MS: Respiratory viruses - play a role in disease onset. RSV inf has OR 2.6; HRV OR 9.8. URTI affects lower airway #AGBT15
9:14pm February 26th 2015 via Hootsuite
MS Cells that line airway important - cilia + goblet mucus-prod cells; asthma is GxE interactions. #AGBT15
9:12pm February 26th 2015 via Hootsuite
MS Airway epithelium - using RNA-seq to also look at respiratory viruses. Asthma is an airway disease w/ complex etiology #AGBT15
9:11pm February 26th 2015 via Hootsuite
Max Seibold, National Jewish Health “Integrated RNA-Seq of Host and Microbe in the Nasal Airway of Childhood Asthmatics” #AGBT15
9:10pm February 26th 2015 via Hootsuite
RL: Not solved yet but steps made toward original aim. Microfluidics not yet, want to speed up library prep and make mobile. #AGBT15
9:07pm February 26th 2015 via Hootsuite
RL: Showed embedded Raspberry Pi movie, w/ same analysis for field deployment. #AGBT15
9:06pm February 26th 2015 via Hootsuite
RL: Best fragment size on the order of 500-2kb length #AGBT15
RL: Opt yield: don't need very long reads for this application; took lambda HindIII digest, seq on MinION shows reads/length #AGBT15
9:05pm February 26th 2015 via Hootsuite
RL: Greenhouse, outside tree air sampled; findings were consistent. #AGBT15
9:04pm February 26th 2015 via Hootsuite
RL: Venn diagram of spp counts: 1391 illumina, 41 oxford, 99 common. #AGBT15
9:03pm February 26th 2015 via Hootsuite
RL: Air-seq: 100-300L air/min; 10^9 enrichment; 1000L air -> 1ul DNA. illumina lib -> @nanopore library #AGBT15
RL: At low, med & high G-C - graph of k-mers, build a tool based around kmers and compared to library; called 'Kontaminant' #AGBT15
9:00pm February 26th 2015 via Hootsuite
RL: Longest stretch of perfect bases - 302bp. Finds k-mer similarity. #AGBT15
8:59pm February 26th 2015 via Hootsuite
RL:Metagenomics on MinION: HMP mock community, 20 diverse bacteria; 20K reads, 98% aligning to one of the references #AGBT15
8:57pm February 26th 2015 via Hootsuite
RL: Build NanoOK to generate FASTA, quality stats, PDF report. Finds most reads aligning, 80-85% accurate. Stretches of perfect seq #AGBT15
8:56pm February 26th 2015 via Hootsuite
RL:512 pores, simple sample prep, inexpensive; long reads. Trend is upwards - better quality and yield. 'It actually works.' #AGBT15
8:54pm February 26th 2015 via Hootsuite
RL: Early access since April 14; experience 'effectively alpha or beta'; 'frequent updates'. #AGBT15
8:53pm February 26th 2015 via Hootsuite
RL:Perhaps combination of MinION + microfluidics + cloud computing? Is it practical? #AGBT15
8:52pm February 26th 2015 via Hootsuite
RL: One of the first @nanopore talks here. Aim: in-field surveillance. Env monitoring of air. #AGBT15
Richard Leggett, The Genome Analysis Centre UK “Towards Real-Time Surveillance Approaches Using Nanopore Sequencers” #AGBT15
8:49pm February 26th 2015 via Hootsuite
BW: Mainly gene bodies, promoters and fn elements; tissue-spec, sometimes not the proper cell types avail. #AGBT15
8:42pm February 26th 2015 via Hootsuite
BW: Used Agilent methyl-seq capture (84Mbp), >10x increase in diff methylated C's. 80% hypomethylation agrees w/previous obs. #AGBT15
8:41pm February 26th 2015 via Hootsuite
BW: See up-regulation; example of 2 genes shown, NXF3 and RUFY4. Data suggested epigenetic priming in vitro #AGBT15
8:40pm February 26th 2015 via Hootsuite
BW: Cp of model data to pt data: filtered consistent genes against normal RNA-Seq data, potential biomarkers & therapeutic targets #AGBT
8:39pm February 26th 2015 via Hootsuite
BW: Exp signatures recapitulated; showed changes in AML reg networks. #AGBT15
8:38pm February 26th 2015 via Hootsuite
BW: Barabe et al Science 2007 paper: http://t.co/QoRfuCydjl Model in mice; less noice than in original pts. #AGBT15
BW: Adapt human cord blood model system; healthy cord blood from single donor, use retrovirus, expanded, xenografted #AGBT15
8:36pm February 26th 2015 via Hootsuite
BW: Celton 2014 ref: http://t.co/QRcim8XMLz for GATA2. 'Complex recomb. of SNVs are not experimentally tractable' #AGBT15
8:35pm February 26th 2015 via Hootsuite
BW: 430 adult AML, RNA-Seq. 'Long tail is more like a deep pool' Many examples of germ-line contributions - GATA2 example #AGBT15
8:33pm February 26th 2015 via Hootsuite
BW: Begins with figure from 24 br ca samples from Stratton's 2009 Nature paper http://t.co/SqLlJJgn5o 'long tail' of mutations #AGBT15
8:31pm February 26th 2015 via Hootsuite
Brian Wilhelm, Univ Montreal “Integrated Genetic and Epigenetic Analysis of Model and Patient Acute Myeloid Leukemias” #AGBT15
8:30pm February 26th 2015 via Hootsuite
.@bioinfomagician Never mind! <confusion cleared up>
8:18pm February 26th 2015 via Hootsuite in reply to
.@bioinfomagician Is it Lab7 Systems or Seven Bridges? Thx.
8:17pm February 26th 2015 via Hootsuite in reply to
JK: 10 AML samples; no normal tissue; low-coverage WGS and RNA-Seq. Unpublished data, will honor request #AGBT15
8:15pm February 26th 2015 via Hootsuite
JK:Chr banding most common for cytogenetics; another method multiplex FISH; third is aCGH '05 Nature Rev Gen http://t.co/g9xbef4M03 #AGBT15
8:14pm February 26th 2015 via Hootsuite
JK: Listed common translocations; 2013 NEJM piece: http://t.co/ChKYOTdqWt #AGBT15
8:12pm February 26th 2015 via Hootsuite
JK:Can we use NGS to complement or replace trad methods? Leukemia - ALL is blockage of certain differentiation; blasts result #AGBT15
8:10pm February 26th 2015 via Hootsuite
Jaeseung Kim, Ontario Inst Cancer Res “Identification of Cryptic Genomic Lesions in Complex Karyotype Leukemia” #AGBT15
8:09pm February 26th 2015 via Hootsuite
(Foundation) Q:Did you look at structure overall? A:No, mut freq for targeted approach similar tho #AGBT15
8:04pm February 26th 2015 via Hootsuite
(Foundation) Bargraph of genomic landscape of PACC's distinct from other panc tumors #AGBT15
7:59pm February 26th 2015 via Hootsuite
(Foundation) IHC for p-ERK:6/7 positive; neg samples 6/28 stain positive. 4 had other MAPK activating events #AGBT15
7:58pm February 26th 2015 via Hootsuite
(Foundation) Vanderbilt's W. Pau - functional char of SND1-BRAF activates MAPK pathway; tested MEK inhibitor, pan-RAF inh in models #AGBT15
7:57pm February 26th 2015 via Hootsuite
(Foundation) Also BRAF fusions w/novel upstream partners. (Kinase domains in BRAF always intact.) #AGBT15
7:56pm February 26th 2015 via Hootsuite
(Foundation) In their db of 15k samples; found 1 Cancer of Unk Primary #AGBT15
7:55pm February 26th 2015 via Hootsuite
(Foundation) 11 samples for RNA, for 33 genes. Found recurring SND1-BRAF fusion; fusion partners the same, breakpoints differ #AGBT15
7:54pm February 26th 2015 via Hootsuite
(Foundation) Difficult to target this tumor type - common drivers not there. 44 samples 287- or 485-genes on DNA, then RNA #AGBT15
7:53pm February 26th 2015 via Hootsuite
(Foundation Med) "Pancreatic Acinar Cell Carcinomas Harbor Recurrent RAF Fusion and Frequent Inactivation of DNA Repair Genes” #AGBT15
7:52pm February 26th 2015 via Hootsuite
DJ: 2x250 PCR-free + DISCOVAR de novo (tool built); tool for 10x ('tool building') #AGBT15
7:49pm February 26th 2015 via Hootsuite
DJ: 'Remarkably, it works!' Shows 160kb on one chromosome; DISCOVAR branching graphs: 'some resolvable if close enough' #AGBT15
7:48pm February 26th 2015 via Hootsuite
JF: Describes 10X Genomics tool. 200K droplets, each w/own barcode, each w/100kb long molecules (slide says '100' but it's 100kb) #AGBT15
7:42pm February 26th 2015 via Hootsuite
