Sequencing By Expansion
Sequencing By Expansion (SBX) is a DNA sequencing method that uses a simple biochemical reaction to encode the sequence of a DNA molecule into a highly measurable surrogate called an Xpandomer. This single molecule approach produces enough Xpandomer in a single drop reaction to sequence an entire human genome 100X over. To achieve this, an Xpandomer replaces each DNA sequence with a sequence of large, high signal reporter molecules using the SBX molecular expansion technology. The DNA sequence is then read out as the Xpandomer reporters pass sequentially through a nanopore detector. SBX is a molecular engineering platform that benefits from core design principles that separate the multiple molecular functions. This systems approach enables efficient development and incorporation of improvements to SBX and is key to reconfiguring and optimizing Xpandomer measurement for different detection platforms.
SBX Proof of Concept
Sequence read-out of an Xpandomer using a wild-type alpha-hemolysin nanopore. Data presented is averaged with a 1 ms filter and the overlaid red lines are autocalled state levels. Repeated bases (homopolymers) are resolved by alternately encoding between the normal base state and an additional homopolymer reporter state (Hp). The base type associated with an Hp state is determined by the previous state it transitioned from.
SBX had been demonstrated using X-probes, illustrated in the animation and proof of concept above, and expandable nucleotides, called X-NTPs, which are described in more detail below.
SBX – Disruptive NGS Technology
Much like with PCR, Xpandomer synthesis is based upon the natural function of DNA replication. Stratos Genomics has developed expandable nucleoside triphosphates, called X-NTPs, that are highly engineered substrates for template-dependent, polymerase-based replication. Four X-NTPs, one for each DNA base, are required for Xpandomer synthesis. Custom engineered polymerases use these next generation building blocks to synthesize Xpandomers from targeted DNA templates. With this elegant advancement, the SBX single molecule sequencing technology will have a similar disruptive impact on the NGS market as PCR did for Molecular Diagnostics.