Parallel Sequencing of Fetal Genome and RNA in the Presence of Ultrasound Warning Signs: a Complementary Approach for the Prenatal Diagnosis of Rare Diseases.

NCT07790536 | Not Yet Recruiting

• 2 other identifiers: APHP251082N° IDRCB
• Study Type: observational
• Target: 100
• Locations: 1 country
• Sites: 1

Brief Summary

Prenatal exome sequencing (ES) is increasingly used for fetuses with ultrasound-detected anomalies but yields 10-15% variants of uncertain significance (VUS), limiting diagnostic performance, particularly in prenatal settings with incomplete phenotypes. This study aims to evaluate the added value of combined prenatal genome sequencing (GS) and RNA sequencing (RNA-Seq), which are not currently part of routine care. Conducted at AP-HP, it will compare the diagnostic yield of GS + RNA-Seq with the current standard approach (chromosomal microarray analysis + ES), according to variant type (coding, non-coding, and structural). The contribution of systematic RNA-Seq to rapid VUS resolution will be specifically assessed. Overall, this project will assess the feasibility, diagnostic performance, and clinical utility of implementing GS + RNA-Seq in prenatal diagnosis, supporting future integration into routine care in France.

Conditions

Couples Eligible for Prenatal Exome Sequencing

Keywords

Prenatal diagnosis (PND); Invasive / Non-invasive prenatal diagnosis (NIPD); Exome sequencing (ES); Genome Sequencing (GS); RNA sequencing; Circulating cell-free fetal DNA (cffDNA)

Outcome Measures

Primary Outcomes (1)

• Evaluation of the diagnostic contribution of RNA sequencing (RNA-Seq) performed in parallel with genome sequencing (GS) in prenatal diagnosis, compared with chromosomal microarray analysis (CMA) and exome sequencing (ES).

  Comparison of variants identified by each strategy and the number of additional diagnoses achieved using genome sequencing (GS) combined with RNA sequencing (RNA-Seq) compared with chromosomal microarray analysis (CMA) and exome sequencing (ES) in the prenatal setting. Diagnostic yield will be analyzed according to variant type (single-nucleotide and structural variants) and genomic location (coding vs non-coding regions).

  18 months

Secondary Outcomes (4)

• Comparison of turnaround times for result delivery between genome sequencing combined with RNA sequencing (GS + RNA-Seq) and the current standard approach of chromosomal microarray analysis and exome sequencing (CMA + ES) in prenatal diagnosis.

  18 months

• Comparison of the costs associated with GS + RNA-Seq versus CMA + ES in prenatal diagnostic settings.

  18 months

• Evaluation of the feasibility and analytical performance of non-invasive prenatal genome sequencing performed on circulating cell-free fetal DNA extracted from maternal blood.

  18 months

• Identification and characterization of potential challenges and obstacles to the implementation of these diagnostic methods in clinical practice.

  18 months

Study Arms (1)

Genome Sequencing (GS) + RNA-Sequencing (RNA-Seq)

Couples (pregnant woman and partner) with a fetal indication requiring prenatal exome sequencing, reviewed and approved by a multidisciplinary prenatal diagnosis center, will be included. Fetal samples (amniotic fluid, including cell cultures) and parental blood samples collected during routine care will be used for standard genetic analyses (chromosomal microarray and exome sequencing) and for research analyses, including genome sequencing (GS), RNA sequencing (RNA-Seq), and bioinformatic evaluations. Non-invasive genome sequencing performed from maternal blood samples (for couples included at Necker-Enfants Malades Hospital only) will be conducted for research purposes only; results will not be returned to couples and will not influence clinical management.

Diagnostic Test: Genome Sequencing (GS) + RNA-Sequencing (RNA-Seq)

Interventions

Genome Sequencing (GS) + RNA-Sequencing (RNA-Seq) DIAGNOSTIC_TEST

Couples whose indication for trio exome sequencing is approved by a multidisciplinary prenatal diagnostic center are enrolled during a pre-test genetic consultation, during which written informed consent is obtained from both partners. As part of routine care, fetal samples are collected by amniocentesis and parental blood samples are obtained for chromosomal microarray analysis (CMA) and trio exome sequencing (ES), analyzed locally. Amniotic fluid cell cultures are systematically prepared and stored. For research purposes, portions of fetal and parental samples are processed at Pitié-Salpêtrière and sequenced at SeqOIA for trio genome sequencing (GS). Bioinformatics analysis is performed using the MOABI platform, with interpretation via the Gleaves-P interface. RNA sequencing (RNA-Seq) is performed on RNA extracted from amniotic fluid cell cultures at Necker Hospital. For couples included at Necker only, maternal plasma DNA is also sequenced. Non-invasive GS results are for rese

Genome Sequencing (GS) + RNA-Sequencing (RNA-Seq)

Eligibility Criteria

• Age: 18 Years+
• Sex: all
• Healthy Volunteers: No
• Age Groups: Adult (18-64), Older Adult (65+)
• Sampling Method: Non-Probability Sample

Study Population

Couples whose indication for prenatal exome sequencing has been reviewed and approved by a multidisciplinary prenatal diagnostic center.

You may qualify if:

• Participating couple aged ≥ 18 years
• Ongoing pregnancy for which the indication for exome sequencing has been discussed and validated by a Multidisciplinary Prenatal Diagnosis Center (CPDPN).
• While a strict list of indications is not appropriate in the prenatal setting, examples include multiple anomalies not related to a malformation sequence, persistent increased nuchal translucency, hydrops fetalis (anasarca), cleft palate, multiple contractures/arthrogryposis, skeletal dysplasia, bowed femurs, or brain anomalies.
• Sequencing performed on an amniotic fluid sample (chorionic villus sampling is excluded)
• Attendance at a genetic counseling consultation
• Written informed consent obtained for study participation

You may not qualify if:

• Couple not covered by the social security system
• Couple deprived of liberty or under legal guardianship or curatorship
• Monoparental pregnancies

Sponsors & Collaborators

• Assistance Publique - Hôpitaux de Paris: lead
• URC-CIC Paris Descartes Necker Cochin: collaborator
• Imagine: collaborator
• Laboratoire SeqOIA: collaborator
• MOABI: collaborator

Study Sites (1)

Hôpital Necker Enfants malades

Paris, Île-de-France Region, 75015, France

Location

Biospecimen

Retention: SAMPLES WITH DNA

Aliquots of fetal amniotic fluid and parental blood samples will be collected for genome sequencing. Cultured amniotic fluid cells, with or without emetine (a nonsense-mediated mRNA decay inhibitor), will be used for RNA sequencing (RNA-Seq). An additional maternal blood sample (2 × 10 mL) will be collected exclusively from participants enrolled at Necker-Enfants Malades Hospital.

MeSH Terms

Interventions

Base Sequence

Intervention Hierarchy (Ancestors)

Molecular Structure; Biochemical Phenomena; Chemical Phenomena; Genetic Structures; Genetic Phenomena

Study Officials

• Lucile BOUTAUD, Pharm.D PhD

  Hôpital Necker Enfants Malades AP-HP

  PRINCIPAL INVESTIGATOR

Central Study Contacts

Lucile BOUTAUD, Pharm. D PhD

CONTACT

01 44 38 17 47; lucile.boutaud@aphp.fr

Sarah BOUCHARD, Project Manager

CONTACT

01 42 19 28 79; sarah.bouchard@aphp.fr

Study Design

• Study Type: observational
• Observational Model: COHORT
• Time Perspective: PROSPECTIVE
• Sponsor Type: OTHER
• Responsible Party: SPONSOR

Study Record Dates

• First Submitted: August 6, 2026
• First Posted: August 27, 2026
• Study Start (Estimated): September 1, 2026
• Primary Completion (Estimated): March 1, 2028
• Study Completion (Estimated): March 1, 2028
• Last Updated: August 27, 2026

Record last verified: 2026-08

Data Sharing

• IPD Sharing: Will not share

Locations

FR (1)