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Initiative for Clinical Long-read Sequencing

NCT ID: NCT06060184

Last Updated: 2023-09-29

Study Results

Results pending

The study team has not published outcome measurements, participant flow, or safety data for this trial yet. Check back later for updates.

Basic Information

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Recruitment Status

NOT_YET_RECRUITING

Clinical Phase

NA

Total Enrollment

500 participants

Study Classification

INTERVENTIONAL

Study Start Date

2023-12-01

Study Completion Date

2026-12-01

Brief Summary

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The study aims to comprehensively introduce Long-read Genome sequencing (LR-GS) based genetic testing into clinical routine. In order to demonstrate the superiority of untargeted LR-GS over Short-read Genome sequencing (SR-GS) to establish firm genetic diagnoses, the investigators will rely on a multi-center "Translate Nationale Aktionsbündnis für Menschen mit Seltenen Erkrankungen" (Translate National Action Alliance for People with Rare Diseases Germany, TNAMSE) cohort of unsolved patients with neurological, neurodevelopmental, and imprinting disorders that is expectedly enriched for complex genomic variation. Within the framework of genomDE, the investigators will then implement, for the first time, LR-GS in the diagnostic work-up of a prospective cohort of patients with a broad range of clinical indications including rare diseases and cancer predisposition.

Detailed Description

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The proposed study aims to develop a blueprint for the implementation of LR-GS in clinical diagnostics. Hence Standard Operating Procedures (SOPs) and guidelines for library preparation, bioinformatic analysis, and clinical interpretation will be compiled. Furthermore, the investigators intend to develop an open source 'gold standard' bioinformatics pipeline, addressing all relevant types of genomic alterations, thus providing the bioinformatic basis for a streamlined implementation of LR-GS at other sites. In addition to in-depth phenotype information the availability of SR-GS will be instrumental to benchmark the ability to detect different types of genomic variation. Additional relevant issues for genetic testing such as variant calling in difficult-to-map genomic regions, detection of genomic methylation patterns, characterization of repeat expansion and duplicated genes, and haplotype-phased genome de novo assembly will be addressed. Moreover, based on the strong background in Artificial Intelligence (AI) driven variant prioritization in the consortium, the investigators aim to implement and/or develop tools that enable an efficient prioritization of disease-causing variants. Beyond the usage within the context of the proposed study, generated datasets will be made available according to the Findable, Accessible, Interoperable and Reusable (FAIR) principles for national (German Human Genome-Phenome Archive, GHGA) and international (European Genome-Phenome Archive, EGA, Genome-Phenome Analysis Platform, GPaP) data repositories. the investigators aim to establish a population scale reference dataset for Structural variants (SV), which is absolutely mandatory in the context of rare disease diagnostics.

Conditions

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Genetic Predisposition

Keywords

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Long-read sequencing Rare diseases Cancer preposition Translate-NAMSE German initiative for genomic medicine (genomDE)

Study Design

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Allocation Method

NON_RANDOMIZED

Intervention Model

PARALLEL

Parallel Assignment
Primary Study Purpose

DIAGNOSTIC

Blinding Strategy

NONE

Study Groups

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Retrospective cohort

Subjects with unclear molecular cause of the disease. The subjects are clinically characterized in the context of outpatient/ inpatient standard care at the University Hospital Tübingen (UKT) or cooperating locations.

Group Type EXPERIMENTAL

Next-Generation Sequencing (NGS)

Intervention Type GENETIC

Sequencing of genomes (Long read NGS)

Prospective cohort

Subjects with indication for genome diagnostics (e.g. within the initiative for genomic medicine (genomDE) based on §64e German Social Code (SGB) Fifth Book (V) (SGB V).

Group Type EXPERIMENTAL

Next-Generation Sequencing (NGS)

Intervention Type GENETIC

Sequencing of genomes (Long read NGS)

Interventions

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Next-Generation Sequencing (NGS)

Sequencing of genomes (Long read NGS)

Intervention Type GENETIC

Eligibility Criteria

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Inclusion Criteria

* Unclear molecular cause of the disease (retrospective cohort)
* Indication for genome diagnostics (prospective cohort; e.g. within the initiative for genomic medicine (genomDE) based on §64e SGB V)
* Suspected genetic cause of the disease

Exclusion Criteria

\- Missing informed consent of the patient or legal guardian
Eligible Sex

ALL

Accepts Healthy Volunteers

No

Sponsors

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RWTH Aachen University

OTHER

Sponsor Role collaborator

Medical University of Hannover

OTHER

Sponsor Role collaborator

Charite University, Berlin, Germany

OTHER

Sponsor Role collaborator

University Hospital Tuebingen

OTHER

Sponsor Role lead

Responsible Party

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Responsibility Role SPONSOR

Principal Investigators

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Tobias Haack, Dr. med.

Role: PRINCIPAL_INVESTIGATOR

University Hospital Tübingen

Locations

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University Hospital Tübingen

Tübingen, , Germany

Site Status

Countries

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Germany

Central Contacts

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Tobias Haack, Dr.

Role: CONTACT

Phone: +49 7071 29

Email: [email protected]

Olaf Rieß, Prof. Dr.

Role: CONTACT

Phone: +49 7071 29

Email: [email protected]

Facility Contacts

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Tobias Haack, Dr.

Role: primary

Rieß, Prof. Dr.

Role: backup

Other Identifiers

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IonGER

Identifier Type: -

Identifier Source: org_study_id