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

Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE

Publication: Oxford : Oxford University Press
Original Publication: London ; Birmingham, AL : H. Stewart Publications, [2000-

Nanopore Sequencing*/methods ; Microsatellite Repeats* ; Algorithms*; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Genetic Markers ; Alleles

Short-tandem repeats (STRs) are the type of genetic markers extensively utilized in biomedical and forensic applications. Due to sequencing noise in nanopore sequencing, accurate analysis methods are lacking. We developed NASTRA, an innovative tool for Nanopore Autosomal Short Tandem Repeat Analysis, which overcomes traditional database-based methods' limitations and provides a precise germline analysis of STR genetic markers without the need for allele sequence reference. Demonstrating high accuracy in cell line authentication testing and paternity testing, NASTRA significantly surpasses existing methods in both speed and accuracy. This advancement makes it a promising solution for rapid cell line authentication and kinship testing, highlighting the potential of nanopore sequencing for in-field applications.
(© The Author(s) 2024. Published by Oxford University Press.)

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31870079 National Natural Science Foundation of China; 2021QY2004 National Key Research and Development Program of China

Keywords: accurate analysis method; cell line authentication; nanopore sequencing; short tandem repeats

0 (Genetic Markers)

Date Created: 20240925 Date Completed: 20240925 Latest Revision: 20240928

20260130

PMC11424183

10.1093/bib/bbae472

39322627