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Genes
Special Issues
The Genetic Lens: A New Era in Ophthalmology
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The Genetic Lens: A New Era in Ophthalmology

A Special Issue of Genes (ISSN 2073-4425) belonging to the section "Genetic Diagnosis".

Deadline for manuscript submissions: 25 September 2026 | Viewed by 4794

Editors

Dr. Stefania Zampatti

E-Mail Website
Guest Editor
Genomic Medicine Laboratory UILDM, IRCCS Fondazione Santa Lucia, 00142 Rome, Italy
Interests: genetic counseling; neurogenetics; pharmacogenetics; rare disorders; genetic diagnosis
Special Issues, Collections and Topics in MDPI journals
Dr. Emiliano Giardina

E-Mail Website
Guest Editor
1. Genomic Medicine Laboratory UILDM, Santa Lucia Foundation, 00142 Rome, Italy
2. Forensic Genetics Laboratoty, Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy
Interests: forensic genetics; genetic counselling; human identification; neurogenetics; prenatal and postnatal genetic diagnosis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The advent of genomic medicine has fundamentally reshaped the landscape of ophthalmology, allowing for the development of innovative protocols for patient evaluation, diagnosis, and management. In the field of retinal genomics, the integration of these new technologies lays the groundwork for the automated analysis of vast genetic datasets. In fact, cutting-edge machine learning algorithms are now essential for decoding the myriad genomic variants associated with inherited retinal diseases (IRDs). Retinal genomics has definitively shown that a comprehensive genetic assessment is crucial in order to apply precision medicine to patients with both common and rare retinal disorders, such as retinitis pigmentosa, Leber congenital amaurosis, and macular dystrophies. By integrating multi-omics data—including genomics, transcriptomics, and epigenomics—AI models have demonstrated unparalleled abilities. The strategic use of these models, under strict human oversight, can help to identify key disease-related biomarkers, support the prediction of patient-specific treatment responses, and speed up the drug discovery process.

This Special Issue welcomes reviews and original articles that cover many aspects of genetics and its applications in retinal disease. These contributions may include, but are not limited to, new diagnostic, therapeutic, and imaging protocols; functional and molecular evaluations of ophthalmological disorders; the translation of research findings into clinical protocols; new management perspectives; and multi-omics analyses of disease trajectories. This Special Issue of Genes will highlight the undeniable potential of genetics to bridge the gap between groundbreaking research and clinical practice, offering a clear roadmap for future innovations in vision health. By leveraging the computational power of modern genomics, precision medicine can move closer to providing individualized, data-driven solutions for treating retinal disorders, thereby improving patient outcomes and reshaping the future of ophthalmology and healthcare.

Dr. Stefania Zampatti
Dr. Emiliano Giardina
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 short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly 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 2600 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

  • ophthalmology
  • genomics
  • artificial intelligence
  • inherited retinal disease
  • blindness

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Published Papers (5 papers)

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12 pages, 3533 KB  
Article
STOML1 as an Exploratory Candidate Gene for Autosomal Dominant Iris and Chorioretinal Coloboma in a British Family
by Vanita Berry, Manav B. Ponnekanti, Nancy Aychoua, Maddy Ashwin Reddy and Michel Michaelides
Genes 2026, 17(9), 1152; https://doi.org/10.3390/genes17091152 - 20 Sep 2026
Abstract
Background: Ocular coloboma is a congenital eye defect with high genetic heterogeneity. This study investigated a four-generation pedigree to identify candidate variants underlying autosomal dominant iris and chorioretinal coloboma. Methods: Whole-exome sequencing (WES) was performed on a single affected family member. Variants were [...] Read more.
Background: Ocular coloboma is a congenital eye defect with high genetic heterogeneity. This study investigated a four-generation pedigree to identify candidate variants underlying autosomal dominant iris and chorioretinal coloboma. Methods: Whole-exome sequencing (WES) was performed on a single affected family member. Variants were prioritised using the Phenopolis pipeline, filtered for rarity across multiple population databases, and retained where CADD indicated predicted deleteriousness. Candidate variants were then validated by Sanger sequencing in the four family members from whom DNA was available. Variants were classified according to ACMG/AMP criteria. Results: Five rare heterozygous variants were identified: STOML1 (NM_004809.5:c.1100T>C; p.(Leu367Pro)), MTIF2 (NM_002453.3:c.1337G>A; p.(Trp446Ter)), CDH23 (NM_022124.6:c.8906G>A; p.(Arg2969His)), CDON (NM_001378964.1:c.3276+1G>T; p.?), and ERCC6L2 (NM_020207.7:c.19C>T; p.(Gln7Ter)). Four are classified as of uncertain significance; the ERCC6L2 variant is classified as pathogenic in ClinVar. Conclusions: STOML1 is proposed as an exploratory candidate gene for isolated ocular coloboma, requiring replication in independent families and functional validation. The recurrent ERCC6L2 nonsense variant is reported as an incidental finding of potential haematological relevance. Full article
(This article belongs to the Special Issue The Genetic Lens: A New Era in Ophthalmology)
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14 pages, 427 KB  
Article
Exploratory Analysis of Glaucoma-Associated SNPs in a Colombian Cohort Highlights Potential Involvement of Oxidative, Vascular, and Neurodegenerative Pathways
by Carlos Casanova, Claudia Valencia-Peña, Wilmar Saldarriaga-Gil, Edgar Lozano-Cruz and Andrés Castillo
Genes 2026, 17(8), 919; https://doi.org/10.3390/genes17080919 - 4 Aug 2026
Viewed by 377
Abstract
Background/Objectives: Primary open-angle glaucoma (POAG) is a complex multifactorial optic neuropathy involving genetic, vascular, oxidative, inflammatory, and neurodegenerative mechanisms. Despite advances in genome-wide studies, the contribution of genetic variants remains incompletely characterized in underrepresented Latin American populations. This study aimed to characterize the [...] Read more.
Background/Objectives: Primary open-angle glaucoma (POAG) is a complex multifactorial optic neuropathy involving genetic, vascular, oxidative, inflammatory, and neurodegenerative mechanisms. Despite advances in genome-wide studies, the contribution of genetic variants remains incompletely characterized in underrepresented Latin American populations. This study aimed to characterize the genetic landscape of POAG in a Colombian cohort by identifying previously reported glaucoma-associated variants, rare candidate variants, and pharmacogenomic markers and integrating these findings into biologically relevant pathways. Methods: An exploratory descriptive study was conducted in 21 Colombian patients with confirmed POAG. Whole-exome sequencing (WES) was performed at an average sequencing depth of approximately 100×. Variants were quality-filtered, functionally annotated, and prioritized within 446 POAG-associated genes retrieved from DisGeNET. Previously reported glaucoma-associated variants and rare candidate variants were identified, while pharmacogenomic variants related to latanoprost and timolol response were evaluated using ClinPGx/PharmGKB. Identified genes were classified according to major biological pathways relevant to glaucoma pathophysiology. Results: Of the 446 POAG-associated genes, 381 were detected in the patients’ exomes. A total of 10,220 molecular variants were identified, of which 1,187 synonymous variants were excluded, leaving 9,033 variants for downstream analysis. Among these, 955 were non-synonymous SNVs, including 26 variants previously reported in association with glaucoma and 929 potentially novel coding variants. Previously reported variants included loci in SIX6, LOXL1, CYP1B1, NOS3, and SOD2. Two rare candidate variants (minor allele frequency <1%) were identified in FMNL2 and C3. Pharmacogenomic variants in PTGS1, ADRB1, and ABCC4 with potential implications for response to latanoprost or timolol were also detected. Functional integration highlighted pathways involving oxidative stress, extracellular matrix remodeling, vascular regulation, neurodegeneration, and inflammation. Conclusions: This exploratory analysis identifies known glaucoma-associated variants, rare candidate variants, and pharmacogenomic markers in Colombian patients with POAG. The findings support a multifactorial biological framework involving interconnected oxidative, structural, vascular, neurodegenerative, and inflammatory pathways. The FMNL2 and C3 variants represent candidates for further investigation, while the identified pharmacogenomic variants highlight the potential relevance of genomic profiling for personalized glaucoma management. Larger ancestry-informed case–control studies are required to validate these observations and determine their clinical significance. Full article
(This article belongs to the Special Issue The Genetic Lens: A New Era in Ophthalmology)
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24 pages, 1581 KB  
Article
Expanding the Mutation Spectrum of Non-Syndromic Retinitis Pigmentosa in Consanguineous Pakistani Families: Unraveling Novel Pathogenic Variants in RP1, PDE6B, and PRCD Genes for Precision Diagnosis
by Tayyaba Shan, Nimra Mukhtar, Sayyed Hammad Ullah, Asad Ullah, Asfandyar Ahmad Khan, Yumei Li, Meng Wang, Raeesa Tehreem, Amtul Aziz, Kiran Afshan, Rui Chen and Sabika Firasat
Genes 2026, 17(5), 529; https://doi.org/10.3390/genes17050529 - 29 Apr 2026
Viewed by 852
Abstract
Background: Non-syndromic retinitis pigmentosa (RP) is characterized by rod–cone degeneration, resulting in night blindness, visual field constriction, and eventual blindness. Recessively inherited RP is predominantly exacerbated in consanguineous populations, such as Pakistan. This study aimed to perform the genetic analysis of sixteen [...] Read more.
Background: Non-syndromic retinitis pigmentosa (RP) is characterized by rod–cone degeneration, resulting in night blindness, visual field constriction, and eventual blindness. Recessively inherited RP is predominantly exacerbated in consanguineous populations, such as Pakistan. This study aimed to perform the genetic analysis of sixteen non-syndromic RP segregating Pakistani families, and to summarize the mutation spectrum of non-syndromic RP in our population by reviewing related literature. Methods: We screened 16 non-syndromic RP families using targeted capture panel sequencing of 344 genes related to inherited retinal dystrophies. Variants were prioritized based on rarity (minor allele frequency (MAF) < 0.001 in the gnomAD South Asian subset), pathogenicity assessments using ACMG/AMP criteria, and REVEL scores (>0.5). Candidate variants were validated for familial segregation through Sanger sequencing. Results: We identified 15 distinct variants across 14 genes associated with non-syndromic retinitis pigmentosa, comprising 6 missense, 7 nonsense, 1 frameshift, and 2 splice-site variants, including 4 novel variants, i.e., p.(Val220Met) and p.(Pro1282SerfsTer2) in RP1, 1 each in PDE6B (c.2021+5G>A), and PRCD p.(Ser38Ter). Homozygosity predominated, underscoring the impact of consanguinity on the burden of autosomal recessive disease in the present cohort, while the CERKL disease-causing mutation, i.e., p.(Arg257Ter), recurred in two families. Conclusions: This study expands Pakistan’s non-syndromic RP mutational spectrum by identifying novel variants in RP1, PDE6B, and PRCD, alongside recurrent CERKL and RHO mutations of the local population. The literature review suggests that RP1, TULP1, and PDE6B are among the most mutated genes in our population, supporting the value of population-specific genetic panels to enhance diagnostics and carrier screening. Full article
(This article belongs to the Special Issue The Genetic Lens: A New Era in Ophthalmology)
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11 pages, 2071 KB  
Article
Heimler Syndrome Caused by Novel PEX6 Variants: Clinical and Genetic Characterization in a Saudi Cohort
by Basamat AlMoallem
Genes 2026, 17(4), 360; https://doi.org/10.3390/genes17040360 - 24 Mar 2026
Viewed by 1475
Abstract
Background: Heimler syndrome (HS) is a rare autosomal recessive disorder representing the mildest end of the peroxisome biogenesis disorder spectrum. It is caused by hypomorphic mutations in peroxisomal assembly genes, most commonly PEX1 and PEX6, and is characterized by sensorineural hearing loss, [...] Read more.
Background: Heimler syndrome (HS) is a rare autosomal recessive disorder representing the mildest end of the peroxisome biogenesis disorder spectrum. It is caused by hypomorphic mutations in peroxisomal assembly genes, most commonly PEX1 and PEX6, and is characterized by sensorineural hearing loss, amelogenesis imperfecta, and retinal dystrophy. Due to phenotypic overlap with other inherited sensory disorders, particularly Usher syndrome, diagnosis of this condition is frequently delayed. Methods: We investigated two unrelated Saudi families presenting with congenital hearing loss and retinal dystrophy who were initially diagnosed with Usher syndrome. Detailed clinical evaluation, including comprehensive ophthalmologic and audiologic assessments, was performed. Whole-exome sequencing (WES) was conducted to identify the underlying genetic cause, followed by variant filtering and in silico pathogenicity prediction. Results: We identified a novel homozygous missense variant, p.Val97Gly (V97G), in the PEX6 gene that co-segregated with the disease phenotype in both families. This variant was absent from major population databases, including dbSNP, the 1000 Genomes Project, ExAC, and gnomAD, and was predicted to be deleterious by multiple in silico prediction tools. Clinically, affected individuals presented with congenital sensorineural hearing loss, pigmentary retinal dystrophy with electrophysiological evidence of cone–rod dysfunction, enamel abnormalities consistent with amelogenesis imperfecta, and mild dysmorphic facial features, supporting a diagnosis within the Heimler syndrome spectrum. Conclusions: Our findings expand the mutational spectrum of PEX6 and highlight Heimler syndrome as an important differential diagnosis in patients presenting with Usher-like phenotypes. To the best of our knowledge, this study represents the first report of the PEX6 p.Val97Gly variant associated with Heimler syndrome in a Saudi population, underscoring the value of whole-exome sequencing for accurate diagnosis and genetic counseling in individuals with inherited sensory disorders. Full article
(This article belongs to the Special Issue The Genetic Lens: A New Era in Ophthalmology)
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Review

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24 pages, 1518 KB  
Review
Precision Is Not Enough: When Tools Outpace Translation in Ocular Gene Therapy
by Maram E. A. Abdalla Elsayed and Robert E. MacLaren
Genes 2026, 17(3), 283; https://doi.org/10.3390/genes17030283 - 27 Feb 2026
Viewed by 1262
Abstract
Advances in molecular biology have positioned the eye as a leading platform for gene therapy, owing to its surgical accessibility, relative immune privilege, and the ability of the contralateral eye to serve as an anatomical control. We trace the historical evolution of gene [...] Read more.
Advances in molecular biology have positioned the eye as a leading platform for gene therapy, owing to its surgical accessibility, relative immune privilege, and the ability of the contralateral eye to serve as an anatomical control. We trace the historical evolution of gene discovery, synthesize current gene therapy strategies for inherited and acquired ocular disorders, critically evaluating the limitations of CRISPR and related genome-editing technologies, and examine the key scientific and translational challenges that must be addressed for genetic therapies to be integrated into routine ophthalmic practice. Full article
(This article belongs to the Special Issue The Genetic Lens: A New Era in Ophthalmology)
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