PREcision Diagnostics in Rare GenetIC Diseases and Tumors - Long Read Sequencing (PREDICT-LRS)

Scientific Institute for Research Hospitalization and Healthcare (IRCCS)

Status: Enrolling

Conditions: Rare Diseases; Whole Exome Sequencing

Treatments: Genetic: DNA/RNA sequencing and bioinformatic data analysis

Study type: Observational

Funder types: Other

Identifiers

NCT06796751

PREDICT-LRS

PNRR2022 (Other Grant/Funding Number)

Details and patient eligibility

About

Using long-read sequencing (LRS) technology to achieve molecular diagnosis in patients with rare genetic diseases who have already been tested by state-of-the-art genetic analysis with ambiguous or negative results. This will lead to efficient and reliable identification and clinical interpretation of cryptic and complex structural genomic variants, which represent the central challenge for the coming decades in human genetics.

Full description

The application of LRS to a diagnostic setting could have an impact on detection rate and diagnostic yield, leading to a better understanding of the etiology, prognosis and recurrence risk of rare genetic diseases (RGD), but also to a targeted treatment. One of the main benefits of LRS is the detection of balanced and unbalanced structural variants (SVs), including complex rearrangements, with high sensitivity and accuracy, through reliable alignment and precise breakpoint definition.

Among the main challenges of modern genetics, are identified 4 subgroups of patients that would benefit from the application of LRS to better characterize the genetic diagnosis and disease mechanisms.

• The first subgroup of patients are those with SVs of unknown significance or uncertain disease mechanism. In particular, clinical interpretation of duplications is challenging, due to the inability of Array Comparative Genomic Hybridization (aCGH) to detect whether they occur in tandem or are duplicated and inserted elsewhere in the genome, thus possibly disrupting genes involved in the duplication or altering their regulation.
• Other complex rearrangements can be studied with LRS to gain a better understanding of the molecular mechanisms of pathogenicity. A better definition of complex SVs, together with an accurate description of the phenotype, will allow the genotype-phenotype correlation to be determined.
• A third subgroup of patients eligible for the study are those with identified monoallelic alteration in autosomal recessive (AR) genes. The aim is to conduct a targeted analysis of the specific gene in order to look for a second mutation that wasn't detected by previous analysis (i.e. intronic variants, SVs, variants in difficult genomic regions).
• Lastly, patients with a phenotype that is strongly suggestive for a genetic condition, in whom several analyses, including Whole Exome-Sequencing (WES), retrieved negative results, could benefit from LRS. In this context, the aim is to apply a whole genome LRS approach to identify missed coding variants in difficult-to-sequence regions, variants in non-coding regions or SVs.

Enrollment: 30 estimated patients

Sex: All

Ages: 28+ days old

Volunteers: No Healthy Volunteers

Inclusion criteria

• patients/relatives of patients with Copy Number Variations (CNVs), previously detected by aCGH, with uncertain clinical significance;
• patients/relatives of patients with inconclusive WES and aCGH data (no pathogenic/likely pathogenic variant);
• patients/relatives of patients with a known single hit (a pathogenic or likely pathogenic variant) in an AR gene detected with WES or aCGH;
• patients/relatives of patients with a finding of complex structural variants whose molecular disease mechanism is to be elucidated.

Exclusion criteria

• none

Trial design

30 participants in 4 patient groups

Patients with CNVs of unknown significance

Description:

The first subgroup of patients are those with SVs of unknown significance or uncertain disease mechanism.

Treatment:

Genetic: DNA/RNA sequencing and bioinformatic data analysis

Patients with complex genomic rearrengements

Description:

Other complex rearrangements can be studied with LRS (i.e. ring chromosomes, isochromosome, chromosomal translocations, somatic SV found in tumors, etc.) to gain a better understanding of the molecular mechanisms of pathogenicity.

Treatment:

Genetic: DNA/RNA sequencing and bioinformatic data analysis

Patients with a monoallelic variant in an AR gene

Description:

A third subgroup of patients eligible for the study are those with identified monoallelic alteration in autosomal recessive (AR) genes.

Treatment:

Genetic: DNA/RNA sequencing and bioinformatic data analysis

Patients with negative results at WES analysis

Description:

Lastly, patients with a phenotype that is strongly suggestive for a genetic condition, in whom several analyses, including WES, retrieved negative results, could benefit from LRS.

Treatment:

Genetic: DNA/RNA sequencing and bioinformatic data analysis