Hoischen: If the fetal fraction is 10%, only 330 fetal genome copies, for het is only 165 molecules. smMIP can be strand-spec #AGBT16
7:40pm February 11th 2016 via Hootsuite
Hoischen: 2nd app - monogenic NIPT - not NIPT for anueploidy, but for inherited disease #. cfDNA about 10ng, 3300 haploid genomes AGBT16
7:39pm February 11th 2016 via Hootsuite
Hoischen: Timing of de novo mutations - some are inherited from a mosaic parent (!) May have recurrence risk #AGBT16
Hoischen RT @frapaport: AH : MIPs were upgraded to single molecule smMIPs https://t.co/XFtbAO4fIS #AGBT16
7:38pm February 11th 2016 via Hootsuite
Alex Hoischen (Radboud Univ Nijmegen NL) ultra-sensitive mosaic mut. detection for clinical applications #ASHG16 https://t.co/FcBci3FVOj
7:36pm February 11th 2016 via Hootsuite
Burgess:Std Oncology panels with 345 genes, 5.1K probes; smaller one with 53 genes, 635 probees. Custom to go to 1MB, 420 genes #AGBT16
1:50pm February 11th 2016 via Hootsuite
Burgess: Software for probe design, variable efficiency, need for balancing probes and buffers #AGBT16
1:43pm February 11th 2016 via Hootsuite
Burgess: Claims MIPS 'not more widely used' due to no 'off the shelf' commercial solution, and home-brew is hard #AGBT16
1:42pm February 11th 2016 via Hootsuite
Burgess: High Efficiency Amplification Targets - an advanced version of MIPS. Goes back to 1988, Lee Hood #AGBT16
Dan Burgess (Roche) HEAT-Seq massively parallel molecular inversion probes for targeted sequencing #AGBT16
1:36pm February 11th 2016 via Hootsuite
Wylie:Q:How modifiable is this panel? A: Can be done in a few hours, still sequence homology will pick up alternates #AGBT16
1:35pm February 11th 2016 via Hootsuite
Wylie: And then was able to quickly able to dev a real-time PCR assay for tracking. #AGBT16
1:32pm February 11th 2016 via Hootsuite
Wylie: Entervovirus D68 was dominant type in the US in 2014; found in all 50 states. Was able to rapidly enrich and sequence #AGBT16
RT @jgreid: Big question at #AGBT16 SV lunch -- "How do we know when two SVs are the same?" Seems simple, but it is not.
1:27pm February 11th 2016 via Hootsuite
RT @DukeSequencing: Sequel looks pretty cool. On my wish list for sure :)@erichjarvis @PacBio #AGBT16 https://t.co/TV1DU5s9hE
1:26pm February 11th 2016 via Hootsuite
Wylie: 34 viral families, 190 genera, 337 spp - both RNA and DNA. Charted sequence capture capacity - NimbleGen 200MB largest #AGBT16
1:25pm February 11th 2016 via Hootsuite
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
