Nanosens Publishes Proof-of-Concept for Point-of-Care CNV Diagnostic
Here's a killer technological challenge for anyone: design a scheme to detect vanishingly small concentrations of a valuable analyte in a biological fluid. The assay must require zero pipetting, work in the field at ambient temperature, generate results quickly, contain positive and negative controls, be usefully precise and accurate, and be usable by personnel with no formal technical training. Oh, and be dirt cheap as well.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 24, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Nanosens Publishes Proof-of-Concept for Point-off-Care CNV Diagnostic
Here's a killer technological challenge for anyone: design a scheme to detect vanishingly small concentrations of a valuable analyte in a biological fluid. The assay must require zero pipetting, work in the field at ambient temperature, generate results quickly, contain positive and negative controls, be usefully precise and accurate, and be usable by personnel with no formal technical training. Oh, and be dirt cheap as well.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 24, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Beyond Generations: My Vocabulary for Sequencing Tech
Many writers have attempted to divide Next Generation Sequencing into Second Generation Sequencing and Third Generation Sequencing. Personally, I think it isn't helpful and just confuses matters. I'm not the biggest fan of Next Generation Sequencing (NGS) to start with, as like"post-modern architecture" (or heck,"modern architecture") it isn't future-proofed. Not that I wouldn't take a job with NGS in the title, but still not a favorite. High Throughput Sequencing feels a little better, but again doesn't leave room for distinguishing growth -- and HTS as an abbreviation i...
Source: Omics! Omics! - February 20, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Failing to Fetch An Interesting Result on Dog Oncogene Homologs
An idea for a little exploration occurred to me back at Infinity -- that is 7.5 years ago -- that I've never tried out. But I never got around to it. I had some downtime recently to play around so I finally executed the experiment -- alas, it turns out not to be very interesting. Still, a negative result is a negative result.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 7, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Covaris Grabs A Spot on the Liquid Handler Deck
For as long as I can remember, Covaris has been the standard in DNA shearing for high throughput short read sequencing. Their benchtop units had their quirks -- custom tubes being the foremost -- but they were what everyone else compared to. In 2013 when the American Society for Human Genetics was in town, the PacBio folks did me a great favor and loaned me an exhibit hall pass. Multiple companies were offerin g DNA shearing instruments -- and every one compared themselves against Covaris. Now they have a new offering, moving the instrument onto a liquid handling robot deck so that it is available for high-through...
Source: Omics! Omics! - January 30, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Patent Dive: Genapsys
Here's a dangerous statement for me: I actually enjoyed reading some patents recently. Now, before you get any ideas in your head about suggesting more patents for me to read, let me be clear that these were unusual patents -- they're written to be read! -- and were read under strict conditions. The patents in question are from Genapsys --found via my good friend Justia.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 29, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Metabolic Whac-a-Mole
Derek Lowe summarized a really cool paper back in October. I've been meaning to grab a copy, but discovered recently that the MIT library no longer has an easy way for outsiders to slip in an use their subscriptions. So I'm working off his summary, but since this is mostly an excuse for flights of genetic fantasy actually reading the paper would probably just hinder me!Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 28, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
2019 Tech Speculations: Oxford Nanopore
As promised in the last post, I'm segregating out Oxford Nanopore. Admittedly I tend to cover them relatively closely -- though I never seem to quite finish writing up their conferences -- but at the moment ONT is the only major player in the U.S. research sequencing marketnot being run out of (or about to be run out of) Illumina HQ. And I'll be very to the point: ONT has a lot of balls in the air and irons in the fire, but from my point-of-view what matters most is rapid and regular progress on the accuracy front.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 25, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
2019 Sequencing Tech Speculations: Will We Actually See New Entrants?
An astute reader caught a sentence fragment about MGI inlast night's Illumina JPM roundup -- the unfortunate evidence of a a mental battle over whether to put any further comments on MGI in an Illumina-centric post. So now I'll sweep that bit into a general post about not-Illumina (and not-Oxford, that will go in yet another).Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 15, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Illumina JPM Talk
Illumina CEO Francis deSouza delivered his J.P. Morgan Healthcare Conference talk (webcast audio,slides&Q&A audio) a week ago. I can claim that some ofmy speculations came true -- just the most boring and obvious ones. Overall, the presentation was the talk of a confident market leader. Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 14, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
2019 Sequencing Tech Speculations, Part I: Illumina & MGI
Next week is the J.P. Morgan Healthcare Conference. It's striking this year the paucity of companies in the genomics space -- Illumina on Mondayat 6:00 EST and MGI on Wednesday at 5:30 EST and Nanostring at 6:30 EST on Wednesday. Perhaps NVIDIA will say something interesting about their forays into healthcare, such as providing the chops for real time nanopore basecalling, on Thursday at 11:30 EST. There's also some nice polls from Albert Viella on TwitterWhat would you like@illumina to announce at#JMP2019 ?https://t.co/TDn5J0glhi part 2— Albert Vilella (@AlbertVilella)January 5, 2019and some more Twitter s...
Source: Omics! Omics! - January 6, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
2019 Resolutions
2019 is upon us; I'm hoping it will be a bit less eventful than 2018. It wasn't all bad -- I took two trips that delivered scenery I have only right to see once in a lifetime -- but it was essentially bookended bylosing my father anda revolution in my workplace. Mixed in there is the bittersweet pride of seeing one's offspring graduate from high school and proceed on to college.New Year's resolutions are notoriously difficult to keep -- one is fighting entrenched behaviors -- but bringing in some external pressure might help. So I'll make my two resolutions for the year very public: that I post...
Source: Omics! Omics! - January 3, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
An Unfortunate Master Class in Poor Plotting
I hope my admiration for Pacific Biosciences intellectual acumen was clearin my post on the acquisition by Illumina, because now I'm going to be a rabid crab over awebinar they aired yesterday. I take telling scientific stories seriously and an important part of telling such stories is displaying data well. I'm a perfectionist in this department by intention, but not always by execution -- I'm constantly reanalyzing my plots and diagrams for errors and cringing when I find them. The webinar is trying to extol the value of the latest developments in the SMRT platform, but the data graphs often actively f...
Source: Omics! Omics! - December 13, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Flappie vs. Albacore via Counterr
I'm going to go through some analysis of Oxford Nanopore basecalling, running some quick comparisons using afreely-available tool called counterr which was announced at the Nanopore Community Meeting two weeks ago. Counterr was developed byDay Zero Diagnostics, a startup I advise -- though in announcing yet again my COI I will stress I don't get paid to help give away software! This is just a small bit of analysis; nothing as comprehensive asRyan Wick's ongoing analysis with a ready-to-submit preprint masquerading as a README file.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - December 12, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Nanopore Community Meeting 2018: The Clive Report
Given it's late and I just dashed through a classic San Francisco downpour, I'm going to mostly stick to covering Clive Brown's talk tonight. Within it there were a number of announcements, and for anyone following this space I get to point out things I've proposed in the past that are moving to fruition as well as recent statements I made that were quite erroneous.Also note that tweets during his talk have been collected by ONT into aTwitter MomentRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 29, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
