ASeq Newsletter

The ASeq Newsletter explores advancements and challenges within the sequencing technology landscape, focusing on industry dynamics, clinical applications, and market competition. It critically examines the role of major companies like Illumina, emerging technologies, and the impact of sequencing in diagnostics and oncology.

Sequencing Technology Genetics and Diagnostics Market Dynamics Clinical Applications Industry Analysis Technological Innovations Company Profiles

The hottest Substack posts of ASeq Newsletter

And their main takeaways

Twinstrand Further Thoughts

0 implied HN points • 15 Jun 21
  1. The post discusses Twinstrand and its potential utility in reducing error rates in sequencing protocols.
  2. The idea of having a kit to enhance Illumina sequencing for Q60 reads is well-received.
  3. There is a market interest in products that can improve sequencing accuracy.

Further thoughts on Quanterix

0 implied HN points • 30 Sep 21
  1. Quanterix boasts high sensitivity down to 0.01pg/ml.
  2. They offer a large dynamic range of over 100pg/ml.
  3. Quanterix aims for low cost with their approach.

Olink

0 implied HN points • 31 Aug 21
  1. Olink is developing a novel sequencing based proteomics platform with significant revenue growth.
  2. The PEA approach involves antibody pairs designed with oligo tags for protein detection.
  3. Olink's PEA-NGS platform shows promising correlations between qPCR and sequencing for protein analysis.

Illumina acquire GRAIL (maybe)

0 implied HN points • 20 Aug 21
  1. Illumina is moving forward with acquiring GRAIL.
  2. GRAIL focuses on sequencing cfDNA for early cancer detection.
  3. The acquisition of GRAIL by Illumina may impact the sequencing market.

First thoughts on PacBio and Omniome

0 implied HN points • 22 Jul 21
  1. PacBio is acquiring Omniome for $600 million.
  2. PacBio aims to offer low error rate short reads at high throughput.
  3. The acquisition is similar to Illumina's proposed acquisition of PacBio.
Get a weekly roundup of the best Substack posts, by hacker news affinity:

Welcome to ASeq

0 implied HN points • 14 Jun 21
  1. The ASeq newsletter by Nava Whiteford focuses on new approaches to DNA sequencing.
  2. The newsletter's content is similar to blog posts shared at 41j.com.
  3. Readers can get a general feel for the content by visiting the linked blog posts.

Solexa

0 implied HN points • 06 Aug 21
  1. Solexa made significant contributions to next-gen sequencing.
  2. Solexa's acquisition of Manteia's cluster generation technology was transformational.
  3. Illumina's acquisition of Solexa in 2007 was considered a bargain.

A few thoughts on Seer

0 implied HN points • 11 Jul 21
  1. Seer is a Proteomics sample prep company that aims to compress the dynamic range of proteins.
  2. Seer uses SPIONs (super-paramagnetic iron oxide nanoparticles) to capture subsets of proteins across the dynamic range.
  3. Seer simplifies protein sample prep and aims to automate the workflow for mass spectrometry analysis.

Somalogic

0 implied HN points • 05 Oct 21
  1. Somalogic is developing an aptamer-based protein detection platform with modified nucleotides to address the aptamer problem.
  2. Somalogic's platform shows potential for a large dynamic range and high resolution on their readout compared to other platforms like Olink and Nautilus.
  3. Challenges faced by Somalogic include binding issues between aptamer-protein and aptamer-array, as well as environmental factors impacting results.

Dreampore - Protein Sizing

0 implied HN points • 06 Jul 21
  1. The patent discusses identifying impurities in protein samples using nanopores
  2. The patent highlights the use of aerolysin nanopores for size determination at the single amino acid level
  3. The patent describes a potential application in measuring enzymatic activity on a single cell level

Nautilus Biotechnology

0 implied HN points • 30 Jun 21
  1. Nautilus Biotechnology is focused on developing a high throughput single-molecule protein fingerprinting platform.
  2. Their technology involves arraying single proteins on a surface using a structured DNA nanoball approach.
  3. They aim to identify and fingerprint proteins by using a variety of affinity reagents and comparing binding signals to a database of known protein fingerprints.

Other Nanopores - Part 1

0 implied HN points • 01 Dec 22
  1. Various companies are exploring tunneling current for DNA sequencing, but challenges remain in detecting individual nucleotides.
  2. Roswell Biotechnologies is investigating backbone conduction for DNA sequencing, showing potential for a unique sensing mechanism.
  3. Part 2 of the post will cover field and optical nanopore sequencing approaches, emphasizing the continuous exploration in the field.

Illumina's Nano-imprinted flowcells

0 implied HN points • 03 Oct 22
  1. Illumina is using Nano-imprinted flowcells to reduce manufacturing costs and maintain margins.
  2. Nano-imprinting is a process where masters make direct contact with substrates to create tiny structures at lower cost.
  3. Bringing nano-imprinting in-house allows Illumina to potentially reduce costs associated with outsourcing and gain more process control.

Quanterix

0 implied HN points • 27 Sep 21
  1. Quanterix is a company focused on building a high-sensitivity single molecule detection platform for proteomics applications.
  2. Their approach involves isolating antigens in wells to amplify detection of target proteins using an ELISA process.
  3. Quanterix's platform claims to offer increased sensitivity in measuring concentrations down to 0.01 pg/ml, showing potential value in applications like monitoring HIV viral load.

Guardant and Twinstrand

0 implied HN points • 04 Aug 21
  1. Twinstrand is suing Guardant for alleged patent infringement over their duplex sequencing approach.
  2. Guardant uses a targeted sequencing approach with high coverage and low error rates.
  3. Twinstrand was likely motivated by Guardant's success with digital sequencing when they were founded.

QuantumSi Prospectus Review

0 implied HN points • 02 Jul 21
  1. QuantumSi's protein sequencing involves fragmenting proteins and using transient binding characteristics to identify amino acids.
  2. Their chip uses semiconductor fabrication, but may lack accuracy in classification for full protein sequences.
  3. The product consists of sample prep box, sequencing instrument, and cloud-based analysis service, targeting a $21 billion market.

Nautilus Prospectus Review

0 implied HN points • 01 Jul 21
  1. The Nautilus prospectus provides insight into their scaffold technology and chip capacity.
  2. The arraying approach seems efficient with over 95% of sites being active.
  3. The document hints at complex reagent systems and potential high consumable costs.

Everything Wrong With: "Illumina: The Measurement Monopoly" Part 5/8

0 implied HN points • 03 Jan 24
  1. During the early 2000s, Illumina faced competition from companies like Pacific Biosciences, 454 Life Sciences, and Solexa Inc.
  2. Other sequencing startups existing back in 2005 included Reveo, SeiRad, DNA Electronics, Intelligent Biosystems, Complete Genomics, and Oxford Nanolabs.
  3. 454 Life Sciences and Solexa were the primary platforms showing data at the time, with Helicos and PacBio launching later.

Macklemore: Next-gen Sequencing Evangelist

0 implied HN points • 03 Nov 23
  1. Macklemore is a leading figure in next-gen sequencing, revolutionizing the field
  2. Macklemore believes that PacBio's Revio is the new clinical standard in human genetics
  3. PacBio and the Revio could become the new clinical standard in whole genome sequencing

Oxford Nanopore Acquires Northern Nanopore Instruments

0 implied HN points • 07 Nov 23
  1. Oxford Nanopore acquired Northern Nanopore Instruments, known for solid state nanopore research tools.
  2. Northern Nanopore used controlled breakdown approach for creating small nanopores in silicon membranes.
  3. Vincent Tabard-Cossa lab's method involved applying voltage slowly until membrane breakdown occurred, then modulating voltage post-breakdown.

Nanopore Sequencing Companies: Geneus

0 implied HN points • 15 Feb 25
🕹 Technology Biotechnology Medical Devices Genomics Startups Innovation
  1. Geneus is a nanopore sequencing company claiming 99% accuracy in their technology. They use special features that allow many sequencing units to fit on a tiny chip.
  2. Their sequencing method seems to be different from others, focusing on synthesizing a complementary strand with unique tags. This method helps identify the sequence of DNA more effectively.
  3. The advancements in size and technology from Geneus might be huge, but details on how they achieved this remain unclear.

Oxford Nanopore Layoffs

0 implied HN points • 18 Feb 25
💼 Business Startups Investments Layoffs Workforce Technology
  1. Oxford Nanopore has laid off around 60 employees, which is about 5% of its workforce. It's tough for those affected, and many were talented individuals.
  2. These layoffs come after reports of new investments in the company, suggesting there might be some uncertainty about reaching profitability soon.
  3. Despite having great technology and good people, the leadership at Oxford Nanopore seems to make questionable decisions, which raises concerns about the company's future.

Roche Nanopore: First Thoughts (pt2)

0 implied HN points • 20 Feb 25
🕹 Technology Biotechnology Genomics Medical Devices Innovation Research
  1. Roche is developing a new duplex approach that improves sequencing accuracy significantly, moving from Q20+ to around Q39. This is a big upgrade for DNA sequencing.
  2. The company aims to launch their product in 2026, but early access is expected in 2025. There's a chance they could face challenges during execution.
  3. While Roche's reads are shorter and competitive with other platforms, they will need to handle pricing and compete with long-read technologies from companies like Oxford and PacBio.

Oxford Nanopore Simplex Error Rate STILL >5%?

0 implied HN points • 08 Nov 23
  1. The Simplex Error Rate for Oxford Nanopore is still greater than 5%.
  2. Despite some slight improvement in accuracy, the overall error rate is at 5.74%.
  3. Current accuracy of Oxford Nanopore seems to be worse than first generation Illumina sequencers.

That New Nanopore Protein Sequencing Paper

0 implied HN points • 24 Oct 23
  1. The study designed synthetic proteins for nanopore sequencing with the ClpX unfoldase.
  2. Results showed single amino acid changes in a static context with some classification efficiency.
  3. Challenges remain in sequencing proteins due to the complexity of possible states and electron limitations.

Roche Nanopore: Instrument Cost

0 implied HN points • 27 Feb 25
🔬 Science Biotechnology Genetics Data Analysis Research Methods Instruments
  1. Roche is working on new nanopore sequencing technology, focusing on how much the instruments will cost to produce. Understanding these costs is important for the technology's success.
  2. The nanopore sequencing process involves collecting a large amount of data quickly, which means the data rates are extremely high. This could lead to challenges in storing and processing such vast amounts of information.
  3. Since the raw data volume is so large, it's unlikely that most users will store it all. Instead, they will probably need to focus on analyzing only the most crucial information collected.

Element@JPM

0 implied HN points • 16 Jan 25
💼 Business Biotechnology Partnerships Research Innovation Finance
  1. Element Biosciences is focused on partnerships aimed at diagnostics and proteomics. This shows they are expanding their technology for better healthcare solutions.
  2. The company's presentation at the JPM conference was notable, even if the details are not easily found online. It hints that their innovations are gaining attention.
  3. The updates are specifically for paid subscribers, indicating that there's exclusive information available for those who support the publication.

The PacBio Vega Chips

0 implied HN points • 12 Nov 24
🕹 Technology Data Analysis Chip Design Genetics Biotechnology Innovation
  1. The PacBio Vega Chips are similar to the Revio chips, but they provide much less data. This means they might not be as powerful for certain tasks.
  2. The data from the Vega chips is available for analysis, and people can check it out for deeper understanding.
  3. This information is part of a subscription service, which means you can get more insights if you become a paid member.

PacBio@JPM - Market/Financials

0 implied HN points • 15 Jan 25
💼 Business Market Trends Financial Analysis Corporate strategy Investment Insights Revenue growth
  1. The Onso sequencer was barely mentioned in the recent PacBio presentation, which is surprising given its high accuracy.
  2. There seems to be a new short read sequencer coming soon, called SuperOnso, which is expected to show results by late 2025.
  3. On a positive note, the revenue from consumables is growing, and PacBio has managed to significantly reduce their financial losses.

JPM In Review

0 implied HN points • 21 Jan 25
💼 Business Finance Technology Market Analysis Healthcare Investments
  1. Oxford Nanopore's revenue is growing, but it's unclear if they'll be profitable by 2027. Their growth is mostly due to a product called Plasmidsaurus, but future short-term growth is uncertain.
  2. Pacific Biosciences is struggling with revenue and sticking to their short reads strategy, which isn't performing well. However, their technical advancements and research look promising.
  3. Illumina's revenue is stable, which is good given current market challenges. They are focusing more on clinical applications, aiming to provide high-quality insights at lower costs.

More Money For Oxford

0 implied HN points • 05 Nov 24
🔬 Science Biotechnology Research Innovation Funding Education
  1. Oxford Nanopore is receiving increased funding. This suggests that there is a growing confidence in its potential.
  2. More money flowing to Oxford indicates a belief in innovation and growth. It's a positive sign for their future developments.
  3. Investors are likely seeing value in what Oxford Nanopore can offer. This could lead to exciting advancements in their technology.

ONT Not Suing MGI?

0 implied HN points • 04 Nov 24
🔬 Science Genomics Biotechnology Research Health Ethics
  1. ONT has decided not to sue MGI after all. This means there won't be legal issues between these companies right now.
  2. The decision was reported by GenomeWeb, highlighting a significant change in ONT's approach.
  3. This could impact the business relationship between ONT and BGI, since they are linked in some way.

Electronic Biosciences Magnetic Motion Control

0 implied HN points • 19 Nov 24
🔬 Science Biosciences Technology Patents Research Innovation
  1. Electronic Biosciences is a company that has been around for a long time, focusing on nanopore technology for detection methods. They're known for getting funding from DARPA since around 2008.
  2. The company is developing new ways to control motion using magnetism, which could be cool in tech applications.
  3. The information about their patents shows they are continuing to innovate and explore different possibilities in the bioscience field.

All Aboard The NanoTrain! Chu Chu!

0 implied HN points • 31 Oct 24
🔬 Science Biotechnology Genetics Sequencing Research Technology
  1. Universal Sequencing Technology is gaining attention again after being quiet for a while. People are curious about their progress and what they are focusing on now.
  2. They seem to have shifted their focus from single molecule sequencing to developing various sample preparation kits. This shows they are adapting to changes in the field.
  3. This update may be particularly interesting for those who follow advancements in sequencing technology and want to know about new tools or methods in the industry.