Introducing Roche Sequencing by Expansion (SBX) Technology

Technological Concept: Sequencing by Expansion (SBX)

Core challenge

• DNA bases are separated by only ~3.4 angstroms (a few atoms wide).
• Conventional sequencing methods struggle to resolve distances at this scale.

SBX solution

• SBX creates a longer, more easily measurable surrogate molecule called an Xpandomer.
• The Xpandomer encodes the DNA sequence in large, high signal-to-noise reporters.

Xpandomer Design and How It Encodes DNA

Xpandomer length

• The Xpandomer is >50× longer than the original target DNA, improving resolution.

Building blocks

• SBX uses novel nucleotides (X-NTPs).
• There are four X-NTP types, corresponding to DNA bases A, C, G, and T.

Structure and encoding mechanism

• Each X-NTP includes:
  • A base linked via a tether to a reporter region.
  • A reporter with a high signal-to-noise element whose identity reflects the DNA base.
  • A central Translocation Control Element (TCE) that controls movement of the Xpandomer during sequencing.

Proprietary Synthesis Mechanism (DNA Template → Xpandomer)

Modified DNA replication process

• Xpandomers are synthesized by sequentially linking X-NTPs along a DNA template.
• This uses a proprietary enzymatic process.

Double-stranded helix formation

• The synthesis process forms a double-stranded helix.

Selective incorporation

• Only the X-NTP that correctly complements the next template base is incorporated.

Template removal and expansion

• After synthesis:
  • A reagent degrades the DNA template.
  • Cleavable bonds between X-NTP base components are broken.
  • This enables the backbone to expand, producing the final Xpandomer.

Detection Method: Nanopore Readout with Deterministic Control

Electrical threading

• The Xpandomer is threaded through a biological nanopore in a deterministic manner.

Signal generation

• As the Xpandomer advances:
  • The TCE holds the reporter in the nanopore, altering the pore’s electrical resistance.
  • The resistance change produces one of four distinct signals, identifying the base (A/C/G/T) present.

Controlled stepping

• After each measurement, a short high-voltage pulse advances the Xpandomer reliably to the next reporter.

Throughput and Scalability Claims

• Massively parallel operation: Runs in parallel across millions of wells.
• Hardware platform: Uses a CMOS-based sensor module.
• Speed claim: Potential real-time sequencing rates of hundreds of millions of bases per second.
• Scalability: SBX is described as flexibly scalable for a broad set of applications, aiming to establish a new paradigm for next-generation sequencing.

Main Speakers / Sources

• No individual speaker is identified in the provided content.
• The overview is presented as Roche’s SBX technology.