Preprint introduces sequencing-by-expansion chemistry for scalable single-cell isoform profiling

A bioRxiv preprint describes sequencing-by-expansion (SBX), a new sequencing chemistry developed to resolve transcript isoforms at single-cell resolution without the throughput and cost constraints that have limited existing long-read platforms in large-scale applications.

Standard single-cell RNA sequencing (scRNA-seq) relies on short-read sequencing technology, which can quantify gene expression but cannot reliably distinguish between the multiple transcript isoforms a single gene may produce through alternative splicing. Alternative splicing is a widespread mechanism through which a single gene can generate proteins with distinct functions; the inability to capture it systematically at single-cell resolution has been an acknowledged gap in the field.

Long-read sequencing platforms, such as those from Oxford Nanopore Technologies and Pacific Biosciences, can in principle resolve full-length transcripts, but their per-base costs and throughput have made them impractical for datasets involving hundreds of thousands or millions of cells. The preprint authors report that SBX addresses this by optimising the sequencing chemistry for high-throughput, low-cost operation at single-cell scale, enabling isoform-level analysis in large cellular datasets.

The work is a preprint and has not yet undergone peer review. Performance claims, including throughput figures and isoform-resolution accuracy, should be treated as preliminary until independent validation is available.