Mohlke: 2nd T2D example: CDC123/CAMK1D, similar footprinting to promoter region mutants in nuclear extracts. FOXA1/A2 pref. binding #AGBT14
9:57am February 13th 2014 via Hootsuite
Mohlke: Looking at two promoters P1 and P2 - P1 has a significant SNP risk variant, P2 doesn't. #AGBT14 Work in AJHG: http://t.co/Lfx2RPVOLp
9:55am February 13th 2014 via Hootsuite
Mohlke: In 2.7K Europeans, fine mapping the area, found strong signal. Overlapped with island open chromatin and promoter marks #AGBT14
9:52am February 13th 2014 via Hootsuite
Mohlke: T2D - looking at underlying variation in GWAS loci ID in 2010 Arap1 #AGBT14 2010 Nature Gen paper here: http://t.co/qRVriNMFLn
9:51am February 13th 2014 via Hootsuite
Mohlke: HDL-cholesterol GWAS manhattan plot: global lipid consort paper (Nat Gen 2013 paper here http://t.co/8lQD2GA79j) #AGBT14
9:49am February 13th 2014 via Hootsuite
Next up: Karen Mohlke (Univ NC) "Regulatory variants at GWAS loci for complex metabolic traits" #AGBT14
9:46am February 13th 2014 via Hootsuite
Chakravarti: Q: (E. Green): Other chromosomes / genes for enhancers? A: Second enh not highly conserved. Need approp. mouse lines #AGBT14
9:44am February 13th 2014 via Hootsuite
Chakravarti: Q: Genetics reminiscent of Autism (enteric morbidity)? A:ENS/CNS not looked at carefully in Autism (yet) #AGBT14
9:43am February 13th 2014 via Hootsuite
Chakravarti: Q (Gibbs): Are RET muts additive? A: Interaction of sets, enh. muts are brought into family by marriage; then penetrant #AGBT14
9:41am February 13th 2014 via Hootsuite
Chakravarti: (Ratios of prior list: 3% / 14% / 18% / 65% - isolated, whole variety of defects) #AGBT14
9:38am February 13th 2014 via Hootsuite
Chakravarti: Looking at 4 types of pts: single gene syndromic, large CNV syndromic, multiple abnormalities, isolated #AGBT14
9:36am February 13th 2014 via Hootsuite
Chakravarti: SOX10 impt xcr factor for gut development; can segment HSCR on the basis of genes that come into play #AGBT14
@KMeltzSteinberg What we might have expected from Eichler's talk: http://t.co/FUYBjbsz2U Recent paper: http://t.co/K97nQV7NLA #AGBT14
9:33am February 13th 2014 via Hootsuite
Chakravarti: Genesis and fate of neural crest cells contributing to the ENS: genes involved in earliest stages are involved w/ HSCR #AGBT14
9:32am February 13th 2014 via Hootsuite
Chakravarti: Newer less-confident data: high incidence of CNV in HSCR; chrom abnormalities, deletions: 42% unique pts have a CNV #AGBT14
9:28am February 13th 2014 via Hootsuite
Chakravarti: Looking for function - via ubiquination gene Ubr4 (E3 ligase), loss of fn in zebrafish gut develpment shown #AGBT14
9:27am February 13th 2014 via Hootsuite
Chakravarti: List of genes enriched for deleterious SNVs - 71% of pts have min 1. ID from RNA-Seq from mouse gut; ID 64 new genes #AGBT14
9:26am February 13th 2014 via Hootsuite
Chakravarti: Sema2D and Sema3C are likely ENS genes. RNA in-situ stains (perhaps ACBio technology) #AGBT14
9:20am February 13th 2014 via Hootsuite
Chakravarti: RET polymorphisms have multiple levels of regulation, 'shadow' enhancers; examine mut's in embryonic mice. Common risk #AGBT14
9:17am February 13th 2014 via Hootsuite
Chakravarti: RET-EDNRB has critical interaction; epistasis in both mice and human. Carrasquillo et al AGBT14 Publ: http://t.co/dec3MfLRNV
9:14am February 13th 2014 via Hootsuite
Chakravarti: Q: how does HSCR develop, and which genes involved? GPCR gene, RET cancer gene: It's disruption of cellular interaction AGBT14
9:12am February 13th 2014 via Hootsuite
Chakravarti: List of many genes via linkage, assoc., gene dosage - past 20y many genetic features now explained. AGBT14
9:11am February 13th 2014 via Hootsuite
Chakravarti: 1/5K Europeans; 2x Asians: no nervous supply to the gut. Multi-factor inh.; 4% recurr. risk to sibs. 4:1 male:female AGBT14
9:10am February 13th 2014 via Hootsuite
Chakravarti: Enteric Nervous System - same sets of genes expressed as CNS. Arose in echinoderms; Hirschsprung - no enteric ganglia AGBT14
9:09am February 13th 2014 via Hootsuite
Up first: A. Chakravarti (Hopkins): Hirschspring Disease AGBT14
9:06am February 13th 2014 via Hootsuite
RT @erlichya: Great summary of #AGBT14 day1 http://t.co/lxm8KoR2sA by @Genohub
9:05am February 13th 2014 via Hootsuite
Quantitative targeted RNA sequencing | PNAS http://t.co/egMBQD5aWh Barcoding individual cDNAs - an idea I first hear yrs ago h/t @sjcockell
6:23am February 13th 2014 via Hootsuite
RT @iontorrent: Caption this photo and DOWNLOAD the Amazing Century of Science calendar at http://t.co/iklF8hFIqJ http://t.co/nThwYxW1WV
4:25am February 13th 2014 via Hootsuite
RT @Genohub: Schnieder: switch now: http://t.co/0bGZivR2kq #AGBT14
6:27pm February 12th 2014 via Hootsuite
Schneider:: Existing aligners are not alt loci-aware; tools 'in development' #AGBT14
6:23pm February 12th 2014 via Hootsuite
Schneider: Using alt loci, paralogues can now be analyzed with important implications; gave example of deletion allele #AGBT14
6:21pm February 12th 2014 via Hootsuite
Schneider: Now alt loci scaffolds - capturing alternative haplotypes instead of combining them. Retain linear chromosome models. #AGBT14
6:20pm February 12th 2014 via Hootsuite
Schneider: Gave example of paralogous genes of HYDIN2 (300kb), and how sequences were mixed in prior assy; is it a SNP or not? #AGBT14
6:18pm February 12th 2014 via Hootsuite
Schneider: GRC took centromere models and filled in 3Mb gaps based on new data, should open up a new area of centromere biology #AGBT14
6:14pm February 12th 2014 via Hootsuite
Schneider: Karen Miga centromere data reference in Genome Res http://t.co/YWMdo1ixrC #AGBT14
6:11pm February 12th 2014 via Hootsuite
Schneider: Arrays vary between individuals, a complex challenge. Collab with UCSC, recently published in Genome Res #AGBT14
6:10pm February 12th 2014 via Hootsuite
Schneider: Repetitive centromeric sequence - alpha satellites, 17bp repeats. And arranged in longer arrays... #AGBT14
6:09pm February 12th 2014 via Hootsuite
Schneider: Centromere sequences are impt - and include variation. Common conception is 'difficult to seq' - but assembly is missing #AGBT14
Schneider: 100 genes now have coding alleles due to improved quality of the assembly #AGBT14
6:08pm February 12th 2014 via Hootsuite
RT @deannachurch: #agbt14 more data and stats at http://t.co/KXrYVh4Cyt and @NCBI annotation is out: http://t.co/0b5CEgXTV4 #bioinformatics
6:07pm February 12th 2014 via Hootsuite
Schneider: GRC collaborating with TGP - 15,244 with MAF=0, other areas from other groups used to update 20k bases total #AGBT14
6:05pm February 12th 2014 via Hootsuite
Schneider: Example TWIST2 gene on Chr 2, referred to Jim Knight and Stephan Schuster's poster here at mtg #AGBT14
6:03pm February 12th 2014 via Hootsuite
RT @StevenNHart: I just can't wait to go home and redo all my work from the last year. #AGBT14 #hg38
6:02pm February 12th 2014 via Hootsuite
Schneider: Other changes had not been released - 1K of them. 178 regions with alt loci; 261 alt loci scaffold. 3.6Mb sequence #AGBT14
6:01pm February 12th 2014 via Hootsuite
Schneider: 2009 rel - had alternate assembly regions. Different kinds of patches - new sequence and 'fix' patches 8MB added. #AGBT14
5:59pm February 12th 2014 via Hootsuite
Schneider: CRCh38 new assembly released Dec 24 2013. "It was time for an update... whether or not it was on your wishlist" #AGBT14
5:58pm February 12th 2014 via Hootsuite
RT @wateresa: Next up, Valerie Schneider of @NCBI on GRCh38 (hg20), the latest human #genome reference assembly. #AGBT14
5:56pm February 12th 2014 via Hootsuite
I'm enjoying @neilhall_uk 's Genome Biology piece, 'It's only human", comparing Illumina's approach to the X Ten as a cartel.
RT @becky_kusko: Too bad Jeanne Lawrence is unable to make it to #AGBT14 to give her talk, I'm so glad I was able to hear her at #ASHG
5:27pm February 12th 2014 via Hootsuite
A snowboarding hero meets cancer survivors in Sochi | Washington Post http://t.co/lJqZUmOfrQ
5:25pm February 12th 2014 via Hootsuite
