweetDeck
Bale: If you are gene expert, 'volunteer to be a curator for that gene' #ASHG2013
5:58pm October 24th 2013 via TweetDeck
Bale: Can evaluate variants by number and ID of submitters. Eventually curated, even by prof. society #ASHG2013
5:56pm October 24th 2013 via TweetDeck
Bale: Two projects, 'sharing clinical reports' and 'free the data' http://t.co/EUSkQ1CKNb #ASHG2013
5:47pm October 24th 2013 via TweetDeck
Bale: Some 5800 BRCA1/2 variants now; 'we need BRCA1/2 data!' #ASHG2013
Bale: ClinVar - one-stop shop, with high confidence in the data (expert curation), also free access. #ASHG2013
5:45pm October 24th 2013 via TweetDeck
Bale: Clinical labs are seq single genes like BRCA1/2 where much data is proprietary. Distributed in many places. #ASHG2013
5:44pm October 24th 2013 via TweetDeck
Bale: ClinVar URL is here: http://t.co/bJREXNLDx6 #ASHG2013
5:43pm October 24th 2013 via TweetDeck
Sherri Bale, GeneDx/BioReference. "Using ClinVar as a resource to eval. genomic variation" #ASHG2013
5:41pm October 24th 2013 via TweetDeck
Geraghty: CEH region targeted 790kb. Would like to eliminate use of fosmids next. #ASHG2013
2:58pm October 24th 2013 via TweetDeck
Geraghty: MiSeq: PE500 Velvet -> Phrap; PB 'no finishing req'. #ASHG2013
2:55pm October 24th 2013 via TweetDeck
