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Intellectual DisabilityDEFIDIAGNCT04154891

Genome Sequencing Strategies for Genetics Diagnosis of Patients With Intellectual Disability

A study testing Whole Genome Sequencing in people with Intellectual Disability, run by Institut National de la Santé Et de la Recherche Médicale, France at 14 sites in France.

Completed

Finished. The study has ended and is not enrolling. Results may be posted on the official record.

Official record
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Trial summary

Introduction : Intellectual Disability (ID) is the most common cause of referral in the pediatric genetic centers and is characterized by an extreme genetic heterogeneity corresponding to a myriad of rare diseases that complicates the identification of ID's. Read more about this study

Who is it for?
Any ageHealthy volunteers can take part
Conditions the study is for
Intellectual Disability
What is being tested?
Whole Genome Sequencing
Could I receive a placebo?
No, everyone receives an active treatment
How many people
3,825 participants
Where
14 sitesFrance
Study dates
13 Mar 2020to 16 Jun 2025
Phase
Interventional
Are there results?
None posted in the registry

Key requirements

Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.

  • Ages Any age
  • All sexes
  • Healthy volunteers accepted
  • Child, Adult, Older adult
  1. Inclusion criteria for children or adults with ID of unknown etiology (index case) In order to be eligible to participate in this study, an individual must meet all the following criteria:
  • Age:
  1. Between 0 and 5 years with stringent criteria (severe delayed development in terms of motor skills, language, and/or sociability) OR
  2. ≥ 6 years: patients with ID, whatever the severity (but with proven ID by ad hoc neuropsychological testing) and the associated manifestations
  • Without any obvious diagnosis identified during a genetic consultation in one of the participating center (i.e., an obvious syndrome with ID with well-known molecular diagnosis is excluded);
  • Provision of signed and dated of "participant" consent form;
  • Stated willingness to comply with all study procedures and availability for the duration of the study. Patient with a social security in compliance with the French law (Provisions relating to research involving the human person provided for in Articles L 1121-1 et seq. of the French Public Health Code).
  1. Inclusion criteria for biological parents
  • Provision of signed and dated of both parents consent form.
  1. Non-inclusion criteria
  • An individual, who presents any condition which in the investigator's opinion makes it undesirable for the subject to participate in the trial or which would jeopardize compliance with the protocol, will not be eligible;
  • Patients with isolated learning disabilities;
  • One or both parents with ID;
  • Parent placed under judicial protection (tutelle, curatelle et sauvegarde de justice) ;
  • Patient with a known etiological diagnosis (non-genetic, previously proven Fra-X syndrome, know chromosomal anomaly, known pathogenic or probably pathogenic variant identified in an ID gene by any technique).
  • For patient concerning by biobank project: hypersensitivity to local anesthesia

Trial locations and contacts

14 sites in 1 country.

14 sites in 1 country

France14 sites
  • CHU d'Angers

    Angers, 49000

  • CHU Bordeaux

    Bordeaux

  • Hospices Civil de Lyon

    Bron

  • CHU Dijon

    Dijon

  • CHU de Grenoble-Alpes

    La Tronche, 38700

  • CHRU Lille

    Lille

  • Assistance publique - Hôpitaux de Marseille

    Marseille

  • CHU Montpellier

    Montpellier

  • CHU Nantes

    Nantes

  • Assistance publique - Hôpitaux de Paris - Groupe Hospitalier Pitié Salpétrière

    Paris

  • Assistance publique - Hôpitaux de Paris - Hôpital Necker - Enfants malades

    Paris

  • CHU Rennes

    Rennes

  • CHU Rouen

    Rouen

  • CHU Strasbourg

    Strasbourg

Other trials in France

About this study

Official title: Etude Pilote Des différentes stratégies de séquençage Haut débit du génome Pour le Diagnostic génétique Des Patients Atteints de déficience Intellectuelle

Introduction : Intellectual Disability (ID) is the most common cause of referral in the pediatric genetic centers and is characterized by an extreme genetic heterogeneity corresponding to a myriad of rare diseases that complicates the identification of ID's.

Overall today in France, for non-syndromic ID affected patients, the Fra-X detection, the chromosomal microarray analysis and Gene Panel Strategy of 44 ID selected genes leads to a global diagnostic yield for 1/3 patients leaving 2/3 of patients still with no diagnosis.

Read more

The advent, and burst, of Next Generation Sequencing (NGS) technologies has clearly revolutionized the approaches to diagnosis and research in the field of rare diseases at an international. That's why the main hypothesis of DEFIDIAG is that Whole Genome Sequencing (WGS) could allow to improve the diagnostic performance and cost-effectiveness for French patients with ID.

Objective : The main objective of this study is to compare ther percentage of genetic causal diagnosis identified in ID patients by performing trio WGS analysis vs the use of the current French reference strategy (ACPA, X-Fra, DI 44).

Methods and design : This is a prospective study. The investigators expect to include 1275 index case with his/her 2 biological unaffected parents.

Being tested
Whole Genome Sequencing
Keywords
Rare disease, Next generation sequencing genome, Diagnostic study, Medico-economic study
Medical subject headings
Intellectual Disability, Rare Diseases, Disease

What participants receive

What participants receive. In a randomised study each person is assigned to one group by chance.

  • Whole Genome SequencingGenetic

    The analysis will follow a consensus protocol that contains 3 obligatory steps: first of all, de novo variants (SNV, CNV and others SV) will be examined in the whole genome data set; then, a SNV/CNV/other SV analysis will be performed under a AR or X linked Mendelian mode hypothesis in the whole genomic regions of a OMIM extended list (that contains all genes already involved in human genetic diseases). Finally, analysis will focus on inherited pathogenic variants under an AD mode hypothesis (analysis of variations already reported as pathogenic in clinVar or HGMD pro; CNV or truncating variation in OMIM genes, etc). When these 3 steps analysis is completed then variants of interest identified at each step will be recorded until examination by a specific multidisciplinary meeting.

Study groups in NCT04154891
Study groupRoleWhat they receive
GeneticOtherEach included patient will be his own control; he will benefit from the two main strategies compared, in parallel. The diagnostic yield of Whole Genome Sequencing using a simplex strategy (WGSs) will be also investigated in parallel to the two main strategies but only in a randomized subgroup of the overall population coming for a first genetic advice. The results of the different strategies will be interpreted blindly, each participating laboratory being in charge for a given investigation center, either of 1) the trio or 2) the 44GPS (part of the reference strategy) and, for the randomized sub-population of the overall population coming for a first genetic advice, simplex analyses. Fra-X and chromosomal microarray analysis corresponding to the reference strategy will follow the routine circuit, which is mainly independent from the WGS circuit.
Receives: Genetic: Whole Genome Sequencing

What is being measured

The primary outcome is the main question the study is designed to answer.

  1. Diagnostic Yield

    The primary study endpoint is the identification of a causal diagnosis of ID defined as the identification of one class 4 or 5 variant (or two in case of autosomal recessive inheritance) that explains the symptoms presented by the patient. In addition variants classified as 3+, anticipated to become future 4 will be recorded. Specific analysis and follow up of the variant classified as 3+ (i.e. with a high probability of pathogenicity) will be done after the end of the protocol to determine the class 3+ to class 4-5 switch proportion and to describe the new genes/mechanisms involved in ID and revealed by DEFIDIAG.

    Measured: 12 months

Secondary outcomes (7)
  1. Causal structural change

    Identification of causal structural changes (CNV, translocation, inversion) in the first investigation population (confirmed during the MDM for the WGS strategies)

    The clinical characteristics of patients and the diagnostic yield at each step of the incremental selection within WGS analyses (44GPS, OMIMOME, WES, WGS) according to the results of the preceding step as well as according to the results of chromosomal microarray analysis and 44GPS will also be parameters of interest in the whole population.

    Measured: 12 months

  2. Incremental cost-effectiveness ratio

    The cost-effectiveness endpoint will be an efficiency criterion based on the estimation of an incremental cost-effectiveness ratio, expressed in terms of cost per additional positive diagnosis.

    Measured: 24 months

  3. Mean cost of wavering diagnostic research

    Estimation of the cost of wavering diagnostic research

    Measured: 24 months

  4. Percentage of at least one modification in medical, medico-social, rehabilitative and psychological follow-up

    Measured: 24 months

  5. Number and type of secondary data

    The number and type of SFs (class 4 or 5 mutation(s)) identified in the parents that specifically consent to this study will be recorded in a specific report. The outcome will be defined by the percentage of SFs in the studied population and the number and type of medical consequences following their identification.

    Measured: 12 months

  6. Median time and type of skills required for analyzing genetic data and for genetic confirmation

    Measured: 12 months

  7. Median time to obtain results

    Measured: 12 months

Timeline

From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.

  1. First posted7 Nov 2019
  2. Study start13 Mar 2020
  3. Primary completion31 Dec 2023
  4. Study completion16 Jun 2025

Resources

More details

For doctors and researchers: how the study is designed, who runs it, and its registry IDs.

Study design
Study type
Interventional
Phase
Phase N/A
Primary purpose
Diagnosis
Allocation
Not applicable
Intervention model
Single group
Model description
Prospective multicenter diagnostic study comparing the percentage of Intellectual Deficiency (ID) causal diagnosis obtained using 2 main different strategies (Whole Genome Sequencing using a trio strategy (WGST), and reference strategy) applied blindly to consecutive patients with no obvious diagnosis. Each included patient will be his own control; he will benefit from the two main strategies compared, in parallel. The diagnostic yield of Whole Genome Sequencing using a simplex strategy (WGSs) will be also investigated in parallel to the two main strategies but only in a randomized subgroup of the overall population coming for a first genetic advice.
Masking
None (open label)
Enrolment
3,825 participants (actual)
IDs, dates and publications
ClinicalTrials.gov ID
NCT04154891
Sponsor's protocol ID
C16-110
Other IDs
2018-A00680-55
Acronym
DEFIDIAG
Status last verified
Sep 2025
First submitted
29 Oct 2019
Last updated
23 Jun 2026
Results posted
No
Data monitoring committee
No
FDA-regulated drug
No
FDA-regulated device
No

Publications

  • Binquet C, Lejeune C, Faivre L, Bouctot M, Asensio ML, Simon A, Deleuze JF, Boland A, Guillemin F, Seror V, Delmas C, Esperou H, Duffourd Y, Lyonnet S, Odent S, Heron D, Sanlaville D, Frebourg T, Gerard B, Dollfus H. Genome Sequencing for Genetics Diagnosis of Patients With Intellectual Disability: The DEFIDIAG Study. Front Genet. 2022 Feb 1;12:766964. doi: 10.3389/fgene.2021.766964. eCollection 2021.

    PubMed 35178068
  • Lejeune C, Robert-Viard C, Meunier-Beillard N, Borel MA, Gourves L, Staraci S, Soilly AL, Guillemin F, Seror V, Achit H, Bouctot M, Asensio ML, Briffaut AS, Delmas C, Bruel AL, Benoit A, Simon A, Gerard B, Hadj Abdallah H, Lyonnet S, Faivre L, Thauvin-Robinet C, Odent S, Heron D, Sanlaville D, Frebourg T, Muller J, Duffourd Y, Boland A, Deleuze JF, Esperou H, Binquet C, Dollfus H. The Economic, Medical and Psychosocial Consequences of Whole Genome Sequencing for the Genetic Diagnosis of Patients With Intellectual Disability: The DEFIDIAG Study Protocol. Front Genet. 2022 Apr 4;13:852472. doi: 10.3389/fgene.2022.852472. eCollection 2022.

    PubMed 35444683
  • Meuwissen M, Verstraeten A, Ranza E, Iwaszkiewicz J, Bastiaansen M, Mateiu L, Nemegeer M, Meester JAN, Afenjar A, Amaral M, Ballhausen D, Barnett S, Barth M, Asselbergh B, Spaas K, Heeman B, Bassetti J, Blackburn P, Schaer M, Blanc X, Zoete V, Casas K, Courtin T, Doummar D, Guerry F, Keren B, Pappas J, Rabin R, Begtrup A, Shinawi M, Vulto-van Silfhout AT, Kleefstra T, Wagner M, Ziegler A, Schaefer E, Gerard B, De Bie CI, Holwerda SJB, Abbot MA, Antonarakis SE, Loeys B. Heterozygous variants in CTR9, which encodes a major component of the PAF1 complex, are associated with a neurodevelopmental disorder. Genet Med. 2022 Jul;24(7):1583-1591. doi: 10.1016/j.gim.2022.04.003. Epub 2022 May 2.

    PubMed 35499524
  • Ravindran E, Lesca G, Januel L, Goldgruber L, Dickmanns A, Margot H, Kaindl AM. Case report: Compound heterozygous NUP85 variants cause autosomal recessive primary microcephaly. Front Neurol. 2023 Feb 9;14:1124886. doi: 10.3389/fneur.2023.1124886. eCollection 2023.

    PubMed 36846113
  • El Chehadeh S, Heide S, Quelin C, Rio M, Margot H, Genevieve D, Isidor B, Goldenberg A, Guegan C, Lesca G, Willems M, Ormieres C, Caumes R, Busa T, Bonneau D, Guerrot AM, Marey I, Vera G, Marzin P, Philippe A, Garde A, Coubes C, Vincent M, Michaud V, Mignot C, Charles P, Sigaudy S, Edery P, Lacombe D, Boland A, Nowak F, Bouctot M, Humbert-Asensio ML, Simon A, Chennen K, Sabour N, Delmas C, Nicolas G, Saugier-Veber P, Lecoquierre F, Cassinari K, Keren B, Courtin T, De Sainte Agathe JM, Malan V, Barcia G, Tran Mau-Them F, Safraou H, Philippe C, Thevenon J, Chatron N, Januel L, Piton A, Haushalter V, Gerard B, Lejeune C, Faivre L, Sanlaville D, Heron D, Odent S, Nitschke P, Schluth-Bolard C, Lyonnet S, Deleuze JF, Binquet C, Dollfus H; DEFIDIAG study group. Genome sequencing for the diagnosis of intellectual disability as a paradigm for rare diseases in the French healthcare setting: the prospective DEFIDIAG study. Genome Med. 2025 Oct 3;17(1):110. doi: 10.1186/s13073-025-01527-4.

    PubMed 41044778

Questions about this trial

What is this clinical trial studying?

A study testing Whole Genome Sequencing in people with Intellectual Disability, run by Institut National de la Santé Et de la Recherche Médicale, France at 14 sites in France.

The full registered description is in the About this study section and the official record.

Is this clinical trial currently recruiting?

The record says: finished, as of the sponsor's last update on 23 Jun 2026. Status can change between updates, so confirm with the study contact before making plans.

Where is the study taking place?

The record lists 14 sites in France. Whether a site is taking part right now should be confirmed with that site. See every site.

What are the possible benefits and risks?

They depend on the study and the treatment, and no study can promise a benefit. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.

Are results available for this study?

The study is completed, but results are not available in the source record. That does not mean the treatment did or did not work.

How can a doctor refer a patient or contact the research team?

The record lists no contact. The official record names the sponsor, who can be asked directly. AzTrials does not enrol participants or take referrals.

What does the primary outcome measure?

Diagnostic Yield (time frame: 12 months). It is what the study was designed to measure, not a finding.

Where can I read the original study information?

On the ClinicalTrials.gov record for NCT04154891, which also lists 5 linked publications.

Does a listing mean the treatment is approved or proven to work?

No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.

How often is this information updated?

AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 23 Jun 2026.

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