Cost-efficient long-read trio-barcoded adaptive sequencing improves rare disease diagnosis.

Nanopore long-read trio sequencing on a single flow cell: all three family members are barcoded and phenotype-selected disease-gene panel regions are enriched during sequencing (adaptive sampling).

TBAS (Trio-barcoded Oxford Nanopore Adaptive Sequencing) enables long-read analysis of an affected child and both parents on a single flow cell. Clinical features are used to select broad disease-gene panels, whose regions are enriched during sequencing rather than targeting a known causal locus. In benchmark regions, TBAS increased coverage and accurately detected small variants, structural variants, tandem repeat expansions, methylation and read-backed phasing. Estimated sequencing consumable costs fell to 32.2% of conventional three-flow-cell trio long-read sequencing. Across 13 trios, TBAS recovered all five known diagnoses and prioritised candidates in five of eight unresolved cases.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

The barrier to long-read trio sequencing is primarily cost, and cutting consumable costs by two-thirds makes it feasible for cases left unsolved by short-read sequencing. The trade-off is reliance on phenotype-driven panel selection: a gene outside the selection remains invisible, which runs counter to the whole-genome logic. With 13 trios, the candidates prioritised in five unresolved cases still need confirmation before any gain in diagnostic yield can be claimed.

Analysis by Dr Thibaut Benquey