The evolution of nucleic acid sequencing and what it means for Genomics and IP

The journey from deciphering individual DNA strands to sequencing entire genomes in hours represents one of biotechnology's most impressive transformations. The first human genome, completed through the Human Genome Project, took around 13 years to sequence and cost billions of dollars, whereas modern sequencing methods can now deliver a genome in hours for a few hundred dollars. For those interested in patents and life sciences, understanding the technical evolution of sequencing methods offers insights into how fundamental scientific advances translate into valuable patent portfolios.
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First Generation: Sanger

Developed in 1977, Sanger sequencing established the foundation for modern DNA sequencing. The technique relies on modified nucleotides called dideoxy nucleotides (ddNTPs) that, when incorporated during DNA synthesis, terminate the growing chain due to their lack of a 3'-OH group. By creating DNA fragments of varying lengths that can be separated and analysed, the Sanger method can be used to determine DNA sequences base by base.

Despite its ground breaking nature, Sanger sequencing is labour-intensive and costly. Its maximum read length is around 1,000 base pairs and throughput is limited by its sequential nature. Nevertheless, it remained the gold standard for over two decades and powered the completion of the Human Genome Project. Its high accuracy, at approximately99.9%, still makes it useful for validating short sequences and verifying genetic variants in clinical settings today.

Second Generation: The NGS Revolution

The introduction of next-generation sequencing (NGS) in the mid-2000s transformed genomics by enabling massively parallel sequencing, processing millions of DNA fragments simultaneously, rather than one at a time. This shift reduced sequencing costs by orders of magnitude and improved access to genomic analysis.

Illumina Sequencing-by-Synthesis

Illumina's platform dominates the NGS market through its sequencing-by-synthesis (SBS) approach. Genomic DNA is first fragmented, ligated to adaptors and loaded onto a flow cell, where each fragment is immobilised and clonally amplified into a cluster by bridge amplification. During sequencing, fluorescently labelled nucleotides are added sequentially in cycles. Each nucleotide incorporation produces a distinct fluorescent signal captured by optical detectors. This results in millions of short reads that are computationally aligned (e.g. to a reference genome) to reconstruct the original longer sequence.

Illumina systems deliver high accuracy, with fragment read lengths typically between 50-300 base pairs. Their scalability ranges from benchtop instruments for small laboratories to production-scale sequencers generating terabases of data per run. This combination of accuracy, throughput, and declining costs has positioned Illumina as the current market leader in this space.

Ion Torrent: Semiconductor Sequencing

Ion Torrent technology, owned by Thermo Fisher, eliminated the optical detection systems used by Illumina. Instead, it detects hydrogen ions (H+) released during nucleotide incorporation. When a nucleotide binds to a growing DNA strand, it releases a hydrogen ion, causing a pH change detected by ion-sensitive field-effect transistors (ISFETs) embedded in a semiconductor chip.

DNA fragments are clonally amplified on beads via emulsion PCR (PCR in water-in-oil droplets to compartmentalise individual templates with beads), then loaded into microwells on a semiconductor chip and exposed to sequential nucleotide flow cycles,similar to SBS. Base incorporation is detected electronically by measuring pH changes and converting these signals directly into sequence data, enabling fast runs (as short as a few hours) and lower instrument costs by avoiding complex optics. However, accuracy can suffer in homopolymer regions (stretches of identical bases), where multiple incorporations in a single cycle make ion-based quantification harder, leading to slightly higher error rates. That said, the speed and cost benefits make Ion Torrent attractive for applications such as microbial genomics.

DNBSEQ: DNA Nanoball Technology

Another short‑read platform worth a mention is the MGI (a subsidiary of the BGI Group) DNBSEQ platform, which represents a distinct second‑generation approach using DNA nanoballs (DNBs). DNA fragments are circularised, amplified by rolling‑circle amplification into compact nanoballs, and loaded onto patterned nanoarrays. Sequencing is then performed using combinatorial probe-anchor synthesis (cPAS),an SBS‑like cyclic chemistry in which fluorescently labelled nucleotides are incorporated and the array is imaged each cycle to determine the sequence.

DNBSEQ technology is reported to achieve accuracy comparable to Illumina platforms while offering a user-friendly platform with competitive pricing, which could contribute to increased adoption in China and other Asian markets.

Third generation: long-read, single molecule sequencing

While second-generation methods revolutionised throughout and cost, their short-read lengths create challenges for assembling complete genomes from fragments. Third-generation technologies address these limitations by sequencing single DNA molecules in real time,producing reads measuring thousands to even millions of bases. These approaches have also opened the door to direct RNA sequencing.

Oxford Nanopore Sequencing

Oxford Nanopore Technologies(ONT) pioneered a unique approach: passing DNA or RNA strands through protein channels (nanopores) embedded in a synthetic membrane. An electrical current flows through the pore, and as nucleotides of the strand pass through, they cause characteristic disruptions in this current. Sophisticated algorithms decode these current fluctuations into sequence information.

Nanopore sequencing runs can be analysed as data are generated and read lengths can span from short fragments to multi‑mega base lengths. Notably, the technology can also be used to call certain base modifications (including methylation) and can directly sequence RNA strands. These properties can be leveraged where rapid, on‑site sequencing is useful, such as pathogen identification or field sampling.

Recent chemistry improvements and advanced base calling algorithms have further improved accuracy, making this exciting technology increasingly competitive for diverse genomic analyses.

Pacific Biosciences SMRT Sequencing

Single Molecule Real-Time (SMRT)sequencing, developed by Pacific Biosciences (PacBio), monitors individual DNA polymerase enzymes as they synthesise DNA in real time. The technology uses zero-mode wave guides (ZMWs), which are tiny observation chambers where a single polymerase molecule is attached to a DNA template. As the polymerase incorporates fluorescently labelled nucleotides, brief fluorescent pulses are detected and decoded into sequence information.

SMRT sequencing can generate long reads, and in circular consensus sequencing (CCS) mode the same circular template is read multiple times and combined into a high‑accuracy consensus (HiFi) read. Analysis software also supports epigenetic research by measuring the rate of DNA base incorporation during sequencing. The long reads of SMRT sequencing can be useful for de novo genome assembly and for detection of structural variants and repetitive regions.

Emerging technology: the fourth generation

Roche Sequencing by Expansion(SBX)

Roche has introduced a new approach called sequencing by expansion (SBX), designed to further enhance signal‑to‑noise performance in nanopore‑based sequencing. SBX first uses a biochemical conversion step to encode the sequence of a target nucleic acid (DNA or RNA) into a longer, engineered surrogate polymer (an “Xpandomer”) built from expandable nucleotide triphosphates (X‑NTPs). The resulting expanded molecule is then read using Roche’s nanopore sensing system, with the goal of enabling faster, high‑accuracy single‑molecule sequencing across a range of read lengths. It will be interesting to see whether SBX achieves broad uptake and becomes a widely adopted platform.

Patent landscape and IP strategy

The nucleic acid sequencing field exemplifies both the value of fundamental biotech platform patents and the emerging importance of algorithmic innovations in competitive strategy.

Platform Patents Remain Crucial

Foundational patents covering sequencing chemistries, hardware architectures, and new biochemical processes continue to command significant market power and generate substantial licensing revenue or settlement payments. The July 2022 settlement between Illumina and BGI (including Complete Genomics) illustrates this, where Illumina reportedly agreed to pay $325 million to resolve patent infringement claims and terminate multiple pending lawsuits.

Despite sequencing becoming more commoditised, core platform technologies remain fiercely protected and highly valuable. The sequencing industry has a long track record of patent and competition disputes, and multiple legal proceedings between major players and newer entrants remain ongoing across jurisdictions, continuing to influence commercial strategy and market dynamics.

Algorithmic innovation

Sequencing advances increasing lyhinge on computation and machine learning, particularly for improved error correction and base/variant calling. This raises IP issues distinct from, and sometimes intersecting with, biochemical inventions. For instance, software and algorithm focussed claims can face tougher eligibility scrutiny and should be directed to concrete technical improvements (e.g., higher accuracy, lower compute, or new processing architectures), not abstract mathematics implemented on a computer.

For sequencing algorithms, companies must weigh patents against trade secrets or find ways of utilising both. Patents can block competitors but require full disclosure; where methods can be hard to reverse-engineer from outputs (as with many “black box” base callers), trade secrets may preserve advantage longer than a 20‑year patent term while avoiding disclosure that enables design‑around.

Balancing protection strategies

The most sophisticated IP strategies in sequencing combine multiple protection mechanisms, including platform patents for core hardware and chemistry, a mix of patents and trade secrets for algorithmic improvements, and copyright protection for software implementations. Companies must also consider that maintaining trade secrets requires robust confidentiality measures and does not provide any protection against independent third-party innovation, while patents demand ongoing prosecution costs and eventual public disclosure.

For both startups and established companies, navigating this complex landscape requires careful assessment of each innovation's characteristics, competitive dynamics, reverse-engineering risk, and long-term business strategy. The substantial settlements and ongoing litigation demonstrate that getting IP strategy right can determine market position and company valuation in this competitive sector.

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