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

Microsatellite Repeats Nanopore Sequencing / methods Algorithms Humans Genetic Markers Sequence Analysis, DNA / methods High-Throughput Nucleotide Sequencing / methods Alleles
accurate analysis method cell line authentication nanopore sequencing short tandem repeats

Journal

Briefings in bioinformatics
ISSN: 1477-4054
Titre abrégé: Brief Bioinform
Pays: England
ID NLM: 100912837

Informations de publication

Date de publication:
23 Sep 2024
Historique:
received: 14 04 2024
revised: 14 08 2024
accepted: 10 09 2024
medline: 26 9 2024
pubmed: 26 9 2024
entrez: 25 9 2024
Statut: ppublish

Résumé

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.

Identifiants

DOI: 10.1093/bib/bbae472 PMID: 39322627
pubmed: 39322627
pii: 7774877
doi: 10.1093/bib/bbae472
pii:
doi:

Substances chimiques

Genetic Markers 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Subventions

Organisme : National Natural Science Foundation of China
ID : 31870079
Organisme : National Key Research and Development Program of China
ID : 2021QY2004

Informations de copyright

© The Author(s) 2024. Published by Oxford University Press.

Auteurs

Zilin Ren (Z)

Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, No. 573 Yujinxiang Street, Jingyue District, Changchun 130012, China.
School of Information Science and Technology, Northeast Normal University, No. 2555 Jingyue Street, Jingyue District, Changchun 130117, China.
ORCID: 0000-0002-3621-1024

Jiarong Zhang (J)

School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Taiyuan 030001, China.

Yixiang Zhang (Y)

Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, No. 573 Yujinxiang Street, Jingyue District, Changchun 130012, China.
School of Information Science and Technology, Northeast Normal University, No. 2555 Jingyue Street, Jingyue District, Changchun 130117, China.

Tingting Yang (T)

School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Taiyuan 030001, China.

Pingping Sun (P)

School of Information Science and Technology, Northeast Normal University, No. 2555 Jingyue Street, Jingyue District, Changchun 130117, China.

Jiguo Xue (J)

Advanced & Interdisciplinary Biotechnology, Academy of Military Medical Sciences, No. 27 Taiping Road, Haidian District, Beijing 100850, China.

Xiaochen Bo (X)

Advanced & Interdisciplinary Biotechnology, Academy of Military Medical Sciences, No. 27 Taiping Road, Haidian District, Beijing 100850, China.
ORCID: 0000-0003-1911-7922

Bo Zhou (B)

Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, No. 573 Yujinxiang Street, Jingyue District, Changchun 130012, China.

Jiangwei Yan (J)

School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Taiyuan 030001, China.

Ming Ni (M)

Advanced & Interdisciplinary Biotechnology, Academy of Military Medical Sciences, No. 27 Taiping Road, Haidian District, Beijing 100850, China.

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Séquences répétées en tandem › Répétitions microsatellites › NASTRA: accurate analysis of short tandem...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage par nanopores › NASTRA: accurate analysis of short tandem...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Algorithmes › NASTRA: accurate analysis of short tandem...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › NASTRA: accurate analysis of short tandem...
questionsmedicales.fr › Phénomènes génétiques › Phénotype › Marqueurs génétiques › NASTRA: accurate analysis of short tandem...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › NASTRA: accurate analysis of short tandem...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › NASTRA: accurate analysis of short tandem...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Gènes › Allèles › NASTRA: accurate analysis of short tandem...