Discover and read the best of Twitter Threads about #epigenomics
Most recents (9)
1/ We've just finished 3 papers on #transposons #infection #epigenomics #graphGenomes, the result of an amazing collaboration with @LB_Barreiro and Tomi Pastinen. Start of a long 🧵 
2/ The first paper by lead author @katiearacena is:
Epigenetic variation impacts ancestry-associated differences in the transcriptional response to influenza infection
tinyurl.com/ytvrk5hn
Epigenetic variation impacts ancestry-associated differences in the transcriptional response to influenza infection
tinyurl.com/ytvrk5hn
3/ @LB_Barreiro just talked about this paper at #BoG22 and @katiearacena has a poster so I'll let them explain their results!
Reviewing the Oxford @nanopore presentation now available to replay. Two highlights/thoughts that I didn't tweet about before:
1) Spike-in for re-training
2) Strand-specific DNA modifications
1) Spike-in for re-training
2) Strand-specific DNA modifications
1) Looking at the kind of stuff presented, where temperature settings, salt, etc. are being more available to end-users, there is an opportunity here to retrain models and improve basecalling for specific datasets.
On a much simpler level, Illumina sequencer did and still do some of that: one would need to spike-in a certain amount of PhiX for the machine to calibrate itself. For low-complexity applications, like 16S sequencing, this could be as high as 25-50% of the reads/throughput.
Epigenomic biomarkers are becoming more established for #LiquidBiopsy and #CancerScreening, and we have seen the big players positioning themselves in this #epigenomics race recently.
Catching signs of #cancer early is crucially important to the disease management and survival rates, so the question is: how can we find out if there is something wrong going on early enough, ideally in a low-cost assay that can be performed regularly on healthy individuals?
@sbarnettARK Epigenomic biomarkers are becoming more established for #LiquidBiopsy and #CancerScreening, and we have seen the big players positioning themselves in this #epigenomics race recently.
@sbarnettARK Catching signs of #cancer early is crucially important to the disease management and survival rates, so the question is: how can we find out if there is something wrong going on early enough?
@sbarnettARK The first generation of high-throughput technologies was predicated on finding mutated (tumor) DNA in the individual's body (somatic), different from their (normal) DNA. Tumor/Normal (T/N) comparisons of the individual's samples, biopsies or ctDNA will indicate if there
#JPM2021 #BiologicalDynamics @BiodynSD My Highlights: I'll cover this from the point of view of #LiquidBiopsy and #Epigenomics profiling, which is where my interest lies: their next-gen multiomics intro is about exosomes (and EVs, exosomal vesicles?)
The slide about Verita Biomarker Isolation Platform seems to be about isolating cells, with the right-most image showing "Visualized EV", which I presume is exosome vesicles
Later on, they do mention methylation markers, above the exosomes image, so I wonder if it's only DNA inside or bound to the exosomes?
#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'
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.
#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).
#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.
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.
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.)
#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.
