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

Genopore - Nanopore Protein Detection

7 implied HN points • 08 Jan 25
🔬 Science Biotechnology Research Health Innovation Diagnostics
  1. Genopore is an Israeli company focused on a new way to detect proteins. They are more interested in detection methods rather than just fingerprinting or sequencing proteins.
  2. The technology they are developing is considered novel, suggesting it could bring new advancements to protein detection.
  3. Their patents and website indicate they have a clear direction towards enhancing protein detection capabilities.

QuantumSi - Routes Forward

21 implied HN points • 24 Nov 24
🕹 Technology Semiconductors Electronics Chemistry Data processing
  1. QuantumSi has recently laid off employees as they restructure due to poor sales. This is tough for those affected, and it's hoped they find new jobs soon.
  2. To reach billions of reads, QuantumSi is exploring chip reuse but it's tricky since they might need to clean the chip quickly and keep it working well after many uses.
  3. They are also looking at using multiple imaging regions to help with throughput instead of reusing chips, which could be a more practical solution for their counting goals.

The NextSeq 2000 Optical System

14 implied HN points • 13 Dec 24
🔬 Science Biology Physics Chemistry Technology Engineering
  1. The NextSeq 2000 utilizes structured illumination to improve imaging quality. This technology allows for clearer images of very small features that were hard to see before.
  2. This updated information aims to reach a broader audience, moving from a previous platform to this one.
  3. The content is exclusive for paid subscribers, highlighting the value in subscribing for more detailed insights.

Announcing Biofound - Connecting Biotech Founders

29 implied HN points • 02 Nov 24
💼 Business Startups Entrepreneurship Networking Biotech Funding
  1. A new mailing list called Biofound has been started to connect biotech founders and people who want to help. It's a place for them to meet each other and collaborate.
  2. People can post about their startups if they're looking for co-founders, advisors, or technical help. You can even do this anonymously if you prefer.
  3. Unlike a previous list focused on funding, Biofound aims to facilitate general connections, helping people network beyond just seeking investment.
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Biomemory - Enzymatic Data Storage

14 implied HN points • 11 Dec 24
🕹 Technology Data Storage Startups Investments Biotechnology
  1. A French startup called Biomemory has raised $18 million for its new enzymatic data storage technology. This is surprising because other companies in the same field are struggling.
  2. Biomemory's first product includes a card that can encode data into DNA, specifically a message of 'Hello World!' using a unique encoding method. This method has some inefficiencies, as it uses more bases than necessary.
  3. The startup faces challenges with encoding data, particularly with homopolymers, which might complicate their technology. Future developments could look into improving these encoding issues.

Ion Torrent Proton Chip Manifold

14 implied HN points • 09 Dec 24
🕹 Technology Innovation Engineering Hardware Design Manufacturing
  1. The Ion Torrent Proton uses a unique chip manifold design that is quite intricate and beautiful. It seems it can't be made from a single piece; instead, it might need to be made in two parts and then joined together.
  2. The chip manifold's complexity showcases advanced engineering in its design and fabrication process. This attention to detail highlights the innovation in developing such technology.
  3. The information shared is for paid subscribers, indicating that there are exclusive insights available for those who support the content. It's a way to provide deeper knowledge to interested readers.

That GenomeWeb Article On Spatial Growth...

7 implied HN points • 03 Jan 25
🔬 Science Biology Technology Innovation Health Research
  1. New technology is emerging in the field of single-cell sequencing, making it easier to analyze large amounts of data. Companies like Parse and 10x are leading the way with new products.
  2. The market for bio-tech is growing, but there are signs it may slow down in the upcoming year. Keeping an eye on industry trends will be important.
  3. Illumina is preparing to launch new technology in 2025, which could have a big impact on gene expression studies. It's worth watching how these advancements will change research.

The Ion Proton Fluidics System

14 implied HN points • 06 Dec 24
🕹 Technology Engineering Systems Devices Innovation
  1. The Ion Proton Fluidics System has a complex fluidics setup that is important for its function. It may look confusing at first, but breaking it down can help understand how it works.
  2. Understanding the fluidics system is crucial for improving its performance. Learning about its components can lead to better maintenance and efficiency.
  3. This post is specifically tailored for paid subscribers, indicating there is exclusive content available for those who support the platform. Being a paid member might offer more in-depth insights.

The PacBio Vega - More Tech Details

21 implied HN points • 07 Nov 24
🕹 Technology Engineering Biotechnology Research Instruments Computing
  1. The PacBio Vega is designed for small labs and minimizes downtime between runs. Users can load new samples while a run is ongoing, making it efficient.
  2. The technology in the Vega seems to be similar to the Revio but aims to reduce costs, likely making high-quality sequencing more accessible to small research centers.
  3. There's curiosity about how PacBio has managed to incorporate advanced computing power into a compact design, which is crucial for producing quality data without needing expensive equipment.

QuantumSi - Chips No More!

14 implied HN points • 21 Nov 24
🕹 Technology Quantum Computing Bioengineering Investments Startups
  1. QuantumSi shared new information during their investor day, showcasing their advancements. They seem to be moving beyond traditional chips in their technology.
  2. The QuantumSi project is gaining attention, and many connections are being made in the community. It's a good time to get involved and learn more.
  3. Readers are encouraged to check out the investor day presentation for deeper insights into QuantumSi's direction. It might be useful for those interested in tech innovations.

Year In Review - Long Reads

7 implied HN points • 18 Dec 24
🕹 Technology Genomics Sequencing Biotechnology Medical Research Health tech
  1. PacBio faced challenges in the stock market but still aims to provide high-quality clinical genomic sequencing. They are seen as a strong competitor in the long-read space despite financial struggles.
  2. Oxford Nanopore has been active in raising funds but has dealt with internal issues and departures of significant team members. Profitability remains an elusive goal for both them and PacBio.
  3. New competitors are emerging in the long-read sequencing market, including Roche and BGI, who are exploring nanopore sequencing technology. This could shake up the landscape for current players.

More Nanopore Nonsense...

14 implied HN points • 08 Nov 24
🔬 Science Biotechnology Genetics Research Innovation Health
  1. Clive Brown has left Oxford Nanopore, and there are mixed reports about his last day at the company.
  2. Oxford Nanopore attempted to prevent Estonia from acquiring PacBio sequencers for a population sequencing project.
  3. The details of the dispute regarding the sequencers can be found in a public document shared by a user on Discord.

The PacBio Benchtop - The Vega

14 implied HN points • 07 Nov 24
🕹 Technology Biotechnology Genomics Instrumentation Data Analysis Healthcare
  1. The new PacBio Vega is a benchtop DNA sequencer that provides 60Gb of data in just 24 hours and costs $169,000. There's also a lower cost option for labs that need less capacity.
  2. When compared to Oxford Nanopore's PromethION, the Vega appears to deliver better accuracy and more consistent results, making it a suitable choice for smaller labs needing reliable output.
  3. The launch of the Vega could help PacBio increase revenue and broaden its market presence, as it appeals to labs that want access to high-quality sequencing without breaking the bank.

Western Civilization And Genomics

14 implied HN points • 06 Nov 24
🔬 Science Genomics History Biology Humanity Philosophy
  1. Western civilization has thrived for about 2500 years, with many achievements in science and knowledge. This long history has shaped our understanding of complex topics like genomics.
  2. Key figures like Isaac Newton helped establish scientific methods, moving society away from superstition to rational thinking. This paved the way for discoveries in inheritance and DNA.
  3. Today, we can sequence human genomes more easily than ever before. This ability can change how we understand our biology and ourselves in profound ways.

Ion Proton - FPGAs!

7 implied HN points • 10 Dec 24
🕹 Technology Hardware Software Data Engineering Innovation
  1. The Ion Proton DNA sequencer uses specific hardware for DNA acquisition, which is important for its function.
  2. This hardware is expensive and involves custom designs, making it a significant cost for the sequencer.
  3. The upcoming summary will focus on the disassembly of the Ion Proton, which reveals more about its inner workings.

Horrors Of The Theoretical Maximum

14 implied HN points • 30 Oct 24
🕹 Technology Bioinformatics Data Analysis Genomics Research Methods
  1. Vendors sometimes quote theoretical maximums for data output, which can be misleading. It's important to understand that these numbers might not reflect actual performance.
  2. Comparing different technologies can be complicated because they have different specifications and capabilities. Each technology, like PacBio, Oxford Nanopore, and Illumina, has its unique strengths and limitations.
  3. In the real world, the difference between what is theoretically possible and what is actually achieved can be significant. This means we should be cautious and not rely solely on theoretical figures.

ONT Suing BGI Again!

7 implied HN points • 07 Dec 24
🕹 Technology Biotechnology Intellectual Property Legal issues Product Development
  1. Oxford Nanopore Technologies (ONT) is taking legal action against BGI in the UK. This follows their earlier decision to pause a lawsuit in the US.
  2. Users of Oxford Nanopore products might face limitations due to user agreements, which could affect their ability to develop competing technologies.
  3. Currently, there isn't concrete evidence proving that BGI has violated ONT's patents, suggesting that the situation could require more careful consideration and evidence before further legal actions.

A Q&A With... Me.

72 implied HN points • 26 Feb 24
🎙 Podcasts
  1. The post is a Q&A session with Nava Whiteford, shared on Substack, a platform for paid subscribers.
  2. Nava was asked to participate in a Q&A for a conference, but it's uncertain when or how it will be published.
  3. The post is exclusive for paid subscribers, and interested individuals can subscribe on Substack to access it.

Clive's Departure from Oxford Confirmed

7 implied HN points • 11 Nov 24
🕹 Technology Startups Leadership Innovation Biotechnology Company Culture
  1. Clive has left Oxford Nanopore, and Rosemary Sinclair Dokos and Lakmal Jayasinghe are taking over his roles. They seem like good choices for the company.
  2. Clive's leadership was important to the company's vision and success, and many believe it could have struggled without him.
  3. There have been several senior departures from Oxford in the past year, which might have changed the company's culture, but product and strategy changes are still unclear.

Nanostring Vendors

51 implied HN points • 05 Mar 24
💼 Business Bankruptcy Instruments
  1. The post discusses Nanostring creditors identified in bankruptcy proceedings, indicating a Google document with detailed creditor breakdowns and mentions suppliers of 'Compelling presentations for litigation'.
  2. The focus of interest lies in the technical components used in Nanostring instruments, narrowing down the list significantly.
  3. Access to the full post is restricted to paid subscribers.

Those 10X Patents

51 implied HN points • 24 Feb 24
🕹 Technology Patents Lawsuits Enforcement Imaging
  1. 10X Genomics has been involved in several lawsuits related to their patents in the spatial space, with most patents set to expire around April 2031.
  2. There is one patent that expires in 2036, which seems to be focused on imaging systems.
  3. If 10X Genomics continues to enforce their patents effectively, they could maintain dominance in the spatial market for the next 7 years.

Some Atto-532 In A MiSeq

51 implied HN points • 15 Feb 24
🔬 Science Imaging Research
  1. The post discusses experimenting with Atto-532 in a MiSeq for epi-fluorescent microscopy, highlighting the process of preparing and imaging on a microscope slide.
  2. Images taken show varying brightness in different color channels, with Atto-532 matching well with the green LED used in MiSeq technology.
  3. There's an anticipation of potential dye crosstalk, with the expectation of leakage from the G dye into the T channel, suggesting Atto-532 as a good match for the G dye.

I Am A Sequencing Absolutist

80 implied HN points • 06 Oct 23
🏥 Health & Wellness Genetics Diagnosis Testing Medical care
  1. The author strongly believes in the power and importance of DNA and RNA sequencing in diagnostics.
  2. Many clinicians tend to delay diagnostic tests unless absolutely necessary, relying on common symptoms and tests first.
  3. Despite the potential of advanced genetic testing, clinicians may be hesitant to order tests if there are no clear treatment options available.

Rationalizing The Illumina Instrument Lineup

51 implied HN points • 09 Jan 24
🕹 Technology Biotechnology Instruments
  1. Illumina has a variety of sequencing instruments in their lineup, which includes different models and variations.
  2. The cost of production for these instruments varies based on the technology and components used.
  3. Rationalizing the Illumina instrument lineup could involve withdrawing some current models and introducing new, more cost-effective options.

The Fall Of The Kingdom Of Illumina

80 implied HN points • 19 Aug 23
⚔ Fiction Fantasy Adventure Drama
  1. King Flatley ruled the kingdom of Illumina for 17 years, but an evil wizard infiltrated causing chaos.
  2. The evil wizard DeSouza's reign of terror led to the kingdom's downfall as he sought the power of the Holy GRAIL.
  3. Prince Icahn rose to challenge DeSouza, leading to a battle that ultimately determined the fate of Illumina.

Oxford Nanopore - Baseless Rumors

36 implied HN points • 24 Feb 24
🕹 Technology Rumors Layoffs Strategy Management Technology
  1. Rumors about layoffs and nepotism at Oxford Nanopore are circulating, potentially impacting the company's share price.
  2. The company's delayed announcement of layoffs raises questions, with some seeing it as a strategic move and others as a demotivational tactic for employees.
  3. The overall strategy of Oxford Nanopore is being called into question, with suggestions that changes may be needed for the company to succeed.

Ultima Genomics - More Reads Per Bead?

36 implied HN points • 20 Feb 24
🔬 Science
  1. In DNA sequencing, methods that ensure one bead and one template per droplet can significantly increase throughput.
  2. Ultima Genomics has been working on a method that allows 100% of beads to have product from a single template, potentially doubling throughput.
  3. Ultima's approach shows promise in reducing polyclonal rates, potentially offering an advantage over existing platforms.

4 Reads Per Cluster! Simultaneously Paired End-Sequencing!

36 implied HN points • 31 Jan 24
🔬 Science Genetics Bioinformatics Sequencing Biotechnology
  1. Illumina has a method to potentially double their instruments' throughput, but it may come with a slight decrease in accuracy.
  2. By simultaneously reading both the forward and reverse strands, Illumina can achieve four reads per cluster, doubling the throughput.
  3. Implementing the simultaneous paired-end sequencing approach may be challenging without sacrificing accuracy, but it opens up opportunities for increased throughput in the future.

The HiSeq X Flowcell

43 implied HN points • 18 Dec 23
🔬 Science Research Biotechnology Data Analysis
  1. About 30% of reagents may be wasted in dead volume on the HiSeq X Flowcell.
  2. The flowcell channels on the HiSeq X have a volume range of 15 to 20 uL.
  3. There could be significant cost implications if reagents costs are a large part of the sequencing expenses.

Would You DEFINITELY Buy A Sequencer That Was...

65 implied HN points • 23 Aug 23
🕹 Technology Innovation Electronics Market research Survey Community Building
  1. The post discusses a poll for what people want in a sequencer, without vendors guiding the surveys.
  2. Considerations in the polls include the idea of a sequencer being identical except for one magical different feature from a new vendor.
  3. The poll asks if you would definitely buy the sequencer, potentially changing a planned purchasing decision.

Not MiSeq Beaters

65 implied HN points • 20 Aug 23
🔬 Science Genetics
  1. Some companies are introducing products to compete with Illumina's MiSeq in the lower end of the sequencing market, but they may not pose a strong challenge.
  2. A recent post on GenomeWeb discussed the emergence of kits and instruments targeting the low-throughput market.
  3. The competition to Illumina's dominance at the lower end of the sequencing market continues to evolve.