Levy: Shows @kevinadavies twwet - 10 years ago, sequencing PhiX174 #AGBT16
2:32pm February 13th 2016 via Hootsuite
Shawn Levy (HudsonAlpha) Unique run conditions allow multiplexed phased genomes on the HiSeq X to reveal #AGBT16
2:31pm February 13th 2016 via Hootsuite
RT @Becky_Kusko: What am I supposed to do in a talk when I can't tweet??? Take notes...in a notebook? #AGBT16
2:08pm February 13th 2016 via Hootsuite
MT @obahcall: Our @nature Editorial on portable sequencing & critical need for real time data sharing https://t.co/SYhbRArc2e #AGBT16
2:06pm February 13th 2016 via Hootsuite
Susan Rosenberg (Baylor) “Freeze-frame synthetic proteins trap genome damage intermediates in living cells” #AGBT16 Opts out - no tweets.
2:01pm February 13th 2016 via Hootsuite
Loman:Q:PCR bases easier to seq? A:Mod bases, base damage, affects quality of reads. Metrichor 'doesn't have a good model for it.' #AGBT16
1:58pm February 13th 2016 via Hootsuite
Loman: Acknowledges @nanopore's support, Josh Quick, Jared Simpson and many others. #AGBT16
1:56pm February 13th 2016 via Hootsuite
Loman: @mattloose sequencing E coli, and using an offline 'nanocall' software #AGBT16
Loman: Want an offline basecaller. Showed a photo of sequencing in their hotel room here at #AGBT16 - did 436MB in 24h, Tn lib, N50 16kb
1:55pm February 13th 2016 via Hootsuite
Loman: Shows a 'bentoLab' battery-powered PCR, isothermal amp for sequencing, and read-until barcode balancing #AGBT16
1:54pm February 13th 2016 via Hootsuite
Loman: Major impediment for real-time outbreaks is our ability to organize and complete databases. #AGBT16
Loman: Showed identical results with 'traditional' NGS methods. From Mar '15 through Oct - increasing fraction of the cases #AGBT16
1:47pm February 13th 2016 via Hootsuite
Loman: Using cellphone for data upload wasn't financially feasible. Most runs were 50 minutes or so on PCR product #AGBT16
1:45pm February 13th 2016 via Hootsuite
Thanks to #BDgenomics was able to get this fun photo during the break at #AGBT16 https://t.co/8L5vHjTz1z
1:44pm February 13th 2016 via Hootsuite
Today's #AGBT16 post: Advances in genomic clinical applications - Next Generation Technologist https://t.co/2yK3qkDGmy
1:42pm February 13th 2016 via Hootsuite
Loman: 2d after arrival, able to start sequencing. Great photo. #AGBT16
Loman: Walking through what it took to get a sequencer to West Africa, comparing @iontorrent versus a backpack for @nanopore #AGBT16
1:41pm February 13th 2016 via Hootsuite
Loman:What is the size of a MinION? Funny comparisons to phones, rulers, staplers... #AGBT16
1:38pm February 13th 2016 via Hootsuite
Nick Loman (University of Birmingham) Real-time genome sequencing in the field #AGBT16
1:37pm February 13th 2016 via Hootsuite
Beechem: Q:RNA? A:A natural for Nanostring. Yes will work with it, but still 'a lot of work to do' #AGBT16
11:35am February 13th 2016 via Hootsuite
Beechem:Q:Readlength? A:It is unusual - probes like water, through whatever length the template is (short or very long) #AGBT16
Beechem: At #AACR16 they will show spatially resolved barcodes on FFPE slices (!) (Something to look for!) #AGBT16
11:34am February 13th 2016 via Hootsuite
Beechem: Workflow comparison - <1h. Expect targeted gene panels (100's of genes), focusing on chemistry. #AGBT16
11:33am February 13th 2016 via Hootsuite
Beechem: Not coverage, it is re-interrogating the same template DNA. 2% read twice is Q35. #AGBT16
11:32am February 13th 2016 via Hootsuite
Beechem: An AG pair, run 2100 times, 42 were incorrect for 2.0% First pass at 2.58% ave, 2nd pass 1.6% ave Reading the same base #AGBT16
Beechem: Shows data of raw single pass error rate of ~2%. He comments about how for some tech, he's still waiting! PREACH IT! #AGBT16
11:31am February 13th 2016 via Hootsuite
Beechem: Shows spots - 1M - 4M spots at a time, on a modified Sprint reader. This is single molecule detection, not single fluors #AGBT16
11:30am February 13th 2016 via Hootsuite
Beechem: 150bp tail beyond the 10b hyb region is what encodes sequence of the 6bp. Groups of 6bp are then mini-assembled #AGBT16
11:29am February 13th 2016 via Hootsuite
Beechem: Four bases to detect, the barcode on the tail, the tail gets picked up by a labeled oligo. Hyb spot 1, hyb spot 2, etc #AGBT16
11:28am February 13th 2016 via Hootsuite
Beechem: The color pattern is in a 'cyclic pattern'. Flowcell capture of sequence. Hyb 10-mer in 5sec. Encoded the first base ID #AGBT16
11:27am February 13th 2016 via Hootsuite
Beechem: As it is early, he recognizes Jeffrey Schloss (NHGRI) in the audience. Advisors include Hood, Nusbaum, Shendure. #AGBT16
11:26am February 13th 2016 via Hootsuite
Beechem: Single-molecule technology - a bit of the future - called "Hyb and Seq". No library, enzymes or amplification #AGBT16
11:25am February 13th 2016 via Hootsuite
Beechem: Shows a melanoma case-study, with nice WT vs V600E/V600E volcano plots, surface protein, and phosphoprotein levels #AGBT16
11:22am February 13th 2016 via Hootsuite
Beechem: SNV det in DNA and RNA - designed stem-loop with single base specificity as multiplexed assay. KRAS Exon 2 (codon 12, 13) #AGBT16
11:20am February 13th 2016 via Hootsuite
Beechem: 3D experiment looks at 5ng DNA, 50ng RNA, 500ng protein (min). 700 targets impt to cancer (RNA). And protein, SNV data too #AGBT16
11:19am February 13th 2016 via Hootsuite
Joe Beechem (NanoString) New optical barcode chemistries power 3D biology & sequencing #AGBT16
11:17am February 13th 2016 via Hootsuite
Hendrickson: Launch of NEB's Cancer Hotspot Panel set for April, can be contacted at nebnextdirect@neb.com #AGBT16
11:14am February 13th 2016 via Hootsuite
Hendrickson: Covers uniformity, uniformity by GC. Shows sensitivity down to well below 5%. Input down to 10ng as well. #AGBT16
11:11am February 13th 2016 via Hootsuite
Hendrickson: Individual bait synthesis allows addition to pre-existing panels. Can specify target size from 100 to 500bp's #AGBT16
11:07am February 13th 2016 via Hootsuite
Hendrickson: 2 IDs: i7 index, 120 UIDs available. i5, up to 12 bases of UMI (unique molecule IDs) #AGBT16
11:05am February 13th 2016 via Hootsuite
Hendrickson: Ligate to end of bait plus hyb'd DNA, Automation-friendly, no ampure-bead cleanups, moderate temps #AGBT16
Hendrickson: Input as low as 10ng; hyb is not tile-based, only 3' end for 90m. Bind to SA, Use enzymes to remove off-target DNA #AGBT16
11:04am February 13th 2016 via Hootsuite
Cynthia Hendrickson (Directed Genomics) Fully customizable hybridization-based enrichment technology w/ capture and library prep #AGBT16.
11:02am February 13th 2016 via Hootsuite
RT @sandiegoscience: Vision, tragedy lead Google exec to head Illumina cancer venture https://t.co/ZoU2hhwXgi https://t.co/OOZPmNHyEI
4:20am February 13th 2016 via Hootsuite
Mungall: NTC rearr 49/41 (78%), matching FISH break-apart pattern. BCL2 rearr 20/26 (77%) #AGBT16
9:05pm February 12th 2016 via Hootsuite
Mungall: On target bases ranged from 22-44% - usable from 7% - 24%. Adequate coverage to determine fusions #AGBT16
9:03pm February 12th 2016 via Hootsuite
Mungall: 220bp ave inserts; custom capture uses SureSelect. Pilot capture: 0.5MB, total is 7.8MB. #AGBT16
9:01pm February 12th 2016 via Hootsuite
Mungall: 100ng DNA, covaris, double bead-based size selection, end-repair with NEB, dA, adapter on Biomek FX. 4-6 PCR cycles #AGBT16
9:00pm February 12th 2016 via Hootsuite
Mungall: Automated FFPE DNA and RNA extraction, yields ranged from 200ng to 7ug (!), 120mm2 surface area1-5 10um scrolls #AGBT16
8:59pm February 12th 2016 via Hootsuite
Mungall: Saw a whole collection from 72 BAC clones and biotinylated baits. '15 J Path https://t.co/mVvNEN1VMp #AGBT16
8:57pm February 12th 2016 via Hootsuite
