Couples Eligible for Prenatal Exome SequencingPrenOmicsNCT07790536
Parallel Sequencing of Fetal Genome and RNA in the Presence of Ultrasound Warning Signs: a Complementary Approach for the Prenatal Diagnosis of Rare Diseases.
An observational study of Couples Eligible for Prenatal Exome Sequencing, run by Assistance Publique - Hôpitaux de Paris at 1 site in France.
Trial 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. Read more about this study
- Who is it for?
- Ages 18 years and older
- Conditions the study is for
- Couples Eligible for Prenatal Exome Sequencing
- What is being tested?
- Genome Sequencing (GS) + RNA-Sequencing (RNA-Seq)
- How many people
- 100 participants
- Where
- 1 siteFrance
- Study dates
- Sep 2026to Mar 2028
- Phase
- Observational
- Are there results?
- Not yet: the study is under way
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 18 years and older
- All sexes
- No healthy volunteers
- Adult, Older adult
Study population: Couples whose indication for prenatal exome sequencing has been reviewed and approved by a multidisciplinary prenatal diagnostic center.
Who may be able to join
- 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
Who cannot join
- Couple not covered by the social security system
- Couple deprived of liberty or under legal guardianship or curatorship
- Monoparental pregnancies
Trial locations and contacts
1 site in 1 country. Contact the study team or a site near you to ask about taking part.
France1 site
Hôpital Necker Enfants malades
Paris, Île-de-France Region, 75015
Lucile BOUTAUD, Pharm. D PhD, 01 44 38 17 47 ext. +33, lucile.boutaud@aphp.fr
Sarah BOUCHARD, Project Manager, 01 42 19 28 79 ext. +33, sarah.bouchard@aphp.fr
About this study
Official title: Parallel Sequencing of the Fetal Genome and RNA in the Presence of Ultrasound Warning Signs: a Complementary Approach for the Prenatal Diagnosis of Rare Diseases.
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.
Read the detailed description
Couples will be enrolled during a "pre-test" genetic consultation by a physician or a research-trained collaborator (genetic counselor or another investigator).
As part of routine clinical care: chromosomal microarray analysis (CMA) and exome sequencing (ES) will be performed locally, with interpretation by a biologist from the site providing follow-up to the couple.
For research purposes, after obtaining written consent from both the pregnant woman and her partner: samples will be prepared for pre-analytical processing at Pitié-Salpêtrière and sequenced at SeqOIA. Interpretation will be conducted by a biologist at a site different from the one performing the exome analysis, using the Gleaves-P interface dedicated to the project (MOABI).
Transcriptomic analysis (RNA-Seq) will be performed on RNA extracted from amniotic fluid cultures, with and without emetine (a NMD inhibitor). Sequencing will be carried out after Agilent capture at the Genetics Laboratory of Necker-Enfants Malades Hospital (AP-HP). Bioinformatics analysis will be performed by the Imagine platform. Study biologists will interpret results using the PolyRNASEQ interface (qualitative splice junction analysis) and IGV (semi-quantitative analysis and expression).
All results from CMA + ES and GS + RNA-Seq will be reviewed during weekly meetings. In cases of discordant or unexpected results (anticipated for ~10 couples), a reference method will be applied to provide clinically validated results through an accredited prenatal diagnostic center, ensuring no loss of care opportunity.
Results will be discussed in a multidisciplinary prenatal diagnosis meeting (RCP) and integrated into the prognostic discussion. Couples will be seen during a "post-test" genetic consultation for communication of results.
For couples included at Necker-Enfants Malades Hospital only: two additional maternal blood tubes will be collected during routine pregnancy follow-up before amniocentesis. Circulating DNA will be extracted from maternal plasma and subjected to genome sequencing under the same conditions as the amniotic DNA. The generated data will be analysed using bioinformatic approaches integrating artificial intelligence methods to improve the distinction between fetal- and maternal-derived DNA fragments. Interpretation will be performed via the Gleaves-P interface. Non-invasive prenatal genome sequencing results are strictly for research purposes: they will not be communicated to couples and will not be used for clinical decision-making. Their objective is to evaluate the feasibility, accuracy, and performance of non-invasive genome sequencing.
- Being tested
- Genome Sequencing (GS) + RNA-Sequencing (RNA-Seq)
- Keywords
- Prenatal diagnosis (PND), Invasive / Non-invasive prenatal diagnosis (NIPD), Exome sequencing (ES), Genome Sequencing (GS), RNA sequencing, Circulating cell-free fetal DNA (cffDNA)
What participants receive
What participants receive. In a randomised study each person is assigned to one group by chance.
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
| Study group | Role | What they receive |
|---|---|---|
| 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. Receives: Diagnostic Test: Genome Sequencing (GS) + RNA-Sequencing (RNA-Seq) |
What is being measured
The primary outcome is the main question the study is designed to answer.
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).
Measured: 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.
Time interval between test prescription and receipt of results for GS + RNA-Seq compared to CMA + ES in prenatal diagnosis
Measured: 18 months
Comparison of the costs associated with GS + RNA-Seq versus CMA + ES in prenatal diagnostic settings.
Evaluation and comparison of the costs associated with GS + RNA-Seq and CMA + ES approaches.
Measured: 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.
Correlation of diagnostic results between invasive foetal genome sequencing performed on DNA extracted from amniotic fluid and non-invasive genome sequencing performed on circulating cell-free foetal DNA extracted from maternal plasma.
Measured: 18 months
Identification and characterization of potential challenges and obstacles to the implementation of these diagnostic methods in clinical practice.
List of difficulties encountered at each stage, from pre- to post-analytical.
Measured: 18 months
Timeline
From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.
- First posted27 Aug 2026
- Study startSep 2026 (estimated)
- Primary completionMar 2028 (estimated)
- Study completionMar 2028 (estimated)
Resources
- Official record on ClinicalTrials.govThe registry entry this page is built from, with its full change history.
- Other trials for Couples Eligible for Prenatal Exome SequencingStudies of the same condition, open and under way.
- More trials run by Assistance Publique - Hôpitaux de ParisThe sponsor's other registered studies.
- What the trial phases meanHow a treatment moves from first tests in people to approval.
More details
For doctors and researchers: how the study is designed, who runs it, and its registry IDs.
Study design
- Study type
- Observational
- Observational model
- Cohort
- Time perspective
- Prospective
- Enrolment
- 100 participants (estimated)
Sponsor and investigators
- Lead sponsor
- Assistance Publique - Hôpitaux de Paris
- Sponsor type
- University, hospital or other
- Collaborators
- URC-CIC Paris Descartes Necker Cochin, Imagine, Laboratoire SeqOIA, MOABI
- Responsible party
- Sponsor
- Investigators
- Lucile BOUTAUD, Pharm.D PhD, Principal investigator, Hôpital Necker Enfants Malades AP-HP
IDs, dates and publications
- ClinicalTrials.gov ID
- NCT07790536
- Sponsor's protocol ID
- APHP251082
- Other IDs
- N° IDRCB
- Acronym
- PrenOmics
- Status last verified
- Aug 2026
- First submitted
- 6 Aug 2026
- Last updated
- 27 Aug 2026
- Results posted
- No
- Data monitoring committee
- No
- FDA-regulated drug
- No
- FDA-regulated device
- No
- Individual data sharing
- No
Study at a glance
From the registry record, last updated by the sponsor on 27 Aug 2026. Recruitment status is as the sponsor reported it: confirm with the study team.
- Official title
- Parallel Sequencing of the Fetal Genome and RNA in the Presence of Ultrasound Warning Signs: a Complementary Approach for the Prenatal Diagnosis of Rare Diseases.
- ClinicalTrials.gov ID
- NCT07790536
- Acronym / sponsor ID
- PrenOmics / APHP251082
- Keywords
- Prenatal diagnosis (PND), Invasive / Non-invasive prenatal diagnosis (NIPD), Exome sequencing (ES), Genome Sequencing (GS), RNA sequencing, Circulating cell-free fetal DNA (cffDNA)
- Study type
- Observational
- Recruitment status
- Not yet recruiting
- Enrolment
- 100 participants (estimated)
- Lead sponsor
- Assistance Publique - Hôpitaux de ParisUniversity, hospital or other
- Collaborators
- URC-CIC Paris Descartes Necker Cochin, Imagine, Laboratoire SeqOIA, MOABI
- Study start
- Sep 2026 (estimated)
- Primary completion
- Mar 2028 (estimated)
- Study completion
- Mar 2028 (estimated)
- First posted
- 27 Aug 2026 (actual)
- Results
- Not posted in the source record
Clinical summary
The research question as the sponsor registered it. This describes what the study plans to test, not what it found.
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.
Detailed description
Couples will be enrolled during a "pre-test" genetic consultation by a physician or a research-trained collaborator (genetic counselor or another investigator).
As part of routine clinical care: chromosomal microarray analysis (CMA) and exome sequencing (ES) will be performed locally, with interpretation by a biologist from the site providing follow-up to the couple.
For research purposes, after obtaining written consent from both the pregnant woman and her partner: samples will be prepared for pre-analytical processing at Pitié-Salpêtrière and sequenced at SeqOIA. Interpretation will be conducted by a biologist at a site different from the one performing the exome analysis, using the Gleaves-P interface dedicated to the project (MOABI).
Transcriptomic analysis (RNA-Seq) will be performed on RNA extracted from amniotic fluid cultures, with and without emetine (a NMD inhibitor). Sequencing will be carried out after Agilent capture at the Genetics Laboratory of Necker-Enfants Malades Hospital (AP-HP). Bioinformatics analysis will be performed by the Imagine platform. Study biologists will interpret results using the PolyRNASEQ interface (qualitative splice junction analysis) and IGV (semi-quantitative analysis and expression).
All results from CMA + ES and GS + RNA-Seq will be reviewed during weekly meetings. In cases of discordant or unexpected results (anticipated for ~10 couples), a reference method will be applied to provide clinically validated results through an accredited prenatal diagnostic center, ensuring no loss of care opportunity.
Results will be discussed in a multidisciplinary prenatal diagnosis meeting (RCP) and integrated into the prognostic discussion. Couples will be seen during a "post-test" genetic consultation for communication of results.
For couples included at Necker-Enfants Malades Hospital only: two additional maternal blood tubes will be collected during routine pregnancy follow-up before amniocentesis. Circulating DNA will be extracted from maternal plasma and subjected to genome sequencing under the same conditions as the amniotic DNA. The generated data will be analysed using bioinformatic approaches integrating artificial intelligence methods to improve the distinction between fetal- and maternal-derived DNA fragments. Interpretation will be performed via the Gleaves-P interface. Non-invasive prenatal genome sequencing results are strictly for research purposes: they will not be communicated to couples and will not be used for clinical decision-making. Their objective is to evaluate the feasibility, accuracy, and performance of non-invasive genome sequencing.
Study design
- Observational model
- Cohort
- Time perspective
- Prospective
- Number of arms
- 1
| Arm | Type | Receives |
|---|---|---|
| Genome Sequencing (GS) + RNA-Sequencing (RNA-Seq) | – | Diagnostic Test: 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. |
Who may qualify
- Ages
- 18 years and older
- Sex
- All
- Healthy volunteers
- Not accepted
- Age groups
- Adult, Older adult
- Study population
- Couples whose indication for prenatal exome sequencing has been reviewed and approved by a multidisciplinary prenatal diagnostic center.
Key inclusion criteria (6 listed)
- 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
Key exclusion criteria (3 listed)
- Couple not covered by the social security system
- Couple deprived of liberty or under legal guardianship or curatorship
- Monoparental pregnancies
Eligibility is decided by the study team after screening; this overview does not establish that a patient qualifies. Full inclusion and exclusion criteria.
Interventions
| Intervention | Type | Arms |
|---|---|---|
| Genome Sequencing (GS) + RNA-Sequencing (RNA-Seq)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 | Diagnostic test | Genome Sequencing (GS) + RNA-Sequencing (RNA-Seq) |
Primary outcome
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).
Time frame: 18 months
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).
4 secondary outcomes
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.
Time frame: 18 months
Comparison of the costs associated with GS + RNA-Seq versus CMA + ES in prenatal diagnostic settings.
Time frame: 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.
Time frame: 18 months
Identification and characterization of potential challenges and obstacles to the implementation of these diagnostic methods in clinical practice.
Time frame: 18 months
Results and safety
This study is still under way. Results are not available in the source record yet.
Research links
- Official record on ClinicalTrials.govLast updated by the sponsor 27 Aug 2026.
- Individual participant dataSharing planned: No
Referral and contact
AzTrials does not enrol participants or take referrals. Contact the study team or a site listed below; they decide who can take part.
Lucile BOUTAUD, Pharm.D PhD principal investigator
Hôpital Necker Enfants Malades AP-HP
1 site in 1 country: see every site and its status.
Questions about this trial
What is this clinical trial studying?
An observational study of Couples Eligible for Prenatal Exome Sequencing, run by Assistance Publique - Hôpitaux de Paris at 1 site in France.
The full registered description is in the About this study section and the official record.
Who may be eligible to take part?
The sponsor lists 6 inclusion and 3 exclusion criteria. Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.
Is this clinical trial currently recruiting?
The record says: opening soon, as of the sponsor's last update on 27 Aug 2026. Status can change between updates, so confirm with the study contact before making plans.
Where is the study taking place?
The record lists 1 site 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?
This study is still under way. Results are not available in the source record yet.
How can a doctor refer a patient or contact the research team?
Contact Lucile BOUTAUD, Pharm. D PhD (01 44 38 17 47 ext. +33, lucile.boutaud@aphp.fr), or a site near the patient. AzTrials does not enrol participants or take referrals.
What does the primary outcome measure?
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). (time frame: 18 months). It is what the study was designed to measure, not a finding.
Where can I read the original study information?
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 27 Aug 2026.