Korlach: Direct comparison of bias fto '15 Nat Rev Genet figure https://t.co/T7pSrUdRVO striking comparison to ILMN data #AGBT16
3:28pm February 13th 2016 via Hootsuite
Korlach: K-12 de novo: 6kb library, 4-h acquisition, HGAP. 1 contig, 4.6MB, 9.9992% (QV51) Bias relative to GC content: nice! #AGBT16
3:27pm February 13th 2016 via Hootsuite
Korlach: Poster that used Multiplicom Tumor Hotspot MASTR Plus: got to 1% sensitivity, and cp to MiSeq was more accurate #AGBT16
3:25pm February 13th 2016 via Hootsuite
Korlach: Of 215K reads, 160K QV30 reads, 101K QV40 reads. #AGBT16
3:24pm February 13th 2016 via Hootsuite
Korlach: Shows one of Sebra's slides from workshop: RET driver mutation, T>C and consistent RSII vs Sequel data. #AGBT16
Korlach: Points out ability to read mutations impt in cancer, but not accessible to ILMN chemistry. #AGBT16
3:23pm February 13th 2016 via Hootsuite
Korlach: Showed histogram of RL. Single-pass accuracy is 89% Mode) 84% (mean). #AGBT16 '15 ref https://t.co/xkHOUYI31e direct linked reads
3:22pm February 13th 2016 via Hootsuite
Korlach: Test template - 2kb amplicon; 4h acquisition; 5.1GB, 615K reads; N50 17.7kb; max RL 66kb #AGBT16
3:20pm February 13th 2016 via Hootsuite
Korlach: Sequel is about 6.5x the throughput; ave >10Kb, 99.999% consensus accuracy #AGBT16
3:19pm February 13th 2016 via Hootsuite
Jonas Korlach (Pacific Biosciences) Addressing complex diseases and hidden heritability with the sequel system #AGBT16
3:18pm February 13th 2016 via Hootsuite
Levy:Q:What about small vars? A:Looked at largest vars - 200-500bp. Still ongoing review #AGBT16
2:51pm February 13th 2016 via Hootsuite
Levy: But the other metrics 'are pretty impressive'. Insert size similar, mapping and duplication rates similar (except 1ng input) #AGBT16
2:40pm February 13th 2016 via Hootsuite
Levy: Patterned flowcells take a bit of a hit on higher noise - 'nothing terrible but worth noting'; the biggest negative #AGBT16
Levy: Changed title to 'Early access to 10X Genomics on Chromium'. Shows insert size distribution 350bp a bit wider on 10X #AGBT16
2:39pm February 13th 2016 via Hootsuite
Levy: Testing Chromium 10X Genomics v2: keeping sequencing costs 'manageable' 120Gb, 1ng input (vs 600ng) #AGBT16
2:37pm February 13th 2016 via Hootsuite
Levy: Many methods - LFR, CPT-seq, Moleculo - leverage MPS but get higher-resolution data. May '15 received @10Xgenomics instrument #AGBT16
2:34pm February 13th 2016 via Hootsuite
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
