Integration of New Generation Multi-omics Analyses for the Diagnosis of Genetic Neurodevelomental Disorders (NEXTOMIX)

August 5, 2026 updated by: Centre Hospitalier Universitaire Dijon

Neurodevelopmental disorders (NDDs), including intellectual disability (ID), represent the most common indication for genetic testing. Affecting up to 3% of the general population, NDDs are characterized by significant clinical and genetic heterogeneity. Although short-read genome sequencing (srGS) has driven major advances through the France Genomic Medicine 2025 Plan (PFMG2025), a substantial proportion of patients still lack a molecular diagnosis.

These results are partly explained by the limitations of short-read genome sequencing (srGS). Although effective in many cases, this technology performs poorly in detecting complex structural rearrangements, anomalies within repetitive or GC-rich regions, epigenetic variations, and certain intronic variants. Furthermore, srGS does not allow for the direct assessment of the functional impact of genetic variations on splicing or gene expression. Following a negative srGS result, periodic reanalysis of sequencing data via the PFMG2025 laboratories (AURAGEN and SeqOIA) is the only diagnostic option currently available in routine practice. However, these reanalyses are constrained by financial and staffing limitations as well as strict eligibility criteria, making it difficult for many patients-particularly those with stable neurodevelopmental disorders (NDDs)-to obtain a diagnosis. Moreover, they often consist merely of a data review without bioinformatic updates, and the turnaround times-frequently exceeding one year-contribute to the diagnostic odyssey. Utilizing updated pipelines tailored to the specific characteristics of NDDs for the re-examination of srGS data could serve as an initial source of new diagnoses.

Complementary technologies-such as messenger RNA sequencing (mRNA-seq), optical genome mapping (OGM), and long-read genome sequencing (lrGS)-are available and offer solutions to overcome the limitations of short-read genome sequencing (srGS). In particular, they enable the identification of complex structural variants and the assessment of the functional impact of point variants. Despite their potential, their routine use remains limited due to cost and technical complexity.

Our study proposes a combined strategy to address the limitations of current approaches and improve the diagnosis of neurodevelopmental disorders (NDDs) that remain unresolved after short-read genome sequencing (srGS). It begins with a re-analysis of sequencing data using customized bioinformatics pipelines tailored to the patients' specific clinical profiles. In cases of inconclusive results, innovative multi-omics analyses (mRNA-seq, OGM, and long-read genome sequencing/lrGS) will be employed to investigate complex genetic variants. As multi-omics approaches are not currently integrated into the PFMG2025 framework, the project's findings will be crucial in demonstrating their added value for NDD diagnosis and could pave the way for their inclusion in a future PFMG. By anticipating these developments, NextOmix will help define the diagnostic strategies of the future, aligned with technological advancements and patient needs.

Study Overview

Status

Status

Indicates the current recruitment status or the expanded access status.
Not yet recruiting

Conditions

Conditions

The disease, disorder, syndrome, illness, or injury that is being studied. On ClinicalTrials.gov, conditions may also include other health-related issues, such as lifespan, quality of life, and health risks.

Intervention / Treatment

Intervention / Treatment

A process or action that is the focus of a clinical study. Interventions include drugs, medical devices, procedures, vaccines, and other products that are either investigational or already available. Interventions can also include noninvasive approaches, such as education or modifying diet and exercise.

Study Type

Study Type

Describes the nature of a clinical study. Study types include interventional studies (also called clinical trials), observational studies (including patient registries), and expanded access.
Interventional

Enrollment (Estimated)

Enrollment

The number of participants in a clinical study. The "anticipated" enrollment is the target number of participants that the researchers need for the study.
132

Phase

Phase

The stage of a clinical trial studying a drug or biological product, based on definitions developed by the U.S. Food and Drug Administration (FDA). The phase is based on the study's objective, the number of participants, and other characteristics. There are five phases: Early Phase 1 (formerly listed as Phase 0), Phase 1, Phase 2, Phase 3, and Phase 4. Not Applicable is used to describe trials without FDA-defined phases, including trials of devices or behavioral interventions.
  • Not Applicable

Contacts and Locations

This section provides the contact details for those conducting the study, and information on where this study is being conducted.

Study Contact

Study Contact

The name and contact information for the person who can answer enrollment questions for a clinical study. Each location where the study is being conducted may also have a specific contact, who may be better able to answer those questions.

Study Locations

Participation Criteria

Researchers look for people who fit a certain description, called eligibility criteria. Some examples of these criteria are a person's general health condition or prior treatments.

Eligibility Criteria

Eligibility Criteria

The key requirements that people who want to participate in a clinical study must meet or the characteristics they must have. Eligibility criteria consist of both inclusion criteria (which are required for a person to participate in the study) and exclusion criteria (which prevent a person from participating). Types of eligibility criteria include whether a study accepts healthy volunteers, has age or age group requirements, or is limited by sex.

Ages Eligible for Study

  • Child
  • Adult
  • Older Adult

Accepts Healthy Volunteers

No

Description

Inclusion Criteria:

  • Index case (minor or adult) with severe to profound intellectual disability or syndromic neurodevelopmental disorder without an identified molecular diagnosis. - Index case with a negative srGS result.
  • Sample collection possible from the index case (blood and skin biopsy) and their biological parent(s) (blood) if material is not otherwise available.
  • Signed consent from the adult index case, or from the legal representatives or guardian (as applicable) of a minor index case, and from their parent(s).

Exclusion Criteria:

  • - Index case or parent(s) not affiliated with or not covered by a social security scheme.
  • Diagnostic hypothesis considered highly probable, for which an available targeted molecular test costs less than the proposed strategy.
  • Suspicion of an acquired cause for the symptoms.
  • Minor parent(s).
  • Parent subject to a legal protection measure, or incapacitated or otherwise unable to provide informed consent.
  • Pregnant, birthing, or breastfeeding woman.
  • Participant (index case or parent) who has previously undergone allogeneic hematopoietic stem cell transplantation, rendering blood sample analysis uninformative.

Study Plan

This section provides details of the study plan, including how the study is designed and what the study is measuring.

How is the study designed?

Design Details

  • Primary Purpose: Diagnostic
  • Allocation: N/A
  • Interventional Model: Single Group Assignment
  • Masking: Single

Arms and Interventions

Participant Group / Arm

Participant Group / Arm

A group or subgroup of participants in a clinical trial that receives a specific intervention/treatment, or no intervention, according to the trial's protocol.
Intervention / Treatment

Intervention / Treatment

A process or action that is the focus of a clinical study. Interventions include drugs, medical devices, procedures, vaccines, and other products that are either investigational or already available. Interventions can also include noninvasive approaches, such as education or modifying diet and exercise.
Other: Patient with severe to profound intellectual disability
Diagnostic test: Re-analysis of available srGS data
Re-analysis of available srGS data without further analysis, as the results were positive for the causal diagnosis.
Diagnostic test: Re-analysis of available srGS data, followed by complementary analyses (lrGS sequencing, mRNA, and GMOs)
Re-analysis of available srGS data followed by additional analyses (lrGS sequencing, mRNA-seq, and GMO testing), as the srGS data are negative for the causal diagnosis.
Diagnostic test: srGS sequencing
New srGS sequencing without additional analyses, as it is positive for the causal diagnosis.
Diagnostic test: Short-read sequencing (srGS) followed by long-read sequencing (lrGS,), mRNA-sequencing and GMO testing
New srGS sequencing followed by additional analyses (lrGS sequencing, mRNA-seq, and GMO testing) because the srGS data are negative for the causal diagnosis.
Other: Patient with a syndromic neurodevelopmental disorder with intellectual disability
Diagnostic test: Re-analysis of available srGS data
Re-analysis of available srGS data without further analysis, as the results were positive for the causal diagnosis.
Diagnostic test: Re-analysis of available srGS data, followed by complementary analyses (lrGS sequencing, mRNA, and GMOs)
Re-analysis of available srGS data followed by additional analyses (lrGS sequencing, mRNA-seq, and GMO testing), as the srGS data are negative for the causal diagnosis.
Diagnostic test: srGS sequencing
New srGS sequencing without additional analyses, as it is positive for the causal diagnosis.
Diagnostic test: Short-read sequencing (srGS) followed by long-read sequencing (lrGS,), mRNA-sequencing and GMO testing
New srGS sequencing followed by additional analyses (lrGS sequencing, mRNA-seq, and GMO testing) because the srGS data are negative for the causal diagnosis.
Other: Patient with a syndromic neurodevelopmental disorder without intellectual disability
Diagnostic test: Re-analysis of available srGS data
Re-analysis of available srGS data without further analysis, as the results were positive for the causal diagnosis.
Diagnostic test: Re-analysis of available srGS data, followed by complementary analyses (lrGS sequencing, mRNA, and GMOs)
Re-analysis of available srGS data followed by additional analyses (lrGS sequencing, mRNA-seq, and GMO testing), as the srGS data are negative for the causal diagnosis.
Diagnostic test: srGS sequencing
New srGS sequencing without additional analyses, as it is positive for the causal diagnosis.
Diagnostic test: Short-read sequencing (srGS) followed by long-read sequencing (lrGS,), mRNA-sequencing and GMO testing
New srGS sequencing followed by additional analyses (lrGS sequencing, mRNA-seq, and GMO testing) because the srGS data are negative for the causal diagnosis.

What is the study measuring?

Primary Outcome Measures

Primary Outcome Measures

In a clinical study's protocol, the planned outcome measure that is the most important for evaluating the effect of an intervention/treatment. Most clinical studies have one primary outcome measure, but some have more than one.
Outcome Measure
Measure Description
Time Frame
Identification of a causative diagnosis (class 4 or 5 variant according to American College of Medical Genetics criteria) explaining the phenotype and validated during a multidisciplinary team meeting.
Time Frame: Between 4 and 12 months
Identification of a causative diagnosis (class 4 or 5 variant according to American College of Medical Genetics criteria) explaining the phenotype and validated during a multidisciplinary team meeting.
Between 4 and 12 months

Collaborators and Investigators

This is where you will find people and organizations involved with this study.

Sponsor

Sponsor

The organization or person who initiates the study and who has authority and control over the study.
Centre Hospitalier Universitaire Dijon

Study record dates

These dates track the progress of study record and summary results submissions to ClinicalTrials.gov. Study records and reported results are reviewed by the National Library of Medicine (NLM) to make sure they meet specific quality control standards before being posted on the public website.

Study Major Dates

Study Start (Estimated)

Study Start

The actual date on which the first participant was enrolled in a clinical study. The "anticipated" study start date is the date that the researchers think will be the study start date.
September 1, 2026

Primary Completion (Estimated)

Primary Completion

The date on which the last participant in a clinical study was examined or received an intervention to collect final data for the primary outcome measure. Whether the clinical study ended according to the protocol or was terminated does not affect this date. For clinical studies with more than one primary outcome measure with different completion dates, this term refers to the date on which data collection is completed for all the primary outcome measures. The "anticipated" primary completion date is the date that the researchers think will be the primary completion date for the study.
March 1, 2029

Study Completion (Estimated)

Study Completion

The date on which the last participant in a clinical study was examined or received an intervention/treatment to collect final data for the primary outcome measures, secondary outcome measures, and adverse events (that is, the last participant's last visit). The "anticipated" study completion date is the date that the researchers think will be the study completion date.
March 1, 2029

Study Registration Dates

First Submitted

First Submitted

The date on which the study sponsor or investigator first submitted a study record to ClinicalTrials.gov. There is typically a delay of a few days between the first submitted date and the record's availability on ClinicalTrials.gov (the first posted date).
August 5, 2026

First Submitted That Met QC Criteria

First Submitted That Met QC Criteria

The date on which the study sponsor or investigator first submits a study record that is consistent with National Library of Medicine (NLM) quality control (QC) review criteria. The sponsor or investigator may need to revise and submit a study record one or more times before NLM's QC review criteria are met. It is the responsibility of the sponsor or investigator to ensure that the study record is consistent with the NLM QC review criteria.
August 5, 2026

First Posted (Actual)

First Posted

The date on which the study record was first available on ClinicalTrials.gov after National Library of Medicine (NLM) quality control (QC) review has concluded. There is typically a delay of a few days between the date the study sponsor or investigator submitted the study record and the first posted date.
August 10, 2026

Study Record Updates

Last Update Posted (Actual)

Last Update Posted

The most recent date on which changes to a study record were made available on ClinicalTrials.gov. There may be a delay between when the changes were submitted to ClinicalTrials.gov by the study's sponsor or investigator (the last update submitted date) and the last update posted date.
August 10, 2026

Last Update Submitted That Met QC Criteria

Last Update Submitted That Met QC Criteria

The most recent date on which the study sponsor or investigator submitted changes to a study record that are consistent with National Library of Medicine (NLM) quality control (QC) review criteria. It is the responsibility of the sponsor or investigator to ensure that the study record is consistent with the NLM QC review criteria.
August 5, 2026

Last Verified

Last Verified

The most recent date on which the study sponsor or investigator confirmed the information about a clinical study on ClinicalTrials.gov as accurate and current. If a study with a recruitment status of recruiting; not yet recruiting; or active, not recruiting has not been confirmed within the past 2 years, the study's recruitment status is shown as unknown.
August 1, 2026

More Information

Terms related to this study

Additional Relevant MeSH Terms

Other Study ID Numbers

Other Study ID Numbers

Identifiers or ID numbers other than the NCT number that are assigned to a clinical study by the study's sponsor, funders, or others. These numbers may include unique identifiers from other trial registries and National Institutes of Health grant numbers.
  • MAZEL PHRCI 2024

Drug and device information, study documents

Studies a U.S. FDA-regulated drug product

No

Studies a U.S. FDA-regulated device product

No

This information was retrieved directly from the website clinicaltrials.gov without any changes. If you have any requests to change, remove or update your study details, please contact register@clinicaltrials.gov. As soon as a change is implemented on clinicaltrials.gov, this will be updated automatically on our website as well.

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