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.
Eres: #ASHG18 Comparative gene regulation in non-human primates - diff exp. Shows many studies - not sufficient on the gene exp level.
11:33am October 20th 2018 via Hootsuite Inc.
Good morning #ASHG18 - Investigating 3D Genome Structure. Ittai Eres (Univ Chicago) Reorganization of 3D genome str… https://t.co/navEXD7BA1
11:32am October 20th 2018 via Hootsuite Inc.
RT @Bhoomiee: Data showing low precision in measurements, ease your woes with #FridayFeeling #Copied @palomaperezbel1 please see!! https://…
9:12am October 20th 2018 via Buffer
RT @colinhillucc: Is it time to stop measuring, and put the ‘ology’ back into microbiome research? https://t.co/28jpRGZdlG #behindthepaper
8:08am October 20th 2018 via Buffer
At #ASHG18, Singlera Genomics Presents Data on Cell-Free DNA Methylation Test for Early Cancer Detection | GenomeWe… https://t.co/Nn8hIKNlpc
12:31am October 19th 2018 via Buffer
A LOT of receptions to join in at the Hilton Bayfront at@#ASHG18! Join @singlerinc in Salon A/B https://t.co/iv8UczRmBN
9:30pm October 18th 2018 via Hootsuite Inc.
All at #ASHG18 are welcome to attend a joint UCSD @singlerainc reception at the Hilton Bayside Hotel (past Hall H t… https://t.co/yEHufTBisX
9:09pm October 18th 2018 via Hootsuite Inc.
@singlerainc announces at #ASHG18 the results of a 10-year, 120,000-participant longitudinal study, where cancer co… https://t.co/GLTDovKQES
8:27pm October 18th 2018 via Hootsuite Inc.
@singlerainc announces at #ASHG18 the results of a 10-year, 120,000-participant longitudinal study, where cancer co… https://t.co/APPoKkLnoN
6:09pm October 18th 2018 via Hootsuite Inc.
#ASHG18 #earlydetection @singlerainc announces early-detection of Colorectal Cancer (CRC) and even Advanced Adenoma https://t.co/3TlBytVTlf
3:24pm October 18th 2018 via Hootsuite Inc.
Gore #ASHG18 Now a prospective study is needed, to intervene to change pt outcomes. A study they hope to do in the… https://t.co/lYcV14RpiN
12:59pm October 18th 2018 via Hootsuite Inc.
Gore #ASHG18 Poster yesterday, booth 445. Concludes: power of methylation haplotypes in asymptomatic patients. Pote… https://t.co/0UFw4zPere
12:58pm October 18th 2018 via Hootsuite Inc.
Gore #ASHG18 We don't think we are predicting cancer; we think we are just picking up the signals of cancer already… https://t.co/heUEar6QjS
12:57pm October 18th 2018 via Hootsuite Inc.
Gore #ASHG18 100% sens in CRC, liver. Pre-diagnosis: found in asymptomatic indiv's up to 4y before conventional dx (!!)
Gore #ASHG18 Divided 30% into training set, locked the model, looked at 837 (70%). 5 types of cancer. CRC, esophage… https://t.co/ApKKszdHXg
12:56pm October 18th 2018 via Hootsuite Inc.
Gore #ASHG18 Looking for haplotypes means looking for patterns, rather than 'individual averages'. Spec methylation signals in cis.
12:55pm October 18th 2018 via Hootsuite Inc.
