Characterization and Contribution of Genome-wide DNA Methylation (DNA Methylation Episignatures) in Rare Diseases With Prenatal Onset

Not yet recruiting

• Conditions: Rare Fetal Genetic Diseases; Congenital Malformation
• Interventions: Genetic: Methylation analysis

• Registration Number: NCT06475651
• Lead Sponsor: Assistance Publique - Hôpitaux de Paris

Brief Summary

It is necessary to define reference DNA Methylation Episignatures from fetal DNA. The hypotheses are:

* It is possible to define reference DNA Methylation Episignatures from fetal DNA extracted from amniotic fluid or frozen tissues collected during the postmortem examination

* Fetal DNA Methylation Episignatures may be different to postanal DNA Methylation Episignatures defined on DNA extracted from blood

Detailed Description

Congenital anomalies (CA) complicate 3 to 5% of pregnancies and may be associated with genetic disorders. Diagnosis of genetic diseases is a major medical challenge, especially during pregnancy.

Over the past two decades, next-generation sequencing (NGS) has revolutionized our ability to identify the genetic condition associated with CA. During pregnancy, prenatal exome sequencing identified an additional diagnosis in around 30% of fetuses with CA when standard chromosomal investigations (karyotype and chromosomal microarray analysis, CMA) fail to provide a diagnosis.

Despite these major advances, around 40% of rare diseases remain unsolved, including 10-15% of patients harboring variants of uncertain significance (VUS).

After birth, additional functional analyses ("multi-OMICS"), including genome-wide DNA methylation studies, may be offered to reclassify VUS.

DNA methylation anomalies play an important role in pathologies (developmental disorders and oncology).

DNA methylation Episignatures, defined as the cumulative DNA methylation patterns occurring at multiple CpG dinucleotides across the genome, have been recognized to be intricately associated with many human traits, including age, sex, and disease status. Recently, DNA Methylation Episignatures have been identified in the blood of children or adults for several well-characterized genetic diseases. However, these postnatal DNA Methylation Episignatures cannot be used during pregnancy, because DNA methylation changes from one tissue to another and during time, especially during fetal developpement. In addition, the tissues available during pregnancy are different from those analyzed postnatally (blood).

Study Timeline

• Status Verified: 2024-06
• Study Start: 2024-06
• Study First Submitted: 2024-06-20
• Study First Submitted QC: 2024-06-20
• Last Update Submitted: 2024-06-20
• Study First Posted: 2024-06-26
• Last Update Posted: 2024-06-26
• Primary Completion: 2024-12
• Study Completion: 2024-12

Recruitment & Eligibility

• Status: NOT_YET_RECRUITING
• Sex: All
• Target Recruitment: 63

Inclusion Criteria

• Patient Inclusion Criteria:

  • Fetuses with a postmortem examination as part of the etiological diagnosis of developmental abnormality within the Genomic Medicine of Rare Diseases department of the Necker Children's Hospital, and whose DNA extracted from lung and amniotic fluid is available
  • OR a child cared for in the Genomic Medicine for Rare Diseases department of the Necker Children's Hospital, and whose DNA extracted from whole blood is available
  • with pathogenic or probably pathogenic variation in a gene following CHD7, KMT2D, HYLS1, TCTN3 or FLVCR2
  • whose parents have consented to molecular genetic testing as part of diagnosis and research

• Negative Controls :

  • Fetuses with a postmortem examination as part of the etiological diagnosis of developmental abnormality within the Genomic Medicine of Rare Diseases department of the Necker Children's Hospital, and whose DNA extracted from lung and amniotic fluid are available
  • OR a child cared for in the Genomic Medicine for Rare Diseases department of the Necker Children's Hospital, and whose DNA extracted from whole blood is available
  • does not have pathogenic or probably pathogenic variation in a gene following CHD7, KMT2D, HYLS1, TCTN3 or FLVCR2
  • whose parents have consented to molecular genetic testing as part of diagnosis and research

• For everyone:

  • For living participants: Non-objection by holders of parental authority to the reuse of clinical data and biological samples collected and stored in the context of care (consent of care).

  • For deceased participants:

• Consent of the holders of parental authority to the use of the samples kept for research purposes, signed as part of the treatment

• No mention of opposition to the reuse of clinical data from the treatment in the patient's medical record

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Exclusion Criteria

• Refusal of postmortem examination in case of fetal loss
• Parents' refusal of molecular investigations

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Study & Design

• Study Type: OBSERVATIONAL
• Study Design: Not specified

Arm && Interventions

Group	Intervention	Description
Workpackage 1, group 1	Methylation analysis	Patients (children) with CHARGE syndrome
Workpackage 1, group 2	Methylation analysis	Healthy negative controls (children) matched for age and sex
Workpackage 2, group 5	Methylation analysis	Patients (children) with KABUKI syndrome
Workpackage 1, group 3	Methylation analysis	Fetuses with CHARGE syndrome
Workpackage 1, group 4	Methylation analysis	Fetuses with no genetic pathology
Workpackage 2, group 6	Methylation analysis	Fetuses with KABUKI syndrome
Workpackage 3, group 7	Methylation analysis	Fetuses with hydrolethalus syndrome
Workpackage 3, group 8	Methylation analysis	Fetuses with Meckel/OFD IV syndrome
Workpackage 3, group 9	Methylation analysis	Fetuses with Fowler syndrome

Primary Outcome Measures

Name	Time	Method
Epigenetic signature associated with pathogenic variations in the CHD7 gene (CHARGE Syndrome)	12 months	Evidence of epigenetic signature from fetal tissue DNA in fetuses with pathogenic or probably pathogenic variation
Epigenetic signature associated with pathogenic variations in the KMT2D gene (KABUKI syndrome)	12 months	Evidence of epigenetic signature from fetal tissue DNA in fetuses with pathogenic or probably pathogenic variation

Secondary Outcome Measures

Name	Time	Method
Differential methylation between fetal and postnatal epigenetic signature	12 months	Evidence of differential methylation between fetal an postnatal epigenetic signature
Differential methylation between tissue and amniotic fluid epigenetic signatures	12 months	Evidence of differential methylation between tissue and amniotic fluid epigenetic signatures
Identification of a new epigenetic signature in foetal pathologies	12 months	Identification of news epigenetic signatures of exclusively pathologies associated with the HYLS1, TCTN3 and FLVCR2 genes
Statistical prediction parameter for each epigenetic signature	12 months	Measurement of the statistical prediction parameter for each epigenetic signature

Trial Locations

Locations (1)

Department of Genomic Medicine for Rare Diseases and the Multidisciplinary Center for Prenatal Diagnosis of the Necker-Enfants malades Hospital; 🇫🇷 Paris, France