Mechanisms of Inherited Retinal Dystrophies Using Whole Genome Sequencing and in Vitro and in Vivo Models

"Understanding Genetic Missing Variability and Pathogenetic Mechanisms of Inherited Retinal Dystrophies Using Whole Genome Sequencing and in Vitro and in Vivo Models"

Inherited retinal dystrophies (IRDs), a large group of heterogeneous and rare disorders, may result in irreversible bilateral visual loss and blindness. Characterizing the genetic bases of IRDs will help to understand the pathogenesis underlying the development of retinal damage. Despite the advances in molecular identification of genes causing disease, unsolved IRDs constitute about 40% of all cases.

Goal of this study is to solve missing heritability in IRD using whole genome sequencing (WGS) to identify the genetic causes in clinically well-characterized patients without a molecular diagnosis.

The identification of novel genes that have a role in the development or maintenance of retinal function will lead to the development of new therapeutic approaches and will favour a more prompt diagnosis and improvement of patient management.

Study Overview

• Status: Recruiting
• Conditions: Retinitis Pigmentosa; Macular Dystrophy; Inherited Retinal Dystrophy
• Intervention / Treatment: Diagnostic test: whole genome sequencing

Detailed Description

IRDs are rare neurodegenerative and genetically heterogeneous conditions with a wide spectrum of presentations, even among affected members of the same family. These disorders exhibit a large range of phenotypes with significant overlap, that can be broadly divided into three main groups: those principally affecting the periphery such as retinitis pigmentosa (RP) and choroideremia; those primarily involving the macula, known as 'macular' or 'central' dystrophies; and those affecting both the centre and periphery as seen in cone-rod or rod-cone dystrophies. Collectively, IRDs have an incidence of 1:2000, impacting approx. 2 million people worldwide and patients are progressively visually impaired. Affected individuals can be followed-up by visual acuity measurements, visual field evaluations, electroretinography recordings (ERG), structural imaging with autofluorescence, spectral-domain optical coherence tomography (OCT), and OCT angiography. Although an accurate clinical diagnosis can be reached by these innovative and non-invasive tools, genetic testing is necessary to confirm a specific phenotype, and segregation analysis can address the inheritance pattern. Gene discovery approaches clarified that mutations of about 280 different genes involved in eyes development, photoreceptor survival, phototransduction mechanisms, retinoid cycle, retinal enzymatic function, or cell structure are responsible for these degenerative diseases (RetNet. Available at: https://sph.uth.edu/retnet/) and the inheritance pattern can be autosomal dominant, recessive, or X-linked.

To improve the success rate of genetic/genomic diagnosis, new sequencing technologies have been explored, starting from targeted sequencing focused on multigene panels to whole exome sequencing (WES) and sequencing of the entire genome (WGS). Because of the genetic heterogeneity of IRDs, the congruence of clinical and molecular diagnosis is a necessary goal to characterize exactly the phenotype and to increase the chance of therapeutically beneficial strategies.

A major challenge consists in identifying novel genes encoding for the diseases. This extreme genetic heterogeneity accounts for about 30% of the detection failure of molecular diagnosis. With the possibility of investigating WES or WGS, broader windows are opened for gene discovery.

• Study Type: Observational
• Enrollment (Anticipated): 120

Contacts and Locations

• Study Contact: Name: Viviana Cordeddu, PhD; Phone Number: 3441 +39-06-4990; Email: viviana.cordeddu@iss.it
• Study Contact Backup: Name: Elena Toschi, MD; Phone Number: 6554 +39-06-4990; Email: elena.toschi@iss.it

Study Locations

• Italy
  • Rome, Italy, 00161
    • Recruiting
    • Istituto Superiore di Sanità-Dpt. Oncology and Molecular Medicine
    • Contact: Viviana Cordeddu, PhD; Phone Number: 3441 +39-06-4990; Email: viviana.cordeddu@iss.it
    • Contact: Emilia Stellacci, MS; Phone Number: 3197 +39-06-4990; Email: emilia.stellacci@iss.it
    • Sub-Investigator: Lucia Ziccardi, MD-PhD

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 5 years to 80 years (Child, Adult, Older Adult)
• Accepts Healthy Volunteers: No
• Genders Eligible for Study: All

• Sampling Method: Non-Probability Sample

Study Population

Male and female patients, aged between 5 and 80 years, suffering from retinal or optic nerve degeneration of a hereditary nature. Patients will be recruited at the IRCSS Fondazione Bietti in Rome and undergo ophthalmological examinations and instrumental tests. Candidate subjects are a clinically well-characterized cohort of patients with ocular dystrophies, including IRDs already clinically followed for at least 12 months and without a conclusive molecular diagnosis.

Description

Inclusion Criteria:

• Patients with retinal and optic nerve dystrophy of suspected hereditary nature.
• Probands with clinical follow-up of at least 12 months.
• Patients with an inconclusive molecular diagnosis by means of molecular-genetic tests for the genes known to date for the diagnosed pathology.

Exclusion Criteria:

• Patients with a clinical diagnosis of no proven genetic origin.
• Patients whose parents' or second degree relatives' samples are not available.
• Patients who refuse to be informed of the genetic results obtained, including incidental clinically relevant, validated and actionable for the patient himself and/or his family.

Study Plan

How is the study designed?

Number of groups / cohorts

30

Cohorts and Interventions

Group / Cohort	Intervention / Treatment
FB_001; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_002; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_003; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_004; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_005; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_006; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_007; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_008; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_009; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0010; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0011; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0012; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0013; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0014; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0015; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0016; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0017; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0018; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0019; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0020; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0021; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0022; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0023; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0024; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0025; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0026; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0027; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0028; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0029; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.
FB_0030; Proband affected by IRD and affected and/or unaffected relatives without molecular diagnosis.	Diagnostic test: whole genome sequencing; Whole genome sequencing will be performed in patients whose test was negative for the targeted resequencing and/or clinical exome sequencing.

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Understanding genetic missing pathogenetic variants in IRD	Identification of genetic variants causative of the clinical phenotype	two years

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Gene discovery in IRD	Identification of novel disease genes responsible for IRD.	two years

Other Outcome Measures

Outcome Measure	Measure Description	Time Frame
Assessment of the pathogenicity of the newly identified variant(s) by functional studies.	Functional characterization of new variants by in vivo and in vitro models	three years

Collaborators and Investigators

• Sponsor: Istituto Superiore di Sanità
• Collaborators: Fondazione G.B. Bietti, IRCCS; Ospedale Pediatrico Bambin Gesù
• Investigators: Principal Investigator: Viviana Cordeddu, PhD, Istituto Superiore di Sanità

Publications and helpful links

General Publications

• Cremers FPM, Boon CJF, Bujakowska K, Zeitz C. Special Issue Introduction: Inherited Retinal Disease: Novel Candidate Genes, Genotype-Phenotype Correlations, and Inheritance Models. Genes (Basel). 2018 Apr 16;9(4):215. doi: 10.3390/genes9040215.
• Ziccardi L, Cordeddu V, Gaddini L, Matteucci A, Parravano M, Malchiodi-Albedi F, Varano M. Gene Therapy in Retinal Dystrophies. Int J Mol Sci. 2019 Nov 14;20(22):5722. doi: 10.3390/ijms20225722.
• Cordeddu V, Redeker B, Stellacci E, Jongejan A, Fragale A, Bradley TE, Anselmi M, Ciolfi A, Cecchetti S, Muto V, Bernardini L, Azage M, Carvalho DR, Espay AJ, Male A, Molin AM, Posmyk R, Battisti C, Casertano A, Melis D, van Kampen A, Baas F, Mannens MM, Bocchinfuso G, Stella L, Tartaglia M, Hennekam RC. Mutations in ZBTB20 cause Primrose syndrome. Nat Genet. 2014 Aug;46(8):815-7. doi: 10.1038/ng.3035. Epub 2014 Jul 13.
• Musacchia F, Ciolfi A, Mutarelli M, Bruselles A, Castello R, Pinelli M, Basu S, Banfi S, Casari G, Tartaglia M, Nigro V; TUDP. VarGenius executes cohort-level DNA-seq variant calling and annotation and allows to manage the resulting data through a PostgreSQL database. BMC Bioinformatics. 2018 Dec 12;19(1):477. doi: 10.1186/s12859-018-2532-4.

Study record dates

Study Major Dates

• Study Start (Actual): November 15, 2022
• Primary Completion (Anticipated): May 2, 2024
• Study Completion (Anticipated): November 15, 2025

Study Registration Dates

• First Submitted: March 20, 2023
• First Submitted That Met QC Criteria: March 30, 2023
• First Posted (Actual): March 31, 2023

Study Record Updates

• Last Update Posted (Actual): March 31, 2023
• Last Update Submitted That Met QC Criteria: March 30, 2023
• Last Verified: March 1, 2023

More Information

Terms related to this study

• Keywords: IRD, RP, WGS, molecular diagnosis
• Additional Relevant MeSH Terms: Eye Diseases; Retinal Degeneration; Retinal Diseases; Genetic Diseases, Inborn; Eye Diseases, Hereditary; Macular Degeneration; Retinitis; Retinitis Pigmentosa; Retinal Dystrophies
• Other Study ID Numbers: ISS20-5656c541c257

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: UNDECIDED
• IPD Plan Description: We plan to share anonymized genomic data among the three partners involved in the study by telecall meetings and shared cloud folders.

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No