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Albert Vilella Profile picture
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13 Jan, 4 tweets, 3 min read
#JPM2021 @carisls My Highlights: in the #CancerDiagnostics area, they position themselves favorably wrt Foundation medicine, Tempus, and Personalis (haven't heard of NEO before).
They put #LiquidBiopsy at the end of this trajectory slide: (couldn't see any years in milestones for this)
No indication that #Caris are pursuing #Epigenomics profiling of #LiquidBiopsy: they mention exome and transcriptome in their slides.
#Caris has 13 #NovaSeq machines in 4 locations:

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Albert Vilella Profile picture
15 Jan
#JPM2021 @GenapSys My Highlights: I think it's fair to say I am more excited than most about this #NGS company, as I see them as an example of how to enter the market while keeping a small profile ($249M raised so far). Image
They now are aiming at 2021 to ship two new chips: 50MM read chip and 144MM sensor chip (not sure what the difference is between read/sensor). Image
They show a slide of price per Gb with #Illumina products as a reference, and their products now lined up, I think, for the first time with price per Gb info. Lowest will be the 144MM chip at ~$27/Gb. Image
Read 14 tweets
Albert Vilella Profile picture
14 Jan
#JPM2021 #ExactSciences #LiquidBiopsy My highlights: I will focus on the liquid biopsy / #epigenomics profiling side of the presentation, which is where my interest lies: Exact described the data from Thrive multi-cancer screening, based on 'mutation+protein' Image
The details they gave on their other recent acquisition, #BaseGenomics are illuminating: they will use their bisulfite-free methylation profiling method for their Cologuard 2.0 test for CRC, but also for the multi-cancer test, and possibly the MRD test as well.
So this means that #ExactSciences intend to upgrade their tech in two steps: from current Cologuard 1.0 to a new test that includes Thrive's tech, and then a second upgrade using the #BaseGenomics #Epigenomics profiling tech.
Read 5 tweets
Albert Vilella Profile picture
14 Jan
Some stats and facts about the #Takifugu #rubripes assembly by @genomeark: this is the third iteration of the assembly. The first was completed in 2002. There was another iteration done in 2011. Why was the pufferfish sequenced so early? A lot has got to do with Sydney Brenner... Image
Indeed, as we can see in this archived version of @ensembl, the Fugu genome was the 5th vertebrate genome to be completed, after human/mouse/rat and zebrafish. Even though zebrafish is widely used as a model organism, Sydney Brenner argued that Fugu was worth sequencing ... Image
... The reason is that Sydney Brenner was passionate (obsessed?) with gene duplications and functional diversification. I.e. a gene duplicates in two copies, and over time, each copy can specialize in doing something slightly different. ...
Read 8 tweets
Albert Vilella Profile picture
13 Jan
#JPM2021 @TwistBioscience My Highlights: back to the #DNAWrite field. TwistBio chip: 1M oligos but only as centralised factory setting. Image
Expanding to a new factory in Portland (roadmap 2022) to reduce TAT. Also mentioned the "long tail" of Clonal Ready Gene Fragments. Image
They have a few slides on #DNAasStorage with a denser chip in prototype phase where they think they can archive 1Tb for $100 (pay once, archive forever*) which, if my calculations are correct, would allow for 10-12 years of @awscloud Deep Glacier or similar mth/GB=0.00099*12*1E3 Image
Read 5 tweets
Albert Vilella Profile picture
13 Jan
#JPM2021 #LiquidBiopsy notable by their absence, which is more than excusable in these pandemic times: @freenome, Biocartis, Biodesix, Epic Sciences, ArcherDx (not by this name anyway). Worth following developments for them. In my book, worth following #Freenome of the ones here.
Smaller #LiquidBiopsy #Oncology #Diagnostics players also not at #JPM2021 but important in the field: Personalis, Inivata, Exosome Diagnostics, Epigenomics Ag, Personal Genome Diagnostics, Foundation Medicine, Singlera, Cambridge Epigenetix, and Bluestar Genomics.
Now added #BiologicalDynamics to my #LiquidBiopsy list crunchbase.com/organization/b… which displace #Biocept in the #Top30 bit.ly/liqbiop (thanks Kevin Han for the follow).
Read 5 tweets
Albert Vilella Profile picture
13 Jan
#JPM2021 #AdaptiveBiotech My Highlights: my interest lies in their angle on #LiquidBiopsy for #EarlyCancerDiagnostics, but they also deal with Life Science Research and Drug Discovery. Image
Their T-Detect method is aiming at #MRD monitoring, here shown in a slide that relates it to their ImmunoSEQ T-MAP Cancer mapping tool, and their Identification of clinical TCR candidates. Image
They stress the T-cell Diagnostics angle in different slides. I recall only @freenome explicitly mentioning immune-profiling from the group of companies in early cancer diagnostics and #epigenomics profiling (Grail/GH/Thrive/Freenome/BioStar/CEGX/etc.) Image
Read 5 tweets

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