Wylie:Found unexpected pathogens, not included in a typical panel (eg Astrovirus).Impt to be comprehensive. #AGBT16
1:24pm February 11th 2016 via Hootsuite
Wylie: Second study in febrile children (unexplained fever), both for RNA and DNA viruses. Many diff types of viruses found #AGBT16
1:23pm February 11th 2016 via Hootsuite
Wylie: Vriome can be eukaryotic - look at 100 healthy, 10 body sites. People carry a lot of viruses from many genera. #AGBT16
1:21pm February 11th 2016 via Hootsuite
Wylie: This work was published recently in Genome Res https://t.co/uxjKCqQIRl #AGBT16
1:20pm February 11th 2016 via Hootsuite
Now at the Roche workshop: Kristine Wylie (Washu) "ViroCap - enhance virome seuquencing using targeted sequence capture" #AGBT16
1:19pm February 11th 2016 via Hootsuite
Mason: Many other assays planned - long list, proteomics, allele-spec expression, hydroxymethylation #AGBT16
1:05pm February 11th 2016 via Hootsuite
Mason: Can see drops in coverage when SV's appear. Se TDG gene transposition. #AGBT16
Mason: Cells overall look pretty good, use AllPrep for both DNA/RNA; Used 10X Genomics of 20kb - 100kb 1.4M-1.5M GEMs detected #AGBT16
1:03pm February 11th 2016 via Hootsuite
Mason: They even have a NASA patch! Launch just happened, blood drawn, only 36h in orbit. #AGBT16
1:01pm February 11th 2016 via Hootsuite
Mason: Scott Kelly @StationCDRKelly has a 'superb Twitter feed'. Longitudinal systems biology as one of two twins #AGBT16
Mason: Has a MoBio 5-enzyme cocktail (with ABRF), to improve extraction efficiency #AGBT16
1:00pm February 11th 2016 via Hootsuite
Mason: MetaSUB 2.0 working with CLC - getting any sample from any part of the body; and know taxa. # of spp betw. tools close #AGBT16
12:59pm February 11th 2016 via Hootsuite
Mason: Ref Shendure's PLOS Genet https://t.co/IbuMOB5KAc 'a year of infection in the ICU' 'waiting 3w for a culture is un-ethical' #AGBT16
12:56pm February 11th 2016 via Hootsuite
Mason: The clinical context - precision metagenomics. Live and antibiotic res bacteria: metagenomics reveals distribution of tet-R #AGBT16
12:55pm February 11th 2016 via Hootsuite
Mason: The extreme environment: looking for biosynthetic gene clusters - new small molecules made by microbes even in the subway #AGBT16
12:54pm February 11th 2016 via Hootsuite
Mason: Now the 'Olympiome' in Rio 2016: looking at the urban microbiome before, during and after. Tokyo 2020 #AGBT16
12:53pm February 11th 2016 via Hootsuite
Mason: Uses QIAseqFX for environmental samples, 'mechanical-quality fragmentation' #AGBT16
12:51pm February 11th 2016 via Hootsuite
Mason: New project MetaSUB - Subways and Urban Biomes, now up to 45 cities. (Paper under review.) #AGBT16
Mason:Showed spatial genetic data for white, asian, yoruban, and puerto rican alleles by geography of the subway map #AGBT16
12:48pm February 11th 2016 via Hootsuite
Mason: Mentions Rob Knight's TED talk in the context of the hygiene hypothesis https://t.co/z2yV4BPfM5 #AGBT16
12:46pm February 11th 2016 via Hootsuite
Mason: One spp was from Antarctica, producing a healthy type of fat found in fish. 'Licking subway poles probably fine' says Expert #AGBT16
12:44pm February 11th 2016 via Hootsuite
Mason: Showed interesting stacked chart of an hourly microbiome map. One Gowanus Canal, 'a methanogen haven' due to type of waste #AGBT16
12:42pm February 11th 2016 via Hootsuite
Mason: #AGBT16 Data is live at Pathomap: https://t.co/cINJacTNOx 600 spp ride the subway with you.
12:41pm February 11th 2016 via Hootsuite
Mason: What about NYC subways? Dec 2013, using GIS cloud, a city-scale 'metropolome' 1/2 the DNA is unknown. #AGBT16
12:39pm February 11th 2016 via Hootsuite
Mason: On to microbiome, cool video on the view of life from the microbe's point of view. We're covered, it's everywhere... #AGBT16
12:36pm February 11th 2016 via Hootsuite
Mason: 96 genes x 140 samples, about 50c per target. 'Very happy with this data.' #AGBT16
12:35pm February 11th 2016 via Hootsuite
Mason: Ran library on 1x160 NextSeq, saw switch of leukemia genes in normal bone marrow. #AGBT16
12:34pm February 11th 2016 via Hootsuite
Mason: 6h library prep, worked first time. 'Very good perf metrics' using ERCC material. #AGBT16
12:32pm February 11th 2016 via Hootsuite
Mason: Had 140pt, WES, RRBS, RNA-seq. Only 10ng RNA left. They generated UMIs (for single-molecule barcoding) #AGBT16
Mason: Purine nucleoside treatment - cells were resistant to apoptosis. But muts were hiding at very low levels. #AGBT16
12:30pm February 11th 2016 via Hootsuite
Mason:But lncRNAs are hiding at low-levels. chemo-res clones in ALL: found early relapse resistance mut's #AGBT16
12:29pm February 11th 2016 via Hootsuite
Mason: Shows nice slide of varying methods of sequencing RNA; 19,815 coding, 25,823 non-coding, 14,505 pseudogenes. Some 60K total #AGBT16
12:28pm February 11th 2016 via Hootsuite
Mason: Reviews DEGs (diff expressed genes) Venn diagram: how much richer the data is via RNA-Seq compared to just amts #AGBT16
12:27pm February 11th 2016 via Hootsuite
Whoops, Chris' affiliation is not Columbia, Weill Cornell. Refers to ENCODE as 80% of the genome having some function. #AGBT16
12:26pm February 11th 2016 via Hootsuite
.@mason_lab Chris Mason (Columbia): 'Targeted RNA sequencing, urban metagenomics, and astronaut genetics" #AGBT16
12:25pm February 11th 2016 via Hootsuite
Gammack: Mentions their recent collab w/ @10Xgenomics to drive 'unique insights' #AGBT16
12:24pm February 11th 2016 via Hootsuite
Gammack: They ahve 120K users of their bioinformatics products; >420K sequenced samples uploeaded to Ingenuity cloud #AGBT16
12:23pm February 11th 2016 via Hootsuite
Gammack:Introduces GeneReader, #AGBT16 BTW I wrote it up here: https://t.co/TrJKYPFcHj
12:21pm February 11th 2016 via Hootsuite
Gammack: Mentions QIAseq, their new name for targeted sequencing enrichment; both for targeted RNA-Seq as well as gene panels #AGBT16
12:19pm February 11th 2016 via Hootsuite
Jason Gammack of @QIAGEN introducing their lunchtime workshop at #AGBT16 https://t.co/Zl0GeM0gUK
Sol-Church: One a genetic mutation, another an epigenetic phenomenon: everyone is accounted for in pedigree #AGBT16
12:02pm February 11th 2016 via Hootsuite
Sol-Church: No maternal SNPs were transmitted to offspring.BsrF1 digestion uncovers 'hidden allele'. Turned out to be methyl-sens! #AGBT16
12:00pm February 11th 2016 via Hootsuite
For those listening to #AGBT16 wondering about stats, here's the @symplur analysis https://t.co/L62eiJy13W
11:56am February 11th 2016 via Hootsuite
.@CIgenomics I was told that @nanostringtech will have cool USB light-bulbs ronight (to match the cool batteries in our #AGBT16 backpacks
11:54am February 11th 2016 via Hootsuite in reply to CIgenomics
Sol-Church: XYLT1 - fn is first step in glysosaminoglycan (GAG) chain elongation; affecting ECM and cartilage formation #AGBT16
11:52am February 11th 2016 via Hootsuite
Sol-Church: Went from SOLiD to ILMN but it wasn't the technology; one had splice var XYLT1. Looked for CNV: found 3MB del in 3/7 #AGBT16
11:50am February 11th 2016 via Hootsuite
Sol-Church: Flattened mid-face, broad nasal bridge, cleft palate, dev delay. Resembles Desbuquois (CANT1) #AGBT16
11:49am February 11th 2016 via Hootsuite
Sol-Church: Baratela Scott Syndr. rare recessive, mental disability well-hidden by children, 7 boys from 6 families, not X-linked #AGBT16
Sol-Church: Their work acknowledges the Center for Mendelian Genomics (UW and JHU); researchers, clinicians, community #AGBT16
11:45am February 11th 2016 via Hootsuite
Katia Sol-Church (duPont Hospital for Children) Baratela Scott Syndrome is a rare recessive skeletal dysplasia #AGBT16
11:43am February 11th 2016 via Hootsuite
