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

10X Chromium Controller Component Cost Is Likely <$5000

29 implied HN points • 28 Dec 23
🔬 Science Research Technology Innovation Analysis Equipment
  1. The 10X Chromium Controller component cost is likely less than $5000, significantly lower than its original $35000 price tag.
  2. The key components like Thomas diaphragm pumps range from $200 to $400, making up a portion of the instrument's cost.
  3. Through further cost optimization, it's possible to produce a comparable instrument for much less than $5000.

Death And NanoString

14 implied HN points • 08 Feb 24
  1. Death can be understood in different categories like reversible/natural or irreversible/catastrophic.
  2. Chapter 11 bankruptcy involves a compromise between a debtor and creditors to reorganize a company.
  3. The concept of a 'forever company' raises questions about the necessity of companies dying for market evolution.

Singular Spatial Sequencing

14 implied HN points • 06 Feb 24
🕹 Technology Innovation Startups Biotech
  1. Singular Genomics announced a new spatial instrument called G4X for spatial analysis via in situ sequencing using RNA templates.
  2. The G4X technology is similar to 10X Xenium but appears more limited in terms of addressable targets per cell compared to Xenium.
  3. There are concerns about potential patent issues with 10X's spatial patents and ReadCoor IP, raising commercial uncertainties despite the neat research and technology aspects.
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Is Oxford Nanopore Failing?

21 implied HN points • 11 Jan 24
💼 Business Finance Technology Growth Failure Market Analysis
  1. Oxford Nanopore has about 3.5 years of cash runway based on their current financial situation.
  2. The company received significant amounts of money outside of product sales which impacted their financial numbers.
  3. Oxford Nanopore's growth trajectory and accuracy claims may not align with their goals of surpassing Illumina in the market.

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.

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.

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

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.

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.

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.

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.

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.

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.

An Overview Of The HiSeq X Optical System

14 implied HN points • 15 Dec 23
🔬 Science
  1. The HiSeq X optical system uses TDI imaging to scan across the surface and build up an image line by line.
  2. The system reads out 4 different emission colors which complicates the imaging process.
  3. Various components like ND filters, Powell lens, laser shutter, and dichroic mirror/filter play key roles in enabling accurate imaging on the HiSeq X optical system.

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.

Repeat Expansions - Long and Short Read Sequencing

14 implied HN points • 11 Dec 23
  1. Repeat expansions can be studied through long and short read sequencing to observe differences.
  2. FMR1 gene on the X chromosome can lead to fragile X syndrome due to repeat expansions.
  3. Sequencing technologies like PacBio provide clearer results for repeat expansions compared to short-read data.

Everything Wrong With: "Illumina: The Measurement Monopoly" Part 4/8

14 implied HN points • 10 Dec 23
🔬 Science Biology Chemistry Physics Engineering Technology
  1. The term 'TechBio' may seem superficial, but technology development in biology is complex and involves a mix of disciplines.
  2. The first qPCR machine from 1992 involved intricate instrumentation like photomultiplier tubes and a variety of electronic components.
  3. The development of technology in biology requires navigating complexity and balancing biochemistry and detection techniques to meet market demands.

The MiSeq's Excitation LEDs!

21 implied HN points • 02 Nov 23
🔬 Science Specifications Components
  1. The MiSeq instrument by Illumina uses LEDs for excitation, which are cost-effective compared to lasers.
  2. The LEDs used include a photodiode for power monitoring and specific LEDs like the OSRAM green LED and Luminus red LED.
  3. Overall, the LED-based assembly in MiSeq replaces expensive lasers with affordable components, making it a cost-effective solution in sequencing tools.

Bringing Up An Old EBay MiSeq

14 implied HN points • 06 Dec 23
🔬 Science Biotechnology
  1. Bought an old MiSeq on eBay, faced issues like getting reagents from Illumina and shipping to Japan but managed to resolve them
  2. Had to reset the password for the MiSeq, managed it by using a Linux system to reset and configure passwords
  3. Prepped PhiX control, ran a sequencing run with over-clustered results, but was able to get 20+ bases aligned to PhiX

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.

The MiSeq's Cameras And The Economics of DNA Sequencers

14 implied HN points • 06 Nov 23
🔬 Science Biology Technology Economics Imaging Innovation
  1. DNA sequencers are expensive due to economies of scale, unlike digital cameras that benefit from mass production.
  2. Cheap DNA sequencers could greatly benefit society, but creating them poses technical and sociological challenges.
  3. The cost of components for DNA sequencers, like cameras in the MiSeq, can be broken down to see how much they contribute to the overall expensive price.

Genus Plc And Sex Selection

14 implied HN points • 10 Oct 23
🔬 Science Biotechnology Genetics Agriculture Ethics
  1. Genus Plc focuses on agricultural biotech products, particularly in pig and bovine semen.
  2. They offer Intelligen sexing technologies for selecting the sex of offspring in animals.
  3. The use of similar sex selection technologies in humans raises ethical concerns and has varying levels of effectiveness.

Let's Buy Singular Genomics!

21 implied HN points • 13 Aug 23
🕹 Technology Genomics Sequencing Instruments Market Research
  1. Singular Genomics is struggling with low share price and few instrument sales.
  2. Proposed solution is to develop a cheap MiSeq-class sequencer to target the lower end of the market.
  3. By focusing on cost-effective instrument with minimal field support, the company aims to attract small labs and researchers.

The Utility of Long Reads...

7 implied HN points • 29 Nov 23
  1. Short reads can address a large portion of the human genome efficiently.
  2. Long reads allow us to tackle 5-10% of the genome that short reads alone cannot.
  3. Analyzing genome uniqueness and repeat structure helps evaluate new approaches in genomics.

HiSeq X Cameras and 4 Color Fluorophores

7 implied HN points • 24 Nov 23
  1. HiSeq X cameras use TDI imaging for capturing images.
  2. HiSeq X cameras have two independent sensors each, totaling 4 sensors for 4 color chemistry.
  3. Proper illumination and filtering techniques are crucial to prevent photo-damage in HiSeq X cameras.