search
Back to results

Initiative for Clinical Long-read Sequencing (IonGER)

Primary Purpose

Genetic Predisposition

Status
Not yet recruiting
Phase
Not Applicable
Locations
Germany
Study Type
Interventional
Intervention
Next-Generation Sequencing (NGS)
Sponsored by
University Hospital Tuebingen
About
Eligibility
Locations
Arms
Outcomes
Full info

About this trial

This is an interventional diagnostic trial for Genetic Predisposition focused on measuring Long-read sequencing, Rare diseases, Cancer preposition, Translate-NAMSE, German initiative for genomic medicine (genomDE)

Eligibility Criteria

undefined - undefined (Child, Adult, Older Adult)All SexesDoes not accept healthy volunteers

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

Sites / Locations

  • University Hospital Tübingen

Arms of the Study

Arm 1

Arm 2

Arm Type

Experimental

Experimental

Arm Label

Retrospective cohort

Prospective cohort

Arm Description

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.

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).

Outcomes

Primary Outcome Measures

Number of patients with Rare Disease (RD) or cancer predisposition syndromes with confirmed diagnosis by LR-GS compared to previous diagnostic methods including SR-GS
A molecular diagnosis is considered confirmed when likely pathogenic or pathogenic variants are identified according to the American College of Medical Genetics and Genomics (ACMG). classification.

Secondary Outcome Measures

Full Information

First Posted
September 13, 2023
Last Updated
September 22, 2023
Sponsor
University Hospital Tuebingen
Collaborators
RWTH Aachen University, Medical University of Hannover, Charite University, Berlin, Germany
search

1. Study Identification

Unique Protocol Identification Number
NCT06060184
Brief Title
Initiative for Clinical Long-read Sequencing
Acronym
IonGER
Official Title
Initiative for Clinical Long-read Sequencing - Towards Implementation of Long-read Genome Sequencing in Routine Diagnostics
Study Type
Interventional

2. Study Status

Record Verification Date
September 2023
Overall Recruitment Status
Not yet recruiting
Study Start Date
December 1, 2023 (Anticipated)
Primary Completion Date
December 1, 2025 (Anticipated)
Study Completion Date
December 1, 2026 (Anticipated)

3. Sponsor/Collaborators

Responsible Party, by Official Title
Sponsor
Name of the Sponsor
University Hospital Tuebingen
Collaborators
RWTH Aachen University, Medical University of Hannover, Charite University, Berlin, Germany

4. Oversight

Studies a U.S. FDA-regulated Drug Product
No
Studies a U.S. FDA-regulated Device Product
No
Data Monitoring Committee
No

5. Study Description

Brief Summary
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
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.

6. Conditions and Keywords

Primary Disease or Condition Being Studied in the Trial, or the Focus of the Study
Genetic Predisposition
Keywords
Long-read sequencing, Rare diseases, Cancer preposition, Translate-NAMSE, German initiative for genomic medicine (genomDE)

7. Study Design

Primary Purpose
Diagnostic
Study Phase
Not Applicable
Interventional Study Model
Parallel Assignment
Model Description
Parallel Assignment
Masking
None (Open Label)
Allocation
Non-Randomized
Enrollment
500 (Anticipated)

8. Arms, Groups, and Interventions

Arm Title
Retrospective cohort
Arm Type
Experimental
Arm Description
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.
Arm Title
Prospective cohort
Arm Type
Experimental
Arm Description
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).
Intervention Type
Genetic
Intervention Name(s)
Next-Generation Sequencing (NGS)
Intervention Description
Sequencing of genomes (Long read NGS)
Primary Outcome Measure Information:
Title
Number of patients with Rare Disease (RD) or cancer predisposition syndromes with confirmed diagnosis by LR-GS compared to previous diagnostic methods including SR-GS
Description
A molecular diagnosis is considered confirmed when likely pathogenic or pathogenic variants are identified according to the American College of Medical Genetics and Genomics (ACMG). classification.
Time Frame
Day 1

10. Eligibility

Sex
All
Accepts Healthy Volunteers
No
Eligibility Criteria
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
Central Contact Person:
First Name & Middle Initial & Last Name or Official Title & Degree
Tobias Haack, Dr.
Phone
+49 7071 29
Ext
77696
Email
tobias.haack@med.uni-tuebingen.de
First Name & Middle Initial & Last Name or Official Title & Degree
Olaf Rieß, Prof. Dr.
Phone
+49 7071 29
Ext
72288
Email
olaf.riess@med.uni-tuebingen.de
Overall Study Officials:
First Name & Middle Initial & Last Name & Degree
Tobias Haack, Dr. med.
Organizational Affiliation
University Hospital Tübingen
Official's Role
Principal Investigator
Facility Information:
Facility Name
University Hospital Tübingen
City
Tübingen
ZIP/Postal Code
72076
Country
Germany
Facility Contact:
First Name & Middle Initial & Last Name & Degree
Tobias Haack, Dr.
Phone
+49 7071 29
Ext
77696
Email
tobias.haack@med.uni-tuebingen.de
First Name & Middle Initial & Last Name & Degree
Rieß, Prof. Dr.
Phone
+49 7071 29
Ext
72288
Email
olaf.riess@med.uni-tuebingen.de

12. IPD Sharing Statement

Plan to Share IPD
Yes
IPD Sharing Plan Description
The IonGER study will provide data in a pseudonymised manner to national and international databases set up to increase the diagnostic yield through advanced analysis tools and matchmaking against other cohorts
IPD Sharing Time Frame
Data will become available after analysis and unlimited.

Learn more about this trial

Initiative for Clinical Long-read Sequencing

We'll reach out to this number within 24 hrs