Jared Simpson (OICR Canada) Nanopore sequencing of a human genome #AGBT17
2:02pm February 16th 2017 via Hootsuite
.@TorontoGenomics As time goes on, there will be fewer and fewer who will understand what this X-ray film business is all about!
2:00pm February 16th 2017 via Hootsuite in reply to TorontoGenomics
I wish I had photos of pets to share with #AGBT17. Here's a photo from circa 1993 - enjoy. https://t.co/TlQC6JrpRr
1:56pm February 16th 2017 via Hootsuite
Have another free-of-charge #AGBT17 single-cell RNA-seq reference https://t.co/MuYgtKA3S8
1:43pm February 16th 2017 via Hootsuite
Here's an interesting single-cell spatial gene expression paper that has nothing at all to do with #AGBT17. https://t.co/AgeKmXi1JX
1:40pm February 16th 2017 via Hootsuite
RT @RobAboukhalil: Great talk by Ido Amit on █████ using single-cell sequencing to explore the underlying biology of █████ █ ███ █ #agbt17
1:38pm February 16th 2017 via Hootsuite
Ido Amit (Weizmann Inst Israel) has asked for me not to tweet - so his loss (and ours) #AGBT17
1:33pm February 16th 2017 via Hootsuite
Livelli: Combined w/CRISPR for endogenous biology. Super-resolution microscopy uses HaloTags, single-molecule, single-cell imaging #AGBT17
11:48am February 16th 2017 via Hootsuite
Livelli: Can attenuate affinity between components of donor-acceptor molecules. Thus 2nd prot-prot interaction NanoBIT method #AGBT17
11:47am February 16th 2017 via Hootsuite
Livelli: Able to do kinome-wide profiling w/ a library of NanoLuc-kinase fusions. Suggests it could be used for pers med #AGBT17
11:46am February 16th 2017 via Hootsuite
Livelli: Developed an in-cell target / ligand system called NanoBRET Info here: https://t.co/CyzLQxBfdP #AGBT17
11:44am February 16th 2017 via Hootsuite
Livelli: Able to do directed evolution to increase light output greatly, Donor protein; getting a HaloTag fluorescent acceptor #AGBT17
11:43am February 16th 2017 via Hootsuite
Livelli: Protein degradation, abundance, localization, reporting techology. Oplophorus lucferase - https://t.co/IYu6Qnu6CJ #AGBT17
11:42am February 16th 2017 via Hootsuite
Livelli: Emphasizing the functionalization of genomic info; interrogation of drug/target; molecular sensors; protein interaction #AGBT17
11:40am February 16th 2017 via Hootsuite
RT @Supergecko: @iontorrent @thermofisher presenting S5 kits: 600bp seq kit available, 800bp seq kit in development #agbt17
11:39am February 16th 2017 via Hootsuite
Thomas Livelli (Promega WI) Next generation integrative life science research #AGBT17
Ellis: Shows data from PCR-free from 250ng, feels they can go down as little as 50ng or 25ng at scale 'for the greedy X10's' #AGBT17
9:53am February 16th 2017 via Hootsuite
Ellis: Shows GC curves, answering one question, and automation data for 96-well. Next step is to 384-well. PCR-free has 1ug input #AGBT17
9:52am February 16th 2017 via Hootsuite
Ellis: Next challenge is scaling, unsure the effect of different contaminants on a new fragmentation method, effect on GC coverage #AGBT17
9:50am February 16th 2017 via Hootsuite
Ellis: Have settled on a method, cancer group has indicated quality of data is excellent, similar to bulk DNA cp to LCM #AGBT17
9:47am February 16th 2017 via Hootsuite
Ellis: Duplicate rate held way down - only 30% below 1ng input. LCM to purification still a problem. Staining, buffers, proteases #AGBT17
9:46am February 16th 2017 via Hootsuite
Ellis: Found 10x-15x more library yield compared to other methods; a proxy for complexity. Same complexity graph - down to below 1ng #AGBT17
9:45am February 16th 2017 via Hootsuite
Ellis: Characterization of fragmentation: time-dependent, indep. of DNA input amount 'across several orders of magnitude' #AGBT17
Ellis: NEB's newest (to launch soon) Ultra II-FS, using enzymatic frag, end-repair and A-tail in single-tube. #AGBT17
9:44am February 16th 2017 via Hootsuite
Ellis: Ultra II was a bit better but still large drop-off. Major problem was library complexity (# of duplicate reads) #AGBT17
9:43am February 16th 2017 via Hootsuite
Ellis: Tested their current workflow, NEBNext Ultra II LC (input range 100ng down to 0.75ng) for WES v5. Metrics suffered <10ng #AGBT17
Ellis: LCM may only have 150 cells. Need high-quality WGS, without WGA due to bias issues for mutational signatures #AGBT17
9:41am February 16th 2017 via Hootsuite
Ellis: Gaps: pg-level library const at-scale is required. Cancer genome group - want genomics from every human tissue via LCM #AGBT17
9:40am February 16th 2017 via Hootsuite
Ellis: Library costs are exceeding sequencing cost; increased demand for PCR-free (req 1000ng). Low input library const problem #AGBT17
Ellis: 20K samples/mo; 75% of these get made into libraries. Their instrumentation include Covaris LE220, Agilent Bravo; LabChip Gx #AGBT17
9:39am February 16th 2017 via Hootsuite
Peter Ellis (Wellcome Trust UK) Next generation DNA library construction for high-throughput genomics #AGBT17
9:38am February 16th 2017 via Hootsuite
RT @richardmleggett: At #agbt17 @pacbio promising Sequel thrupt will increase 2x this year, 2x next year, 8x at end of '18 making 32x total.
8:57am February 16th 2017 via Hootsuite
ICYMI: My own take on the @nanostringtech Hyb & Seq technology presented yesterday at #AGBT17 https://t.co/buNCoKLIVB
8:56am February 16th 2017 via Hootsuite
Marth: Also plans to use single-cell sequencing to better understand clonal expansion, improve their model #AGBT17
9:30pm February 15th 2017 via Hootsuite
Marth: Used multiple sampling from a TNBC post-mortem sample set, to 'call into question the cancer's organ of origin' in mBC #AGBT17
9:29pm February 15th 2017 via Hootsuite
@coregenomics has published his thoughts on @nanostringtech Hyb & Seq here: https://t.co/AOO3e6QBUV #AGBT17
9:24pm February 15th 2017 via Hootsuite
Marth: 2nd line Rx same pt example, a clear resistance mutation with recommendation to change Rx #AGBT17
9:21pm February 15th 2017 via Hootsuite
Marth: Ultimate goal - to be informative for individual pts. No evidence for chemoresistance in example given #AGBT17
9:20pm February 15th 2017 via Hootsuite
Marth: Have models of a consensus subclone model; confirmed with single-cell sequencing, pre and post-Rx. #AGBT17
9:18pm February 15th 2017 via Hootsuite
Marth: Often no unique solutions, multiple subclone structures. '14 Genome Biol ref https://t.co/X0eTDKekpy #AGBT17
9:15pm February 15th 2017 via Hootsuite
Marth: Illus primary tumor, groups of variants that disappear in relapse. Can reconstruct primary and relapse AFs #AGBT17
9:14pm February 15th 2017 via Hootsuite
Marth: Somatic muts are dynamic, forming evolving grouops of cells (subclones) #AGBT17
9:13pm February 15th 2017 via Hootsuite
Gabor Marth (Univ Utah) Tracking the evolution of a patient's tumor across multiple time points or multisite metastases #AGBT17
9:12pm February 15th 2017 via Hootsuite
Syvanen: Shows gain and loss of driver muts in ALL cells at relpase, detectable as minority clones at diagnosis. #AGBT17
9:07pm February 15th 2017 via Hootsuite
Syvanen: ID driver genes, ID'd 5 novel for ALL. ATRX, RPL10, KMT21D. MutSig/Oncodrive computational screens #AGBT17
9:01pm February 15th 2017 via Hootsuite
Syvanen: Dx to relapse, used Haloplex 872 ca genes. '16 ref https://t.co/3hZRx5dmQz Graph of mutational burden #AGBT17
8:54pm February 15th 2017 via Hootsuite
Syvanen: Shows pie chart of distribution of sub-types. 30% of pts lack cytogenetic subtype #AGBT17
8:53pm February 15th 2017 via Hootsuite
Syvanen: Nordic oncologists established biobanks of samples early (>1K DNA, >500 RNA, BM at diagnosis) #AGBT17
8:51pm February 15th 2017 via Hootsuite
Ann-Christine Syvanen Uppsala Univ: Deep-targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mut patterns #AGBT17
8:50pm February 15th 2017 via Hootsuite
Nordland: Built classifiers with known subtypes; with unkn samples didn't get the detected they expected, went back to RNA-Seq #AGBT17
8:37pm February 15th 2017 via Hootsuite
