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Cancers
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Long-Read Sequencing in Cancer
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Long-Read Sequencing in Cancer

A special issue of Cancers (ISSN 2072-6694). This special issue belongs to the section "Cancer Informatics and Big Data".

Deadline for manuscript submissions: closed (30 April 2025) | Viewed by 7978

Special Issue Editors

Prof. Dr. Luca Ermini

E-Mail Website
Guest Editor
School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032 Camerino, Italy
Interests: genomics; cancer evolution; cancer biology; third-generation sequencing; bioinformatics
Special Issues, Collections and Topics in MDPI journals
Dr. Patrick Driguez

E-Mail Website
Guest Editor
Core Labs, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
Interests: genomics; third-generation sequencing; sequencing technologies; data analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We use sequencing technologies to understand the complexity of cancer genomes and pinpoint their vulnerabilities to treat cancer. Next-generation sequencing has been widely used for more than a decade, resulting in enormous advances but also limitations, primarily due to short read lengths. Long-read sequencing technology (TGS) has emerged in recent years, ushering in a new era of research, and cancer genomics is one field where TGS can yield significant results.

TGS can generate any length of sequencing read, including extremely long reads that span complex genomic regions. This enables the study of complete structural variations and mutations at a single-allele phased resolution. TGS can directly characterize genome-wide hypo/hypermethylation patterns and identify full-length aberrant transcripts, making it an invaluable resource for immuno-oncology therapeutic targets. TGS can also provide bedside sequencing with rapid results for time-critical situations, as well as sequencing in resource-limited environments or remote locations. 

This Special Issue will focus on the role of TGS in cancer in allits facets, including all omics aspects related to long reads as well as a hybrid approach of long-/short-read sequencing. This Special Issue will look at both basic research and more (pre)clinical studies that advance our understanding of the complex cancer disease.

Dr. Luca Ermini
Dr. Patrick Driguez
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cancers is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • long-read sequencing
  • cancer genetics
  • genomics
  • transcriptomics
  • methylomics
  • cancer research

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Published Papers (3 papers)

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Research

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19 pages, 768 KiB  
Article
From Sanger to Oxford Nanopore MinION Technology: The Impact of Third-Generation Sequencing on Genetic Hematological Diagnosis
by María José Larráyoz, Pablo Luri-Martin, Amagoia Mañu, Oihane Churruca, Natalia Gordillo, Irache Erdozain, Ada Esteban-Figuerola, Carlos de Miguel, Diego Robles, María García-Fortes, José Rifón Roca, Ana Alfonso-Pierola, Felipe Prósper, Beñat Ariceta and María José Calasanz
Cancers 2025, 17(11), 1811; https://doi.org/10.3390/cancers17111811 - 29 May 2025
Viewed by 303
Abstract
Background: Sanger sequencing remains the gold standard for characterizing genetic variants in short DNA fragments (<700 bp). However, the increasing demand for short TATs and high sensitivities in variant detection, particularly in oncohematology, is driving the need for more efficient methods. Next-generation sequencing [...] Read more.
Background: Sanger sequencing remains the gold standard for characterizing genetic variants in short DNA fragments (<700 bp). However, the increasing demand for short TATs and high sensitivities in variant detection, particularly in oncohematology, is driving the need for more efficient methods. Next-generation sequencing (NGS) has improved sensitivity and allows for the simultaneous analysis of multiple genes, but it is still costly and time-consuming. Consequently, Sanger sequencing continues to be widely used. In this study, we have compared Sanger sequencing with Oxford Nanopore technology (ONT), which offers enhanced sensitivity and faster sequencing, delivering diagnostic results within 24 h. Methods: This study involves 164 samples (for a total of 174 analyzed regions of interest) previously characterized using either Sanger sequencing or a next-generation sequencing (NGS) panel, categorized by their genetic alterations. Validation was conducted on 15 genes crucial for the diagnosis, prognosis, or identification of drug resistance in myeloproliferative neoplasms (MPN), myelodysplastic syndromes (MDS), acute myeloid leukemia (AML), and chronic myeloid leukemia (CML). The primary objective was to assess whether MinION could identify the same variants previously detected in these patients. Results and Conclusions: With a 99.43% concordance observed in our comparison, our results support the implementation of MinION technology in routine variant detection in MPN, MDS, AML, and CML cases due to its significant advantages over Sanger sequencing. Full article
(This article belongs to the Special Issue Long-Read Sequencing in Cancer)
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Review

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19 pages, 2541 KiB  
Review
Novel Avenues for the Detection of Cancer-Associated Viral Genome Integrations Using Long-Read Sequencing Technologies
by Larissa-Anna Bergmann, Alicja Pacholewska and Michal R. Schweiger
Cancers 2025, 17(11), 1740; https://doi.org/10.3390/cancers17111740 - 22 May 2025
Viewed by 263
Abstract
Human papillomaviruses (HPVs), like many other viruses, are able to integrate their genomes into the host cellular genome. This integration can activate viral oncogenes or alter the function of cellular oncogenes and tumor suppressor genes, thereby increasing the likelihood of HPV-associated tumor development. [...] Read more.
Human papillomaviruses (HPVs), like many other viruses, are able to integrate their genomes into the host cellular genome. This integration can activate viral oncogenes or alter the function of cellular oncogenes and tumor suppressor genes, thereby increasing the likelihood of HPV-associated tumor development. In particular, HPV types 16 and 18 are responsible for over 70% of all cervical, anal, and oropharyngeal cancers worldwide, with rising incidence. Even more, high-resolution mapping of preferred integration sites using LR-Seq technologies offers deep insights into the molecular mechanisms of HPV integration. LR-Seq enables the detection of complex integration patterns, where the viral genome can be replicated and amplified into virus–host concatemers, including events within large structural variations or highly repetitive genomic regions. Furthermore, aligning LR-Seq data to the latest T2T reference genome (hs1) is necessary to provide new information about viral integration in genomic regions that were previously inaccessible, such as centromeres and other structurally complex repeat-rich loci. In this review, we provide insights into HPV genomic integration revealed by LR-Seq technologies, with a particular focus on how the use of the complete T2T reference genome enhances the detection of integration events in previously uncharacterized, repeat-rich regions of the human genome. Full article
(This article belongs to the Special Issue Long-Read Sequencing in Cancer)
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20 pages, 1397 KiB  
Review
The Application of Long-Read Sequencing to Cancer
by Luca Ermini and Patrick Driguez
Cancers 2024, 16(7), 1275; https://doi.org/10.3390/cancers16071275 - 25 Mar 2024
Cited by 10 | Viewed by 6721
Abstract
Cancer is a multifaceted disease arising from numerous genomic aberrations that have been identified as a result of advancements in sequencing technologies. While next-generation sequencing (NGS), which uses short reads, has transformed cancer research and diagnostics, it is limited by read length. Third-generation [...] Read more.
Cancer is a multifaceted disease arising from numerous genomic aberrations that have been identified as a result of advancements in sequencing technologies. While next-generation sequencing (NGS), which uses short reads, has transformed cancer research and diagnostics, it is limited by read length. Third-generation sequencing (TGS), led by the Pacific Biosciences and Oxford Nanopore Technologies platforms, employs long-read sequences, which have marked a paradigm shift in cancer research. Cancer genomes often harbour complex events, and TGS, with its ability to span large genomic regions, has facilitated their characterisation, providing a better understanding of how complex rearrangements affect cancer initiation and progression. TGS has also characterised the entire transcriptome of various cancers, revealing cancer-associated isoforms that could serve as biomarkers or therapeutic targets. Furthermore, TGS has advanced cancer research by improving genome assemblies, detecting complex variants, and providing a more complete picture of transcriptomes and epigenomes. This review focuses on TGS and its growing role in cancer research. We investigate its advantages and limitations, providing a rigorous scientific analysis of its use in detecting previously hidden aberrations missed by NGS. This promising technology holds immense potential for both research and clinical applications, with far-reaching implications for cancer diagnosis and treatment. Full article
(This article belongs to the Special Issue Long-Read Sequencing in Cancer)
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