ONT Sketches Paths to Long, Selective, Accurate Sequencing
Some sort of summary of London Calling in this space is grossly overdue after getting caught by multiple work firedrills and then several recursive rounds of procrastination. I'm not going to attempt to cover all the company announcements. I'm going to focus on a cluster of announcements that show a long range vision of inexpensive sequencing consisting of very accurate, very long reads. Well, a cluster of visions -- some parts can be mixed and matched and others cannot. This should be a prospect to grab the attention of any current or aspiring ONT competitors. Now before I'm accused of being a gullible...
Source: Omics! Omics! - June 29, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
New Clinical Human Genome Speed Record
Iproposed last year that there should be a regular racing event for human genomics. The only real competitor in is this interesting race seems to be Steven Kingsmore's group at Rady Children's Hospital. I was sent an embargoed press release from Illumina about a new record by that group, which clocks in at 13.5 hours from patient sample to clinical report. ANew England Journal of Medicine paper (hence the embargo, ending just before I post this) reports on the advance but wasn't in the packet I received. Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - June 2, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Matt Meselson Needs a Biographer!
Yesterday was Matt Meselson's 91st birthday. I have only met him a few times and he wouldn't know me from Adam, but he is a particularly interesting individual I've had the good fortune to converse with. I'm putting out a plea now for a skilled biographer to write his life, because it certainly has been an interesting and impactful one, with scientific work stretching from the early beginnings of molecular genetics to a preprint just recently posted onBioRxiv.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - May 25, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
My Latest London Calling Thoughts
The title really says it -- London Calling has actually already begun and here I am pretending to write a"before the conference" piece. Of course, since everything is virtual again this year I can actually do this since I haven't watched anything yet nor have seen any tweets -- and the big technology announcement section isn't for a few hours so I have loads of time to write! Sadly, nor have I gone and looked at what I've written before. Nor have I defended these two days very well - my schedule is cluttered with meetings and appointments. So I haven't prepared in any way, shape or form...
Source: Omics! Omics! - May 20, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
GISAID Broken Down by Sequencing Hardware
The GISAID database has been the workhorse for storing and distributing SARS-CoV-2 sequences during the COVID-19 pandemic and recently passed one million entries. There was some Twitter chatter wondering about the hardware breakdown for this, as it isn't really easy to get out of GISAID. I had done a somewhat arduous partial take at this for my VIB talk last month, but in the meantime GISAID had granted me some additional access to metadata which I've been too busy to tackle. But knowing some others were curious, time to dive back in. Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - April 25, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT21: VizGen Unveils MERSCOPE
More spatial profiling news coming in from AGBT -- Harvard spin-out VizGen is launching in the U.S. an instrument implementing MERFISH technology. This sub-$300K instrument will initially enable panels of up to 500 genes to be profiled, with plans to expand that capacity to 1000. Users either pick from a menu of pre-designed panels or select genes using a Gene Panel Design Tool and VizGen would proceed to manufacturing the panel in around two weeks. VizGen CEO Terry Lo and Senior Director of Marketing Brittany Auclair were kind enough to give me a preview last Friday.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 2, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT21: The LabRoots Presentation Platform is an Unmitigated Disaster
Rant isON! I've been having an utterly miserable experience with the LabRoots conference software that AGBT is using for their virtual meeting. This year has exposed many of us to a wide variety of teleconference and virtual meeting software and many of the glitches are small and hard to pin down. Or matters of personal preference (though if you don't share mine, you are simply wrong!). But now on two major platforms I've come across major issues with LabRootsRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 1, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT21: A Few Pre-Conference Mutterings
Getting some miscellanea out before AGBT21 starts later this morningRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 1, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT21: Rebus Esper for Spatial Sees Things You Wouldn't Believe
My predictionthat spatial would be a hot topic at AGBT was easy to make knowing I was sitting on embargoed news in the spatial space. This morningRebus Biosystems announced the launch of the Rebus Esper system for wide field spatial profiling of gene panels with subcellular resolution. Rebus is promising that this instrument will offer true walkaway automation from fluidics through imaging, and data processing, requiring only one hour of hands-on time.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 1, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT 2021: A Spatial Foundation
I'll call it now -- the big buzz at this year's AGBT will be around spatial profiling. Trust me, it's not just a hunch. The two current players in the field -- nanoString and 10X Genomics -- both have significant presence in the virtual conference. Don't be surprised to see more players on the field -- just sayin'Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 28, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
PacBio With SoftBank's $900M: How Might TheyWork?
Pacific Biosciences continued its roll of successful business development, snagging $900M from Japan's SoftBank two weeks ago. Combined with a recent secondary stock offering and a major deal with Invitae, PacBio has gone from their self-proclaimed near-derelict status during the Illumina acquisition attempt saga to rolling in cash.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 27, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
More Details on 10X's Sample Profiling Trident
10X Genomics had an online event Wednesday called Xperience (as far as I could tell no Jimmy Hendrix music was used, a missed opportunity!) to lay out their development roadmap. This largely paralleled thepresentation given at J.P. Morgan, but there were a few new bits and of course much more technical detail to whet the appetites of scientists -- and judging from a number of very positive tweets I saw today they were successful in that goal. Some of the 10X management was kind enough to walk me through the deck earlier this week as well as permission to borrow images from it, so this summary is based on that as well as...
Source: Omics! Omics! - February 26, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Could I See Myself at J.P. Morgan?
There's a question that others pop my way pretty much every year around J.P. Morgan: would I ever attend myself? I'll confess it never occurred to me before I was asked, but that isn't necessarily a deal breaker. I foolishly didn't attend AGBT until 2013 when Alexis Borisy (then CEO of Warp Drive) suggested I go -- I think it was mostly because he thought it was a good investment and probably only secondarily to keep me off the ski slopes for a week -- I shattered my knee just after AGBT 2012 ended. It's an interesting but complex question which I will answer one way here, but freely admit that...
Source: Omics! Omics! - February 9, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Why I Hated One Genapsys Slide
I claimed in my Miscellanea piece that I was one post away from being done with J.P. Morgan -- oops, forgot I had drafted a minor screed on data display which I'll push out before the last piece - particularly since I hinted I would be taking Genapsys to task on this subject. Unexpectedly good timing too: maybenew Genapsys CEO Jason Myer'sfirst big initiative can be to fix this plot!Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 8, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
J.P. Morgan: Miscellania
Before J.P. Morgan is truly a month ago I should clean up some loose ends as a penultimate post driven by this year's virtual conference (the last post isn't exactly time sensitive). In contrast to the single company focused items that preceded it, this is a grab bag of minor observations and notes.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 6, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
