Albert Vilella Profile picture
Next-Generation Sequencing, Single-Cell and Spatial Biology, Next-Generation Proteomics, Synthetic Biology, Compute Acceleration in Bioinformatics.
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May 18, 2023 9 tweets 3 min read
The tech update from Oxford @nanopore #NanoporeConf now ongoing with @The__Taybor now presenting: Duplex: 1.5% of the time, the complement strand follows the first strand naturally.
Initially, modified the adapters and reached 30% duplex rate. Image
May 17, 2023 10 tweets 3 min read
On library prep at #Nanoporeconf, a description for PCR-free methods showing the difference between ligation (max output) and rapid mode (10minutes, minimal lab equipment needed). Ultralong reads (ULR) also enabled, all Kit14. Image Rapid ULR. Current record is about 4 megabases. Image
Apr 21, 2023 7 tweets 2 min read
I did a deep dive on the different workflow management (WFM) tools for #Bioinformatics Data Analysis a few years ago, and since then there have been a few extra entrants in this segment, still mostly concentrated in serving the Next-Generation Sequencing field. A few years ago, there were two communities dominating the open-source WFM ecosystem in NextFlow and SnakeMake, and two platforms dominating the the commercial offerings in DNAnexus and Illumina BaseSpace.
Apr 21, 2023 8 tweets 3 min read
More interesting Next-Generation Sequencing knowledge in the ASeq Discord channel (by @new299). Illumina patterned flowcells and the etching process to "print" the wells into the flowcell. Could be down to 350nm diameter for some flowcell configurations now. Image If I remember correctly, Illumina started with a 600nm diameter for the patterned flowcell, in the HiSeq X and then later on in the evolution of the platform that used these patterned flowcells.
Apr 20, 2023 4 tweets 1 min read
There have been some acquisitions in #CancerDiagnostics and #CancerScreening recently, some of which signify a trend towards consolidation that is worth describing:
$A Agilent is moving towards some more vertical integration in Cancer Dx and Cancer screening by recently acquiring both announcing a partnership with Akoya Bio and announcing the acquisition of Avida Biomed. Image
Apr 20, 2023 6 tweets 1 min read
It is likely that as Spatial Biology tools become more robust and user-friendly, they will become increasingly popular and widely adopted in the scientific community. This may lead to a shift in the balance between single-cell and Spatial Biology approaches, with the latter eventually becoming more prevalent.
Apr 19, 2023 55 tweets 6 min read
A new post on Single Cell, Spatial Biology Omics and In situ Imaging on the URL in the image. Behind the curtain, some speculative thoughts on possible Mergers and Acquisition moves, including $TXG $NSTG and related companies such as $ILMN $GH $EXAS $RHHBY $ADAP $TMO $BDX , etc. Image In recent years, methods for encapsulating individual cells and analysing their DNA, RNA or protein contents have become more established, with commercial support from Biotech and Life Science Tool providers
Mar 15, 2023 28 tweets 6 min read
The regular Mass Spec market is being challenged by a new wave of companies whose technologies aim to disrupt the well-established market of large Mass Spec instrument vendors. These regular MS instruments tend to be expensive to buy, although not that expensive to run. There are limitations in the type of analysis one can perform with regular Mass Spec. One of the biggest limitations is that performing 'de novo' protein sequencing in MS is not straightforward: the most common way is to digest the proteins into small peptides, and then
Mar 14, 2023 9 tweets 3 min read
In #biotech #stocks news, today we review $TXG @10xGenomics , one of the companies in the #SingleCell and #SpatialBiology sectors. 10x Genomics is a biotechnology company that develops and markets solutions for omics analysis of single cell and spatial biology samples. The company offers several product lines:
Feb 25, 2023 46 tweets 14 min read
As we see videos in social media of the first $PACB PacBio Revio to enter the @broadinstitute , with the promise of the long-read $1000/genome in place, what does it look like today to set up a Next-Generation Sequencing factory/institute? There have been many of these institutes come and go, and probably the @broadinstitute (Cambridge, US) and the @sangerinstitute (Cambridge, UK) are the two referents in historical terms and in their magnitude of achievements in #genomics. So if we take them as an example, what do
Feb 24, 2023 5 tweets 1 min read
One of the rather big announcements by $BLI Berkeley Lights (soon to be renamed PhenomeX) is that there would be a new Beacon instrument released in 2023: the Beacon Quest, a 2-chip optofluidic system for academic research. Image Those of you that have been reading this account for a while will remember that the Beacon is a multi-million dollar large-fridge/freezer instrument that does high-throughput single-cell phenotyping, and the main product in the product line for Berkeley Lights (PhenomeX).
Feb 23, 2023 5 tweets 2 min read
In #NextGenerationSequencing news, $ILMN Illumina has some more details on the website for the NextSeq 1000/2000 kits, now including a 100 cycle kit for the P1 flowcells, and the 600 cycle kits for P1 and P2. Image The interesting detail is that the P2 600 cycles kit gives 300M Reads CPF (Clusters passing filter), compared to the equivalent 300 cycle kit on the same flowcell (400M). So either the diameter of the wells is different, or about 100M Clusters are "lost" in the 600 cycle kit.
Feb 11, 2023 21 tweets 5 min read
The world of Next-Generation Sequencing (NGS) post-#AGBT23:
1) Some will say that $ILMN Illumina is sleep-walking into a cliff: the company has been dominating the field with 80-90%+ of the market-share, but they are unable to retain their technological advantage to competitors: - Illumina doesn't have the most affordable $/Gb platform anymore, currently at $3.2/Gb, and $2/Gb in H2 2023, but others are already at $2/Gb, $1.5/Gb and will be at $1/Gb in Q3 2023.
Feb 10, 2023 13 tweets 8 min read
A summary of announcements/highlights from #AGBT23 (in no particular order): #AGBT23 cfDNA methylation profiling as a blood biomarker for Congestive Heart Failure. This is from the same team that gave you the @GrailBio Methylation Atlas, now applied to biomarker discovery.…
Feb 10, 2023 18 tweets 3 min read
In #NextGenerationProteomics news, today we cover the basics of Proximity ligation assay (PLA) technology, also known as proximity barcoding assay technology, which is a method for detecting protein-protein interactions in cells or tissues. The assay is based on the principle of ligating two probes (such as antibodies) that are in close proximity to each other, typically within a few nanometers. The ligation reaction produces a circular DNA molecule that is amplified by polymerase chain reaction (PCR) and
Feb 9, 2023 4 tweets 2 min read
#AGBT23 More details on the $ILMN Illumina Infinity reads technology from Alex Aravanis (post from LinkedIn). Also first data shared on XLEAP-SBS chemistry for the NextSeq 1000/2000 instruments. Not sure why would anyone buy one of these instruments given the alternatives from @ElemBio and @CompleteGenomic 's G400.
Feb 8, 2023 8 tweets 2 min read
Given all the talk of $100 genomes and tens of thousands of genomes being sequenced per year on a single instrument, the question arises: how many of these sequencing factories are we going to see? how many genome equivalents do we need capacity for? Taking the 50,000 genomes a year mark as a starting number, and considering we have 140 million new-borns a year, we would need 2,800 DNBSEQ T20 factories distributed around the world only to keep up with the new-born human population.
Feb 8, 2023 4 tweets 2 min read
In #NextGenerationSequencing, @CompleteGenomic's new of the <$100/genome with their DNBSEQ T20 available from Q3 2023, and their T7x3 $130/genome pricing, we now have 3 companies that have hit the $200/genome mark with announcements: @ElemBio $ILMN Illumina and Complete Genomics. Both $ILMN Illumina and @CompleteGenomic's will hit the $200/genome and <$100/genome mark in the second half of 2023, but @ElemBio Element Bio AVITIx3 and Complete Genomics T7x3 pricing models are *now* available at $200/genome and $130/genome respectively.
Jan 13, 2023 7 tweets 3 min read
In #JPM2023, $NAUT Nautilus Bio didn't make their slides available, but they have a slide deck from an investor meeting in December 2022. They intend to launch their Proteome Analysis Platform in Mid-2024. They see a market opportunity of $25B, where 50% would be BioPharma customers, and 20% Academic and Research.
Jan 13, 2023 4 tweets 2 min read
In #JPM2023 news, $SEER also presented. They are another of the Next Generation Proteomics Sequencing players. One of their USPs is that they have an approach capable of finding different protein variants that would be undistinguishable with affinity-based approaches. This includes slice variants, where the "Peptide Level" identification allows them to detect meaningful differences where other approaches are not able to.
Jan 13, 2023 4 tweets 2 min read
In #JPM2023 news, $OLK Olink presented and showed good numbers, especially for their high-plex segment. Olink believes they have <5% penetration on the mid-plex TAM