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Overview of sequencing by expansion (SBX) technology

Published on December 31, 2025 | 5 min read

Key takeaways

Sequencing by expansion (SBX) uses a novel strategy to convert DNA information into Xpandomer molecules, helping to overcome signal-to-noise limitations of current nanopore-based sequencing technologies
When combined with high-throughput arrays and real-time processing—this pore-based technology delivers fast, flexible, and accurate single-molecule sequencing at scale
SBX offers two distinct workflows: SBX-D (duplex sequencing), which provides high accuracy for applications like WGS and oncology, and SBX-S (simplex sequencing), which is optimized for ultra-high throughput and is suited for applications like transcriptome analysis and identifying novel isoforms

A new approach to NGS

Roche has responded to the demand for improved performance by developing a new category of next-generation sequencing (NGS) technology, called sequencing by expansion (SBX). This powerful approach to NGS has been designed for flexibility and performance, with headroom to scale into the future.

Fundamentally, SBX technology converts DNA information into a longer, “expanded” molecule, overcoming the spatial challenges of current nanopore technology and enabling higher signal-to-noise for improved accuracy.¹ This expanded molecule, or Xpandomer, is then fed through Roche’s proprietary nanopore, driving single-molecule sequencing at incredibly high rates of speed and facilitating rapid access to usable sequencing data.

Roche's SBX technology across three foundational building blocks

X-NTPs

SBX technology utilizes a proprietary biochemical conversion process to expand and encode the sequence of a DNA template into an Xpandomer molecule

The building blocks of the Xpandomer are expandable nucleotide triphosphates, or X-NTPs. These high signal-to-noise reporters are the result of sophisticated molecular engineering and include an easily differentiated reporter code, a translocation control element for highly controlled transit through the pore, enhancers for robust Xpandomer synthesis, and an acid-cleavable bond for post-replication expansion.

Xpandomer synthesis

Xpandomer synthesis enables precise X-NTP incorporation for high-fidelity sequencing

Each of the four easily differentiated X-NTPs (one for each base) acts as a substrate for template-dependent, polymerase-based replication. The polymerase, XP synthase, has been carefully engineered to incorporate large X-NTP monomers, enabling >99.3% mean raw read accuracy, uniform GC coverage, and longer read lengths. Polymerase enhancing moieties, or PEMs, are also added to the synthesis reaction to assist the polymerase in properly incorporating X-NTPs into the growing polymer.

By stabilizing the extending molecule, PEMs play an important role in increasing read length beyond traditional short-read sequencing technologies. Following synthesis of the surrogate molecule, acid-cleavable bonds are broken, allowing the newly synthesized Xpandomer to extend 50X longer than the original DNA molecule.

Single-molecule measurement

The Xpandomer molecule is then routed through a biological nanopore in a highly efficient and accurate manner.

Movement of the Xpandomer through the pore is guided by voltage pulses that advance the Xpandomer through the pore one reporter code at a time. The highly differentiated reporter codes are easily measured during this translocation process via a scalable complementary metal oxide semiconductor (CMOS)-based array, which combines electrodes, detection circuits, and analog-to-digital conversion.

Because the CMOS array contains roughly eight million microwells (each containing a nanopore), measurement occurs in a massively parallel, highly controlled manner without the convolution issues of traditional nanopore sequencing. The result is the cost-effective measurement of hundreds of millions of bases per second, bypassing the traditional approach of cyclical incorporation and measurement of a single base at a time.

Demonstrated research methods

The versatility of the AXELIOS 1 platform has been successfully demonstrated across a broad range of research methods. Its dual sequencing modes provide maximum flexibility to meet your specific project requirements. The SBX-simplex workflow delivers the high throughput required for data-intensive applications, while the SBX-duplex workflow leverages intramolecular consensus to eliminate artifacts and maximize accuracy. Explore the resources below and contact a representative to learn more.