Next-Generation Sequencing in Rare Genetic Diseases

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: 10 April 2026 | Viewed by 846

Special Issue Editors


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Guest Editor
1. Department of Molecular Medicine, University of Pavia, Pavia, Italy
2. IRCCS Mondino Foundation, Pavia, Italy
Interests: molecular genetics; clinical genetics; next generation sequencing (NGS); molecular karyotyping; prenatal diagnosis; neurogenomics; oncogenomics; bioinformatics
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Guest Editor
Department of Molecular Medicine, University of Pavia, Pavia, Italy
Interests: genetics of rare diseases; bioinformatics; NGS data analysis (exome/genome, long-reads, Hi-C) for the identification of structural variations and germline, de novo, post-zygotic variants

Special Issue Information

Dear Colleagues,

Rare genetic diseases (RGDs) affect more than 300–400 million people worldwide. In a large portion of cases, people with an undiagnosed disease incur in the so-called “diagnostic odyssey”. An accurate diagnosis of an RGD can result in better clinical management, the identification of potential therapeutics, and the avoidance of unnecessary treatments that may have non-negligible side effects. In the last decade, the advent of NGS (next-generation sequencing) and omics sciences, such as genomics, transcriptomics, and methylomics, has completely revolutionized the approach to RGDs. In this new scenario, bioinformatics tools, often based on artificial intelligence (AI) approaches, have evolved significantly in parallel with new technological approaches (e.g., long-read sequencing).

This Special Issue aims to highlight the contribution of these novel approaches to unravel the pathogenetic mechanisms, discover novel disease genes and genotype–phenotype associations, and depict the genetic architecture underlying RGDs and driving novel therapeutic approaches. Original articles, case series, reviews, and descriptions of new methodologies in the field of RDs are welcome to contribute to this Special Issue.

Potential topics include, but are not limited to, the following: innovative approaches (NGS-based) to the diagnosis of RGDs (genomic medicine and multiomics data integration), big data and artificial intelligence, disease gene discovery, network analysis and rare disease (epi)signatures, including multilocus and mosaic disorders.

We look forward to receiving your contributions.

Dr. Edoardo Errichiello
Dr. Paola Dimartino
Guest Editors

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Keywords

  • rare genetic diseases
  • next-generation sequencing
  • bioinformatics
  • multiomics data
  • artificial intelligence
  • gene discovery
  • single nucleotide variants
  • structural variants

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Published Papers (1 paper)

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14 pages, 2427 KB  
Case Report
A Complex Case of Retinoblastoma Solved by the Combined Approach of Humor/Plasma cfDNA-NGS and LR-WGS
by Simona Innamorato, Simona L. Basso, Omaima Belakhdar, Mirella Bruttini, Chiara Fallerini, Heyran Huseynli, Giulia Caccialupi, Elena Pasquinelli, Mariarosaria Adduci, Giorgio Signori, Felice Arcuri, Valeria Malagnino, Maria Chiara Siciliano, Stefano Lazzi, Simone Pesaresi, Daniela Galimberti, Paolo Galluzzi, Sonia De Francesco, Theodora Hadijstillanou, Anna Maria Pinto, Alessandra Renieri and Francesca Arianiadd Show full author list remove Hide full author list
Genes 2025, 16(12), 1399; https://doi.org/10.3390/genes16121399 - 22 Nov 2025
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Abstract
Background: Complex cases of retinoblastoma (RB) often require integrative molecular approaches to define tumor etiology and guide clinical management. Purpose: Our aim was to evaluate the usefulness of combining aqueous humor (AH)/plasma cell-free DNA next-generation sequencing (cfDNA-NGS) and long-read–whole-genome sequencing (LR-WGS) to resolve [...] Read more.
Background: Complex cases of retinoblastoma (RB) often require integrative molecular approaches to define tumor etiology and guide clinical management. Purpose: Our aim was to evaluate the usefulness of combining aqueous humor (AH)/plasma cell-free DNA next-generation sequencing (cfDNA-NGS) and long-read–whole-genome sequencing (LR-WGS) to resolve diagnostically challenging RB cases. Case Description: We report the case of a 3-year-old Caucasian girl, conceived by heterologous assisted reproductive technology (ART), presenting with unilateral, widely infiltrative RB in the right eye. She exhibited limited verbal communication, a glabellar angioma extending to the nasal bridge and philtrum, and mild hypertelorism. Standard blood testing revealed no pathogenic SNVs, CNVs, or methylation abnormalities in the RB1 gene. Targeted cfDNA analysis using the Illumina TruSight Oncology 500 (TSO500) panel on AH and plasma identified a somatic RB1 splice-site variant (c.1498+2T>C) with a variant allele frequency (VAF) of 98.5%, consistent with biallelic inactivation. Additional gains (fold change > 1.5) were found in AH and confirmed in plasma, suggesting a germline 13q duplication. Third-generation LR-WGS, performed with Oxford Nanopore Technology (ONT), on blood confirmed a 24.6 Mb duplication on chromosome 13, compatible with the rare 13q duplication syndrome characterized by psychomotor delay, craniofacial dysmorphism, and hemangiomas. AH-cfDNA revealed additional somatic copy-number alterations, including amplifications (i.e., MDM4 and ALK) and deletions (i.e., BRCA2), indicating progressive clonal tumor evolution. Conclusions: This experience tells us that a combined approach with TSO500 Illumina NGS on cfDNA, along with LR-WGS, is able to help solve complex cases and define the appropriate treatment and surveillance strategy. Full article
(This article belongs to the Special Issue Next-Generation Sequencing in Rare Genetic Diseases)
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