Wang #ASHG18 Genotype and phenotype connection to schizophrenia, bipolar, 81% 70% ref https://t.co/UoAs8GVLUG Now u… https://t.co/i0r3QM7tC9
1:19pm October 20th 2018 via Hootsuite Inc.
D. Wang #ASHG18 Comprehensive functional genomic resource and integrative model for the adult brain
1:18pm October 20th 2018 via Hootsuite Inc.
Claringbould #ASHG18 Announces availability of data on https://t.co/Fk48dewQOb and biorxiv preprint here https://t.co/6JFRVW2NOY
1:12pm October 20th 2018 via Hootsuite Inc.
Claringbould #ASHG18 Immune disease from scRNA-seq '18 ref https://t.co/VX4mHnyCGl Onto neuronal genes '18 ref https://t.co/hBNj1TRo0Y
1:10pm October 20th 2018 via Hootsuite Inc.
Claringbould #ASHG18 Combining cis- and trans-eQTL with polygenic score, come up with sQTL. '18 ref https://t.co/qz10oa3LVn
1:08pm October 20th 2018 via Hootsuite Inc.
Claringbould #ASHG18 Integrate RNAseq and microarray. eQTS effects on 2,568 genes. '16 ref https://t.co/abTu29rkPE
1:05pm October 20th 2018 via Hootsuite Inc.
Claringbould #ASHG18 After all GWAS, connecting to traits at the eQTL level. Trans-eQTL effects are small; setup co… https://t.co/vO7bI1rBJM
1:03pm October 20th 2018 via Hootsuite Inc.
Annique Claringbould (Univ Groningen) #ASHG18 Leveraging gene exp to understand consequences of polygenic risk scor… https://t.co/Q0eBztDtcY
1:02pm October 20th 2018 via Hootsuite Inc.
Lappalainen #ASHG18 Preprint of main and companion papers expected later this winter. Shows Huge GTEx slide of all… https://t.co/ftziZqax2v
12:57pm October 20th 2018 via Hootsuite Inc.
Lappalainen #ASHG18 Cell types contribute to allelic heterogeneity of GWAS-eQTLs. Example: platelet count data.
Lappalainen #ASHG18 Enriched for promoter flanking, enh regions; tissue-spec eQTLs. Improving GWAS interpretation:… https://t.co/xgU2kVW7Xw
12:55pm October 20th 2018 via Hootsuite Inc.
Lappalainen #ASHG18 1280 Neutrophil-interacting eQTLs in blood, and 367 neron-interactig eQTLs in brain: violin plots shown by tissue.
12:54pm October 20th 2018 via Hootsuite Inc.
Lappalainen #ASHG18 Now looking at cell-type composition across 64 celltypes; key importance for interpreting varia… https://t.co/yTh8jDd8of
12:53pm October 20th 2018 via Hootsuite Inc.
Lappalainen #ASHG18 Tissue sharing of reg variation data shown; also mechanisms of tissue-specificity. Post-xcr pro… https://t.co/MnzAT8Ozud
12:52pm October 20th 2018 via Hootsuite Inc.
Lappalainen #ASHG18 Found 178 genes with trans-eQTLs. 25K eQTLs have highly likely consensus causal reg variants
12:50pm October 20th 2018 via Hootsuite Inc.
Lappalainen #ASHG18 Harmonized GWAS data with 114 traits too. Expression and splicing of QTLs in cis and trans: 95%… https://t.co/SJioaVPfR5
12:49pm October 20th 2018 via Hootsuite Inc.
Lappalainen #ASHG18 Raw, derived data 17,382 post-mortem tissue samples, 54 tissues, 838 donors. mRNA-Seq data; 30x… https://t.co/9S8ckebL19
12:48pm October 20th 2018 via Hootsuite Inc.
Lappalainen #ASHG18 Scalable interpretation of GWAS loci, regulatory code, inspiration of GTEx started in '10; '15… https://t.co/9DwMLYylKt
12:47pm October 20th 2018 via Hootsuite Inc.
#ASHG18 Session Genetic and Epigenetic effects on the Transcriptome T Lappalainen The GTEx Consortium atlas of gene… https://t.co/9fspjnqrOy
12:46pm October 20th 2018 via Hootsuite Inc.
Xu: #ASHG18 Shows interesting cMyc expression with large SV detection '18 Nature Genet https://t.co/MVCidt5q0l Also ERBB4 in br ca line
12:26pm October 20th 2018 via Hootsuite Inc.
Xu: #ASHG18 Validated this method via FISH. Formation of 'neo-TADs'. Showing high c-MYC exp in neuroblastoma, assoc'd with large SVs
12:24pm October 20th 2018 via Hootsuite Inc.
Xu: #ASHG18 Developed algorithm to look at inter-chr xl - mapping to reference, gives examples of del and inv as we… https://t.co/6kbCugh07o
12:23pm October 20th 2018 via Hootsuite Inc.
Xu: #ASHG18 Shows translocation and inversion in cancer line. Now onto Hi-C for detection of long-distance, inter-chr translocations.
12:21pm October 20th 2018 via Hootsuite Inc.
Xu: #ASHG18 Shows a scan, 150Kb - 250Kb in length, labeled and mapped by Irys (Bionano's system). NB - description… https://t.co/bICOuImqwB
12:19pm October 20th 2018 via Hootsuite Inc.
Xu: #ASHG18 Lays out method - nicking, GFP green dyes into nick, leaded and read. Shows neat movie of the BNG method.
12:18pm October 20th 2018 via Hootsuite Inc.
Xu: #ASHG18 49% of genome is repetitive; thus with WGS can't effectively detect SVs. These SINE elements can be ove… https://t.co/F2xmJtURyV
Jie Xu (Penn State) #ASHG18 Structural Variation and its impact on 3D genome structure in cancer cells
12:16pm October 20th 2018 via Hootsuite Inc.
Reilly #ASHG18 ID a strong growth defect 'clinically relevant phenotype'. Shows KO, restored fn, showed ChIP data,… https://t.co/zwyd1FMjug
12:14pm October 20th 2018 via Hootsuite Inc.
Reilly #ASHG18 CRISPR knockouts and inh ID distinct sets of elements: see enrichments for essential genes.
12:12pm October 20th 2018 via Hootsuite Inc.
Reilly #ASHG18 TF enrichment at sig CTCF hits; distance, then TF enrichment for particular TFs. Enrichment highest… https://t.co/dXYH3kru6G
12:10pm October 20th 2018 via Hootsuite Inc.
Reilly #ASHG18 Plots 5K neg growth genome-wide, shows CTCF hit 'hotspots', enriched near xl boundaries.
12:08pm October 20th 2018 via Hootsuite Inc.
Reilly #ASHG18 Guides that cut in the core CTCF motifs are most significant. Close to essential genes. Groth in CTC… https://t.co/Zr1MT3eaX0
Reilly #ASHG18 Shows data from 96K perturbations. Controls depleted for growth effects; off-target effects are stri… https://t.co/3qOnbIINWw
12:06pm October 20th 2018 via Hootsuite Inc.
Reilly #ASHG18 '15 PNAS ref https://t.co/r4ARryr2aE Walks thru method - integrates ChIP-Seq to ChIA-PET Hi-C, w/96K… https://t.co/k5O32y61WA
12:05pm October 20th 2018 via Hootsuite Inc.
Rielly #ASHG18 Sabetti's lab - looking for non-coding var that work genome-wide. CTCF is an ideal target - motif de… https://t.co/vn0TtS1GEf
12:03pm October 20th 2018 via Hootsuite Inc.
Steven Rielly (Broad) #ASHG18 Using multiplex non-coding CRISPR deletion libraries to individually perturb CTCF bin… https://t.co/ulQzwnTbzr
12:02pm October 20th 2018 via Hootsuite Inc.
Plewcczynski #ASHG18 Looking at gene exp, built eQTLs and mapped onto struct features. Measured <5K variant chr loo… https://t.co/TKZ0AQ4
12:00pm October 20th 2018 via Hootsuite Inc.
Plewcczynski #ASHG18 Looking at 1K Genome project individuals, can view seq var, chr loops, and ChIP-Seq binding with different genotypes.
11:57am October 20th 2018 via Hootsuite Inc.
Plewcczynski #ASHG18 Allows to see change in 3D structure with deletions, duplications, inversions, insertions (!)
11:56am October 20th 2018 via Hootsuite Inc.
Plewcczynski #ASHG18 Infl of sequence var with interaction loops. 'The methodolgy is simple - it fits one slide'. https://t.co/ShlvnKjBNU
Plewcczynski #ASHG18 Affect of CTCF-mediated 3D genome architecture - '16 ref https://t.co/RPSBWLBHAY on their first model of 3D GNOME
11:55am October 20th 2018 via Hootsuite Inc.
Plewcczynski #ASHG18 Use ChIA-PET and recapitulate Hi-C data Shows data from '15 Cell https://t.co/YwIZd5iKFS with comparative approach
11:52am October 20th 2018 via Hootsuite Inc.
Plewcczynski #ASHG18 Major Q's: genomic interaction targets frequent target for SV's? How does SNPs influence looping? Impact of gene exp?
11:51am October 20th 2018 via Hootsuite Inc.
Plewcczynski #ASHG18 Now collab with JAX; 4D Nucleome NIH project described here https://t.co/CP6ZmPR1ta Sequence infl chromatin structure
11:50am October 20th 2018 via Hootsuite Inc.
Plewcczynski #ASHG18 Points out that it was the 3D structure that nucleic acids were first discovered and character… https://t.co/WT2YAm8X37
11:48am October 20th 2018 via Hootsuite Inc.
Dariusz Plewcczynski (Univ Warsaw) #ASHG18 3D GNOME 2.0 modeling engine of human genome structure at the population level
11:47am October 20th 2018 via Hootsuite Inc.
Eres: #ASHG18 Shows chr to chr differences on a global scale. Summarizes - preprint on the way Yoav Gilad lab, webs… https://t.co/tXwfONmap9
11:43am October 20th 2018 via Hootsuite Inc.
Eres: #ASHG18 Volcano plot - contact freq differences, 'locus-locus contacts are generally conserved in iPSCs' at 5% FDR.
11:37am October 20th 2018 via Hootsuite Inc.
Eres: #ASHG18 Calling sig orthology - complex and difficult, due to ref seq quality differences. Shows unsupervised… https://t.co/JlfC7AoY3T
11:36am October 20th 2018 via Hootsuite Inc.
Eres: #ASHG18 Used iPSC from Chimpanzees, humans. And used Hi-C, along with RNA-Seq data. Thus: 3D and expression Q's to answer.
11:34am October 20th 2018 via Hootsuite Inc.
