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Applications of Nanopore Sequencing in Human Genomics

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (20 December 2024) | Viewed by 1086

Special Issue Editor

1. Department of Bioengineering, Khoury College of Computer Sciences, Northeastern University, Boston, MA 02115, USA
2. Department of Physics, Khoury College of Computer Sciences, Northeastern University, Boston, MA 02115, USA
Interests: genomics; transcriptomics; proteomics; clinical biology
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Special Issue Information

Dear Colleagues,

Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third-generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. These applications show that nanopore technology is promising in the field of biological and biomedical sensing.

This Special Issue aims to debate the most recent advances in nanopore sequencing and technology. Contributions (research and review articles) will focus on applications using nanopore sequencing to cancer biology, pathogen (microbial and viral) detection, and genome assembly. Submissions on nanopore RNA sequencing and modification analysis (DNA and RNA) are welcome.  

Dr. Miten Jain
Guest Editor

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Keywords

  • third-generation sequencing
  • nanopore sequencing
  • direct RNA sequencing
  • epigenetic analysis
  • long-read sequencing

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Published Papers (1 paper)

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Research

20 pages, 12074 KiB  
Communication
ONT in Clinical Diagnostics of Repeat Expansion Disorders: Detection and Reporting Challenges
by Ludmila Kaplun, Greice Krautz-Peterson, Nir Neerman, Yocheved Schindler, Elinor Dehan, Claudia S. Huettner, Brett K. Baumgartner, Christine Stanley and Alexander Kaplun
Int. J. Mol. Sci. 2025, 26(6), 2725; https://doi.org/10.3390/ijms26062725 - 18 Mar 2025
Viewed by 636
Abstract
While whole-genome sequencing (WGS) using short-read technology has become a standard diagnostic test, this technology has limitations in analyzing certain genomic regions, particularly short tandem repeats (STRs). These repetitive sequences are associated with over 50 diseases, primarily affecting neurological function, including Huntington disease, [...] Read more.
While whole-genome sequencing (WGS) using short-read technology has become a standard diagnostic test, this technology has limitations in analyzing certain genomic regions, particularly short tandem repeats (STRs). These repetitive sequences are associated with over 50 diseases, primarily affecting neurological function, including Huntington disease, frontotemporal dementia, and Friedreich’s ataxia. We analyzed 2689 cases with movement disorders and dementia-related phenotypes processed at Variantyx in 2023–2024 using a two-tiered approach, with an initial short-read WGS followed by ONT long-read sequencing (when necessary) for variant characterization. Of the 2038 cases (75.8%) with clinically relevant genetic variants, 327 (16.0%) required additional long-read analysis. STR variants were reported in 338 cases (16.6% of positive cases), with approximately half requiring long-read sequencing for definitive classification. The combined approach enabled the precise determination of repeat length, composition, somatic mosaicism, and methylation status. Notable advantages included the detection of complex repeat structures in several genes such as RFC1, FGF14, and FXN, where long-read sequencing allowed to determine somatic repeat unit variations and accurate allele phasing. Further studies are needed to establish technology-specific guidelines for the standardized interpretation of long-read sequencing data for the clinical diagnostics of repeat expansion disorders. Full article
(This article belongs to the Special Issue Applications of Nanopore Sequencing in Human Genomics)
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