Evaluating the efficiency of nanopore adaptive sampling sequencing in detecting balanced translocation
Meng Gao1,2, Jun Ren1,2, Cuiting Peng1,2
1Department of Medical Genetics/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.
Journal of Medical Genetics
|February 25, 2026
Summary
Nanopore adaptive sampling sequencing effectively detects balanced translocations (BTs), offering a cost-effective alternative to whole-genome sequencing for identifying genetic risks in families. This method improves detection of submicroscopic BTs, aiding in genetic counseling.
Area of Science:
- Genomics
- Genetic diagnostics
Background:
- Balanced translocations (BTs) increase risk of miscarriage and abnormal offspring due to unbalanced gametes.
- Current genetic testing misses submicroscopic or complex BTs.
- Whole-genome long-read sequencing is effective but costly and data-intensive.
Purpose of the Study:
- To evaluate nanopore adaptive sampling sequencing for detecting BTs.
- To assess its cost-effectiveness and efficiency compared to existing methods.
Main Methods:
- Nanopore adaptive sampling sequencing on peripheral blood from 14 participants in 8 families with suspected BTs.
- Karyotyping and Sanger sequencing for breakpoint confirmation.
Main Results:
- Adaptive sampling accurately identified all BT breakpoints (0.8–18 Mb).
- Detection was efficient with a 500 kb flanking region at 20X depth or 5 Mb at 15X depth.
- Achieved comparable depth to whole-genome sequencing with reduced data and cost.
Conclusions:
- Nanopore adaptive sampling sequencing provides high-resolution, cost-effective detection of submicroscopic BTs.
- It is a practical alternative to whole-genome long-read sequencing.
- Suitable for clinical workflows when prior testing suggests BT regions.
