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Fetal Structural AnomaliesPrenatalSEQNCT03936101

Prenatal Genetic Diagnosis by Genomic Sequencing

An observational study of Fetal Structural Anomalies, run by Columbia University at 5 sites in United States.

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

This study is evaluating the impact of prenatal sequencing on the management of fetuses with ultrasound abnormalities. The hypothesis is that a significant subset of fetal abnormalities have a genetic cause that can be identified by sequencing and that prenatal knowledge of this information will improve prenatal care… Read more about this study

Who is it for?
Ages 18 years and olderHealthy volunteers can take part
Conditions the study is for
Fetal Structural Anomalies
What is being tested?
Prenatal Genomic Sequencing
How many people
1,097 participants
Where
5 sitesUnited States
Study dates
28 Jun 2019to 25 Mar 2024
Phase
Observational
Are there results?
Yes, posted in the registrySummary in the doctors' view

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
  • Healthy volunteers accepted
  • Adult, Older adult

Study population: A total of 1,100 pregnancies with fetal structural anomalies and meeting eligibility criteria will be enrolled into the study. Of these, 750 will undergo prenatal genomic sequencing (prenatal sequencing group) and the remaining 350 pregnancies will not have any prenatal genomic sequencing (unsequenced prenatal group). Enrollment of pregnancies with an isolated nuchal translucency measurements ≥ 3.5 mm will be restricted to 5% within each group (sequenced and unsequenced) and isolated estimated fetal weight <5th %ile also will be restricted to 5% for each group (sequenced and unsequenced).

Who may be able to join

  • Prenatal sequencing group
  • Fetus identified by ultrasound and/or MRI with at least one of the following:
  • One or more major structural anomalies (Appendix A)
  • A nuchal translucency measurement of ≥ 3.5 mm
  • A fetus less than 24 weeks 0 days gestation with normal anatomy and sonographically estimated fetal weight <5th %ile without maternal hypertension, type I diabetes, or other maternal disorders known to alter fetal growth.
  • Negative prenatal CMA (or those with CMA findings not related to the ultrasound finding)
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  • Singleton or twin gestation
  • Gestational age less than 36 weeks, 0 days to allow for availability of sequencing results before delivery
  • Unsequenced Group
  • Fetus identified by ultrasound and/or MRI with at least one of the following:
  • One or more major structural anomalies (Appendix A)
  • A nuchal translucency measurement of ≥ 3.5 mm
  • A fetus less than 24 weeks 0 days gestation with normal anatomy and sonographically estimated fetal weight <5th %ile without maternal hypertension, type I diabetes, or other maternal disorders known to alter fetal growth
  • Negative prenatal or postnatal CMA (or those with CMA findings not related to the ultrasound finding)
  • Declined prenatal sequencing
  • Singleton gestation

Who cannot join

  • Prenatal Sequencing Group
  • Prenatal sequencing or planned prenatal sequencing performed outside of the study, including gene panels
  • Maternal or paternal age less than 18 years old
  • Proven infectious or teratogenic cause of fetal anomaly
  • Planned termination of the pregnancy
  • Unavailable blood or saliva samples from both biologic parents prior to sequencing
Show all 16Show fewer
  • Parental unwillingness to participate in 1 year postnatal follow-up
  • Language barrier (non-English or Spanish speaking)
  • Previous consent to the unsequenced prenatal group or enrollment in a previous pregnancy
  • Unsequenced Group
  • Maternal or paternal age less than 18 years old
  • Proven infectious or teratogenic cause of fetal anomaly
  • Positive prenatal NIPT screening for trisomy 21,18 or 13. Positive 22q11.2 prenatal NIPT testing with consistent ultrasound findings is also an exclusion.
  • Planned termination of the pregnancy
  • Parental unwillingness to participate in 1 year postnatal follow-up
  • Language barrier (non-English or Spanish speaking)

Trial locations and contacts

5 sites in 1 country.

5 sites in 1 country

United States5 sites
  • University of North Carolina Chapel Hill

    Chapel Hill, North Carolina, 27514

  • Children's Hospital, Cincinnati Medical Center

    Cincinnati, Ohio, 45229

  • Baylor College of Medicine

    Houston, Texas, 77030

  • UT Health Houston

    Houston, Texas, 77030

  • Columbia University Medical Center

    New York, New York, 10032

Other trials in United States

About this study

Official title: Prenatal Genetic Diagnosis by Genomic Sequencing: A Prospective Evaluation

This study is evaluating the impact of prenatal sequencing on the management of fetuses with ultrasound abnormalities. The hypothesis is that a significant subset of fetal abnormalities have a genetic cause that can be identified by sequencing and that prenatal knowledge of this information will improve prenatal care, reduce unnecessary diagnostic testing, reduce the cost of care, and improve the quality of life for both the child and the family.

Read the detailed description

Whole exome and whole genome sequencing (WGS) have expanded the ability to determine the genetic etiology of previously undiagnosed disorders. This study is a multicenter prospective cohort study to evaluate the emerging technology of sequencing for the management of fetuses with structural anomalies. The hypothesis is that a significant subset of fetal structural anomalies has a genetic etiology identifiable by sequencing and that prenatal knowledge of this information will improve perinatal care, reduce unnecessary diagnostic testing, reduce the cost of care, and improve quality of life for both the child and the family. The aims of this study are to investigate these multiple aspects of prenatal sequencing in a single study with an innovative integrated prospective design, which will permit a robust evaluation of the benefits and risks of delivering diagnostic and prognostic genetic testing results in a prenatal setting.

The study will determine, in a sequential population of pregnancies with selected fetal structural anomalies and a negative or non-causal chromosomal microarray (CMA), the frequency of pathogenic, likely pathogenic, and uncertain genomic variants identifiable by sequencing. To determine the impact of this information on clinical care, a control population of unsequenced pregnancies with similar structural anomalies will be prospectively recruited and the infants from both cohorts will be followed up to 1 year of age. This study component will evaluate differences in healthcare management and cost through discharge from hospital post-delivery, and perinatal and infant outcomes through 1 year of life. The educational, counseling and psychosocial impact of sequencing results during the prenatal period, in the nursery and through 1 year of life also will be evaluated. Since the analytical and clinical tools needed for the full translation of sequencing into care are still developing, optimization of bioinformatic tools to improve identification of pathogenic and likely pathogenic mutations associated with prenatal phenotypes of established disease genes will be investigated, as well as identification of new genes associated with presently undiagnosed fetal/neonatal phenotypes. This study will provide an in-depth evaluation of the prenatal diagnostic value of sequencing prior to its responsible introduction into practice and will provide independent data to guide its translation.

Being tested
Prenatal Genomic Sequencing

What participants receive

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

  • Prenatal Genomic SequencingDiagnostic test

    Whole genome sequencing (which initially will be masked and reported as exome only)

Study groups in NCT03936101
Study groupRoleWhat they receive
Prenatally Sequenced Group750 trios with fetal structural anomalies who receive prenatal sequencing from the study
Receives: Diagnostic Test: Prenatal Genomic Sequencing
No Prenatal Sequencing (Unsequenced) Group350 trios with fetal structural anomalies who do not have prenatal sequencing

What is being measured

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

  1. Number of Participants Who Had Reportable Variants

    Reportable variants: defined as either Pathogenic / Likely pathogenic (P/LP) or variant of uncertain significance (VUS) identified by sequencing and deemed reportable by the Variant Adjudication Committee.

    Measured: At end of study, approx 4 years

  2. Healthcare Costs

    Healthcare costs from time of diagnosis of anomaly to infant discharge between sequenced and unsequenced groups.

    Measured: From time of diagnosis of anomaly to infant discharge

Secondary outcomes (21)
  1. Gestational Age at Delivery

    Gestational age of newborn at delivery (in weeks)

    Measured: At time of delivery

  2. Neonatal Outcomes

    Neonatal outcomes will be compared and outcomes will be measured by the number of newborns who experience: need for ventilator support, sepsis, need for pressor support, need for extracorporeal membrane oxygenation (ECMO), metabolic abnormalities (e.g., acidosis, elevated uric acid, hypo-/hyperglycemia), intraventricular hemorrhage, periventricular leukomalacia, encephalopathy, and seizure.

    Measured: Up to 28 days after birth

  3. Number of Deaths

    Neonatal/infant death at time of discharge and at 12 months of age.

    Measured: From discharge to 12 months postpartum

  4. NICU Stay Duration

    Length of initial NICU stay and number of days spent in the hospital between initial discharge and 12 months of age.

    Measured: From discharge to 12 months postpartum

  5. Length in Centimeters

    Infant length at 12 months of age.

    Measured: 12 months postpartum

  6. Weight in Kilograms

    Infant weight at 12 months of age.

    Measured: 12 months postpartum

  7. Score on Development by Ages and Stages Questionnaire (ASQ-3)

    Developmental outcomes defined by the following parameters: communication, gross motor, fine motor, problem solving and personal-social, at 12 months of age using ASQ-3. Lower scores are associated with developmental delay. For each developmental area, parents may answer YES=10, SOMETIMES=5, or NOT YET=0 by filling in a bubble for each item response. The full score range for each domain is 0 to 60.

    Cutoffs for each domain are: Communication 15.64, Gross Motor 21.49, Fine Motor 34.5, Problem Solving 27.32, Personal-Social 21.73

    Measured: 12 months postpartum

  8. Anxiety by Self-report Questionnaire

    Anxiety following result disclosure (or 8 weeks post enrollment for the unsequenced group), neonatal discharge and 12 months postpartum. The full score range is 0 to 21, where lower numbers represent lower anxiety (better outcome).

    Measured: 2 weeks after disclosure of study sequencing results or 4 weeks after enrollment for the unsequenced group; 1 month after discharge from the hospital or end of the pregnancy if there was a fetal demise or pregnancy termination; 12-15 months postpartum

  9. Depression by Self-report Questionnaire

    Depression following result disclosure (or 8 weeks post enrollment for the unsequenced group), neonatal discharge and 12 months postpartum. The full score range is 0 to 24, where a lower score represents lower depression (better outcome).

    Measured: 2 weeks after disclosure of study sequencing results or 4 weeks after enrollment for the unsequenced group; 1 month after discharge from the hospital or end of the pregnancy if there was a fetal demise or pregnancy termination; 12-15 months postpartum

  10. Quality of Life by Self-report Questionnaire

    Quality of life for the patient and family at 12 months postpartum.

    Measured: Approximately 4.5 years

  11. QALY, Measured in Cost Per Year

    Incremental cost per Quality Adjusted Life Year (QALY).

    Measured: Approximately 4.5 years

  12. Total Number of Identified Phenotypes Associated With Disease- Sequenced Group ONLY

    Phenotypic Expansion: Apparent prenatal phenotypic expansion from currently defined pediatric phenotypes.

    Measured: 12 months postpartum

  13. Number of Participants With VUS - Sequenced Group ONLY

    Variants of uncertain significance (VUS) that have not yet been associated with this disease phenotype.

    This outcome was only intended to be measured in participants in the Sequenced arm, as outlined in the study protocol. Data for this outcome was not collected from any participant in the Unsequenced arm.

    Measured: 12 months postpartum

  14. Number of Participants With Variants Classified as GUS - Sequenced Group ONLY

    VUS subclassified as compelling variants in novel genes that are not yet disease associated (genes of uncertain clinical significance; GUS).

    This outcome was only intended to be measured in participants in the Sequenced arm, as outlined in the study protocol. Data for this outcome was not collected from any participant in the Unsequenced arm.

    Measured: 12 months postpartum

  15. Digital WES - Comparison of Coding and Non-coding Results - Sequenced Group ONLY

    Pathogenic, likely pathogenic and VUS variants identified by sequencing (coding and non-coding regions) compared with coding regions only (digital WES).

    Measured: Approximately 4.5 years

  16. Proband Only Versus Trio - Comparison of Results Between Trio and Proband Only - Sequenced Group ONLY

    Pathogenic, likely pathogenic and VUS variants identified by analysis of a proband alone compared to a proband-parent trio.

    Measured: Approximately 4.5 years

  17. Change in Management (Healthcare) as Determined by NICU Physician and Record Review - Sequenced Group ONLY

    Number of participants who had a change in management decisions attributable to genomic results, defined as changes to the patient's treatment plan or changes to the counseling of the patient/family regarding the immediate or long-term medical management.

    This outcome was only intended to be measured in participants in the Sequenced arm, as outlined in the study protocol. Data for this outcome was not collected from any participant in the Unsequenced arm.

    Measured: From delivery until discharge or death (neonatal)

  18. Parental Support Needs by Self-report Questionnaire - Sequenced Group ONLY

    Assessment of educational/counseling and social support needs of the mother and father. The full score range is 12 to 60, where a higher score represents a higher satisfaction with the experience (better outcome).

    Measured: At sequencing completion, approximately 4.5 years

  19. Parental Understanding by Self-report Questionnaire - Sequenced Group ONLY

    Accuracy of parental understanding of genetic test results. The parental responses to the question "How well do you understand your prenatal genetic test results?" will be collected. All possible responses are: "Not at all", "A little bit", "Moderately", "Quite a bit", and "Extremely"

    Measured: At sequencing completion, approximately 4.5 years

  20. Number of Participants Who Had a Change in the Sequencing Result - Sequenced Group ONLY

    Reinterpretations of sequencing results that lead to a change in classification of sequencing variants.

    This outcome was only intended to be measured in participants in the Sequenced arm, as outlined in the study protocol. Data for this outcome was not collected from any participant in the Unsequenced arm.

    Measured: From sequencing completion to data analysis period, up to 4.5 years

  21. Turnaround Time - Sequenced Group ONLY

    Turnaround time of sequencing components and how it changes over time. This outcome was only intended to be measured in participants in the Sequenced arm, as outlined in the study protocol. Data for this outcome was not collected from any participant in the Unsequenced arm.

    Measured: Time from sequencing initiation until study site result, up to 38 days

Timeline

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

  1. First posted3 May 2019
  2. Study start28 Jun 2019
  3. Primary completion25 Mar 2024
  4. Study completion25 Mar 2024

Resources

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
Case-control
Time perspective
Prospective
Enrolment
1,097 participants (actual)
IDs, dates and publications
ClinicalTrials.gov ID
NCT03936101
Sponsor's protocol ID
AAAS2118
Other IDs
R01HD055651
Acronym
PrenatalSEQ
Status last verified
Oct 2025
First submitted
25 Mar 2019
Last updated
27 Oct 2025
Data monitoring committee
No
FDA-regulated drug
No
FDA-regulated device
No
Individual data sharing
Yes: In accordance with the NIH Genomic Data Sharing policy, sequencing data (including VCF files) and clinical data will be shared with other scientific investigators and through the controlled access dbGAP repository or comparable genomics commons, the Sequence Read Archive, and any NIH Birth Defects Commons that is established. A final dataset containing clinical and phenotypic data will be submitted to the NICHD data repository (DASH). In addition, new algorithms and allele frequency data will be shared with the newly developed Precision FDA platform as applicable.

Questions about this trial

What is this clinical trial studying?

An observational study of Fetal Structural Anomalies, run by Columbia University at 5 sites in United States.

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 16 inclusion and 16 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: finished, as of the sponsor's last update on 27 Oct 2025. Status can change between updates, so confirm with the study contact before making plans.

Where is the study taking place?

The record lists 5 sites in United States. 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?

Yes. Results are posted in the registry (first posted 27 Oct 2025). A summary is in the For doctors view, and the full results are on ClinicalTrials.gov.

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?

Number of Participants Who Had Reportable Variants (time frame: At end of study, approx 4 years). The study lists 2 primary outcomes in all. 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 Oct 2025.

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