NASTRA: accurate analysis of short tandem repeat markers by nanopore sequencing with repeat-structure-aware algorithm

Area of Science:

• Genetics
• Bioinformatics
• Genomic Technologies

Background:

• Short tandem repeats (STRs) are crucial genetic markers in biomedical and forensic fields.
• Current nanopore sequencing methods struggle with accurate STR analysis due to inherent noise.
• Existing analysis tools often rely on database-dependent methods, limiting their scope.

Purpose of the Study:

• To develop an accurate and efficient tool for analyzing autosomal short tandem repeats (STRs) from nanopore sequencing data.
• To overcome the limitations of traditional database-based STR analysis methods.
• To enable precise germline STR analysis without requiring allele sequence references.

Main Methods:

• Development of NASTRA (Nanopore Autosomal Short Tandem Repeat Analysis), a novel computational tool.
• Utilizing unique algorithms to analyze STR genetic markers directly from nanopore sequencing data.
• Validation through cell line authentication and paternity testing scenarios.

Main Results:

• NASTRA demonstrates high accuracy in both cell line authentication and paternity testing.
• The tool significantly outperforms existing methods in terms of speed and accuracy.
• NASTRA provides precise germline analysis of STRs independent of allele sequence databases.

Conclusions:

• NASTRA represents a significant advancement in analyzing short tandem repeats from nanopore sequencing data.
• The tool offers a robust solution for rapid cell line authentication and kinship testing.
• This development underscores the potential of nanopore sequencing for accurate, in-field genetic analyses.