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

Top posts of the year

And their main takeaways

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.

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.

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.

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.
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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.

Illumina Reagent Volumes And Recipes

58 implied HN points • 27 Aug 23
🕹 Technology Research Sequencing Recipes
  1. Illumina does not provide public disclosure on reagent volumes, but you can measure them from kits.
  2. Recipe files for different Illumina sequencing platforms are available online to guide reagent amounts for the flowcell.
  3. A Google doc has extracted reagent steps for a deblock/incorporation cycle from various Illumina recipe files.

Arguments Against Clinical Meta-genomics

58 implied HN points • 31 Jul 23
🔬 Science Sequencing Technology Methods
  1. Funding for surveillance is lacking, so focusing on diagnostics may not be practical.
  2. Existing methods can detect new pathogens, reducing the need for meta-genomic sequencing.
  3. Challenges exist in making meta-genomic sequencing platforms affordable and appealing compared to traditional methods.

PacBio Acquires Apton!

58 implied HN points • 04 Aug 23
🕹 Technology Biotech Acquisition Sequencing Innovation
  1. PacBio is acquiring Apton BioSystems for approximately $110M to enhance their sequencing technology.
  2. The acquisition of Apton seems strategic for PacBio to develop a competitive high-throughput sequencing instrument.
  3. PacBio's new instrument lineup includes a range of sequencers from mid-range short reads to high-throughput long reads.

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.

NextSeq 550 Imaging System

51 implied HN points • 11 Sep 23
🕹 Technology Imaging
  1. The post is about the NextSeq 550 Imaging System.
  2. The author discusses a HiSeq imaging module listing on eBay.
  3. The post is available only for paid subscribers.

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.

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.

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 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.

Compute In The HiSeq X

43 implied HN points • 15 Nov 23
🔬 Science Technology Hardware Storage
  1. HiSeq X uses an external compute server compared to MiSeq's internal computer setup.
  2. HiSeq X has larger storage volumes in various RAID configurations than MiSeq.
  3. HiSeq X offers about 4x the compute performance of MiSeq, while NovaSeq 6000 is 7 times faster than HiSeq X.

Everything Wrong With: "Illumina: The Measurement Monopoly" Part 1/8

43 implied HN points • 03 Nov 23
🕹 Technology Innovation Competition Industry Development Market
  1. Improvement in DNA sequencing has been slow compared to advancements in other industries like semiconductors
  2. Illumina's best selling sequencer is aging and there's a lack of significant competition in the market
  3. Technological advancements in sequencing are mainly incremental, with a focus on adding more cameras and making flow cells bigger

Some Thoughts On 10X Genomics

36 implied HN points • 18 Jan 24
🔬 Science Genomics Competitors Market Growth
  1. Spatial revenue for 10X Genomics is increasing, while single cell revenue growth is slowing down.
  2. There may not be much growth expected in single cell applications for 10X Genomics, but spatial sequencing shows potential for growth.
  3. 10X Genomics faces competition in the single cell market, but may retain a significant market share.

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.

Sequencing In Oncology

36 implied HN points • 23 Jan 24
🏥 Health & Wellness
  1. Clinical sequencing market is surpassing research in sequencing.
  2. Oncology is the largest clinical market, with a significant revenue.
  3. Companies like Exact Sciences are prominent players in precision oncology testing.

How Is A Flowcell Made? How Much Does It Cost?

36 implied HN points • 21 Dec 23
🔬 Science Technology Research Innovation
  1. The construction of a flowcell involves specific materials like Kapton KJ and Black Kapton.
  2. Some tests were done on the channel material, showing properties like self-extinguishing and tackiness at high temperatures.
  3. Channels are formed using a piece of cover glass and a section of the flowcell plastic material.

NextSeq 550 Imaging System and Fluidics Notes

36 implied HN points • 06 Jan 24
🕹 Technology Imaging System
  1. The NextSeq 550 Imaging System uses 6 identical imaging sub-modules.
  2. Each sub-module has its own camera, focusing electronics, and excitation sources.
  3. The post provides a summary of information based on one of these imaging modules and what's available in patents.

All About The MiSeq

36 implied HN points • 04 Sep 23
🔬 Science Genomics Sequencing Technology
  1. The MiSeq is one of Illumina's longest read sequencers.
  2. Illumina released the MiSeq to compete with Ion Torrent sales.
  3. The MiSeq is the oldest next-gen sequencer in the market, released in 2011.

Protein Sequencing And Nanopore Current Ranges...

29 implied HN points • 02 Mar 24
🔬 Science Biology Chemistry Technology Research Innovation
  1. Protein sequencing using nanopores is a topic of interest, with a recent study highlighting a large state space of 10^25 and using an Oxford Nanopore's R9.4.1 pore with a range of ~10pA.
  2. Investigating patents can provide insights into the current range for DNA sequencing and can spark further contemplation about the future of protein sequencing using nanopores.
  3. The detailed post on protein sequencing and nanopore current ranges is available for paid subscribers, emphasizing the exclusivity of the content.

DNA Tubes - The HiSeq X Fluidic System

29 implied HN points • 13 Dec 23
🔬 Science Genomics
  1. The HiSeq X DNA sequencer contains about 100 meters of tubing inside for its fluidics system.
  2. The majority of the tubing in the HiSeq X appears to be around 1.5mm OD and 1mm ID, possibly made of PTFE.
  3. The fluidic path of the HiSeq X is structured similarly to the Solexa Genome Analyzer and uses components from the same vendors.

Thoughts On Pacific Biosciences

29 implied HN points • 14 Sep 23
🔬 Science Sequencing Accuracy
  1. PacBio's raw accuracy has only slightly improved over 4 generations of instruments.
  2. Fundamental issues, like polymerase kinetics, may be limiting the accuracy of PacBio sequencing.
  3. PacBio has prioritized longer read lengths over accuracy, using cyclic consensus sequencing for improved results.