Enriching for Answers in Rare Diseases

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Rare genetic diseases pose significant diagnostic challenges.
• Long-read sequencing offers advantages for complex variant detection but can be costly.
• Efficiently sequencing multiple samples, like trios, on a single platform is desirable.

Purpose of the Study:

• To introduce Trio-barcoded ONT Adaptive Sampling (TBAS) as a cost-efficient long-read sequencing strategy.
• To enable comprehensive genetic analysis of rare-disease trios on a single PromethION flow cell.
• To improve the diagnostic yield and reduce the cost of long-read sequencing for rare diseases.

Main Methods:

• Developed TBAS by combining sample barcoding and adaptive enrichment for long-read sequencing.
• Applied TBAS to sequence rare-disease trios on an Oxford Nanopore PromethION platform.
• Integrated bioinformatics pipelines for variant calling, phasing, and structural variant detection.

Main Results:

• TBAS achieved near-complete variant phasing and high-accuracy detection of small variants, structural variants, and tandem repeats.
• Demonstrated a 77% potential solve rate for rare-disease trios.
• Retained valuable methylation data, crucial for certain genetic diagnoses.
• Showcased scalability and cost-efficiency compared to existing long-read methods.

Conclusions:

• TBAS is a scalable and cost-effective long-read sequencing strategy for rare-disease trio analysis.
• This approach significantly enhances the potential for accurate genetic diagnosis of rare diseases.
• TBAS enables clinically relevant, phenotype-guided long-read diagnostics at reduced costs.