If you want to see @nanopore ‘sequence tasting’ @mattloose has a crowd at #AGBT16 https://t.co/dV7333I9I5
5:41pm February 12th 2016 via Hootsuite
.@GraveleyLab Yes - science as something of a competitive sport.
4:34pm February 12th 2016 via Hootsuite in reply to GraveleyLab
.@h2so4hurts Next best thing to being here! :)
4:33pm February 12th 2016 via Hootsuite in reply to h2so4hurts
Furlan: But Monocle could collapse into 2D, all experiments and conditions. ID'ing DEG across cell-types: 48,988 cells, 6K DEGs #AGBT16
4:32pm February 12th 2016 via Hootsuite
Furlan: Via RNA-seq, identifying structure from single-cell RNA-seq data (pretty 3D globe-style, colored PCA graph) #AGBT16
4:31pm February 12th 2016 via Hootsuite
Furlan:Can separate by flow - use 10X get 2K cells/sample Cole Trapnell dev SW called Monocle for analysis. #AGBT16
4:30pm February 12th 2016 via Hootsuite
Furlan: Single-cell approach to GVHD, using a mixed lymphocyte reaction. Harvest from 2 people - one irradiated, another dyed #AGBT16
4:28pm February 12th 2016 via Hootsuite
Furlan: GVHD: Flow can only query limited number of markers. 'Complexity of tools need to meet complexity of disease' #AGBT16
4:27pm February 12th 2016 via Hootsuite
Scott Furlan (Univ Washington) #AGBT16 Studying the immune system at scale.
4:26pm February 12th 2016 via Hootsuite
NB I need to read @cigenomics and @omicsomicsblog posts on @10xgenomics https://t.co/fHSNcz4gRa and https://t.co/JOtJ8MOYT4. Or just sleep.
4:24pm February 12th 2016 via Hootsuite
Gabriel: Used NA12878, both forms of C4 are present in b37 reference; 'allows us to directly obs phased C4 haplotypes w/o trios' #AGBT16
4:22pm February 12th 2016 via Hootsuite
Gabriel: Major schizophrenia discovery Nature '16 https://t.co/Ai8JV1tiJv on C4 association in MHC; could linked reads have helped? #AGBT16
4:20pm February 12th 2016 via Hootsuite
Gabriel: [Loose-end rescue' to resolve complex tumor re-arrangements. #AGBT16
4:18pm February 12th 2016 via Hootsuite
Gabriel: 8-11Mb phase-blocks. 125kb lengths. #AGBT16
4:15pm February 12th 2016 via Hootsuite
Gabriel: Dan MacArthur picked 4 lines with Titan muts (largest gene in the genome, most difficult to deal with). 1 ng WES #AGBT16
Gabriel T @shgoodwin1: SG: GemCode chromium seems easy to use and scalable. Do need to be gentle with long fragment input DNA #AGBT16
4:14pm February 12th 2016 via Hootsuite
Gabriel RT @TorontoGenomics: SG: working routinely with 1.2 ng DNA #AGBT16
4:13pm February 12th 2016 via Hootsuite
ICYMI: The Genome Technology of #AGBT16 https://t.co/0M98ZpOsG8
4:10pm February 12th 2016 via Hootsuite
Gabriel: Populations, Mendelian, Cancer. Rare disease / cancer can use 10X. ~30 samples processed. Goal assess bias, SNP calling #AGBT16
4:08pm February 12th 2016 via Hootsuite
Gabriel: Context of scale, comparing '06 vs '15: 60Mb vs 5Pb. From 1 human genome to 32,693 #AGBT16
4:05pm February 12th 2016 via Hootsuite
Stacey Gabriel (Broad) The power of linked long reads in human sequencing applications #AGBT16
4:03pm February 12th 2016 via Hootsuite
RT @CIgenomics: Covering the @10xgenomics launch at #AGBT16 https://t.co/mHZQXwEckA
4:02pm February 12th 2016 via Hootsuite
Schnall-Levin: Single-cell RNA-seq using bacodes for human transcriptome. PCA clusters 3 cell lines #AGBT16
4:01pm February 12th 2016 via Hootsuite
Schnall-Levin: Eml4-Alk fusion for Neimann Pick disease compound het. Stacey G, Hakon H will speak later about Titan, others #AGBT16
4:00pm February 12th 2016 via Hootsuite
Michael Schnall-Levin (10X Genomics): Chromium exome does Agilent pull-down with optimized baits, w/rescued regions #AGBT16
3:58pm February 12th 2016 via Hootsuite
RT @KMS_Meltzy: Comic Sans #BINGO #AGBT16
3:38pm February 12th 2016 via Hootsuite
Nickerson:Q:Carrier testing? A:In ClinVar is shared. #AGBT16
Nickerson: Rare Disease Day is coming Feb 29 - can you support it? https://t.co/wrN9UXzaZN #AGBT16
3:37pm February 12th 2016 via Hootsuite
Nickerson: Developng 'MyGene2' where parents of children can get involved. 'We need to think about this for cancer too' #AGBT16
3:35pm February 12th 2016 via Hootsuite
Nickerson: Social media is being used by parents of children with rare disease New Yorker https://t.co/d8EYb6DgPX the Might family #AGBT16
Nickerson: Also mentions Genotype to Mendelian Phenotype https://t.co/2Wbu7a2XUW to promote gene discovery #AGBT16
3:32pm February 12th 2016 via Hootsuite
Nickerson: Mentions GeneMatcher for those with interest in the same gene '15 ref https://t.co/LBesqkGeIJ #AGBT16
3:31pm February 12th 2016 via Hootsuite
Nickerson: What do we mis with exomes? SVs, indels, and impactful var's in non-coding regions #AGBT16
3:30pm February 12th 2016 via Hootsuite
Nickerson: Solve rates is average 55%; solve rate for recessives is 95%. Missing some variation (SVs, indels that are larger) #AGBT16
3:25pm February 12th 2016 via Hootsuite
Nickerson: Mosaicism is important - could explain incomplete penetrance. Hemizygosity in males '13 ref https://t.co/CVbT1lXsxg #AGBT16
3:24pm February 12th 2016 via Hootsuite
Nickerson: Otitis Media - chronic ear infections '15 Nat Genet https://t.co/EZxvZLqffu Novel dupl var, LOD 7.5 Circular pedigree! #AGBT16
3:22pm February 12th 2016 via Hootsuite
Nickerson: Congen heart disease - H3K4 ass'd, Science '15 paper https://t.co/QjhzkIVqfZ 'every child w/this needs to be sequenced' #AGBT16
3:20pm February 12th 2016 via Hootsuite
Nickerson: One case:acromelic frontonasal dysostosis, where father had a slightly flat nose but child severe https://t.co/1npZb5TZMj #AGBT16
3:18pm February 12th 2016 via Hootsuite
Nickerson: Analysis - WES of affecteds, filter var's based on genetic model (de novo, dominant or recessive), filter on allele freq #AGBT16
3:12pm February 12th 2016 via Hootsuite
Nickerson: Genetic models: never sure if it's de novo or dominant, because they are so rare. #AGBT16
Nickerson: There is a 'need for more and robust phenotype information' due to the difficulty of association with low-penetrant genes #AGBT16
3:11pm February 12th 2016 via Hootsuite
Nickerson: ~7700 in OMIM, ~300/y solved, 1/100,000 rare, and hard due to incomplete penetrance or multi-gene effects #AGBT16
3:10pm February 12th 2016 via Hootsuite
Debbie Nickerson, (Univ Washington) “Scaling Mendelian genomics” #AGBT16
3:09pm February 12th 2016 via Hootsuite
Varmus: Splicing pattern of U2AF1-S34F (knock-in, inducible mutant) in mouse resembles human cancer, no obvious phenotype in mice. #AGBT16
2:26pm February 12th 2016 via Hootsuite
Varmus: Build mouse models that had inducible splicing-factor mutations. Data shows WT-U2AF1 essential for viability. #AGBT16
2:24pm February 12th 2016 via Hootsuite
RT @mason_lab: #AGBT16 My slides from Plenary Session: Space Genetics, long reads, and inter-planetary technology! https://t.co/TFAU0ViZCu
2:18pm February 12th 2016 via Hootsuite
Varmus: Story 2: Splicing factor genes in myeloid neoplasms: implications for U2AF1 found in many tumor types. a surprise #AGBT16
2:17pm February 12th 2016 via Hootsuite
Varmus: Ref to this '06 Cancer Res https://t.co/XGNhLArXDD work on melanoma #AGBT16
2:15pm February 12th 2016 via Hootsuite
Varmus: BRAF and NRAS Q61C in melanoma do not co-express, perhaps another oncogene combination #AGBT16
2:14pm February 12th 2016 via Hootsuite
Varmus' work on synthetic lethality explanation of KRAS and EGFR mutation exclusivity MT @frapaport: eLife https://t.co/GZho1Z2B19 #AGBT16
2:12pm February 12th 2016 via Hootsuite
