Working… Menu

Clinical Utility of Prenatal Whole Exome Sequencing (Prenatal WES)

The safety and scientific validity of this study is the responsibility of the study sponsor and investigators. Listing a study does not mean it has been evaluated by the U.S. Federal Government. Know the risks and potential benefits of clinical studies and talk to your health care provider before participating. Read our disclaimer for details. Identifier: NCT03482141
Recruitment Status : Recruiting
First Posted : March 29, 2018
Last Update Posted : July 15, 2020
Information provided by (Responsible Party):
University of California, San Francisco

Brief Summary:
The investigator aims to examine the clinical utility of WES, including assessment of a variety of health-related and reproductive outcomes in undiagnosed prenatal cases.

Condition or disease Intervention/treatment Phase
Structural Anomalies Cardiac Anomalies Central Nervous System Anomalies Thorax Anomalies Genito-urinary Anomalies Gastrointestinal Anomalies Skeletal Anomalies Multiple Anomalies Device: Whole Exome Sequencing (WES) Not Applicable

Detailed Description:

Next-generation sequencing (NGS) is changing the paradigm of clinical genetic testing. Unlike highly focused single-gene tests, NGS allows one to examine gene panels, the exome, and the whole genome. With the broad array of molecular tests now available, ordering physicians face the conundrum of selecting the best diagnostic tool for patients with suspected genetic conditions. Single-gene testing is often most appropriate for conditions with distinctive clinical features and minimal locus heterogeneity. NGS-based gene panel testing, which can be complemented with chromosomal microarray analysis (CMA) and other ancillary methods, provides a comprehensive and feasible approach for well documented but genetically heterogeneous disorders. Whole exome sequencing (WES) and whole genome sequencing (WGS) have the advantage of enabling parallel interrogation of most of the genes in the human genome. To some, WES is preferable to previously used methods due to higher diagnostic yield, shorter time to diagnosis, and improved cost-efficiency.

The ability to survey the exome opens up both new opportunities and new challenges. For example, all coding regions of known genes must be analyzed when applying WES to undiagnosed cases with unclear inheritance patterns. Current limitations on variant interpretation capabilities and clinical validity raise questions about the clinical utility of WES as either a stand-alone or a first-choice diagnostic test. Additional challenges include pre- and post-test counseling with appropriate and robust informed consent, bioinformatics analysis setup and validation, variant interpretation and classification, the need for policies and protocols concerning the discovery and reporting of secondary findings unrelated to the presenting indication, a requirement for validation of WES results, assurance of conformation to quality control standards, data storage and accessibility, and reimbursement issues.

Current clinical standards recommend offering chromosomal microarray (CMA) in the prenatal setting when fetal structural anomalies are detected via prenatal ultrasound. In these cases, clinically relevant copy number variants have been reported in 6.0-9.1% of fetuses with a normal karyotype. However, informed consent processes for prenatal CMA are challenging-particularly in cases with ultrasound anomalies, as parents are absorbing challenging news and under considerable stress. Women have reported being "blindsided" by positive CMA results, or feeling that these results were "toxic information"-information they wished they did not have, particularly in cases of uncertain genetic information or uninterpretable variants. Nonetheless, in that same study women who were referred for CMA because of ultrasound anomalies reported less frequent negative reactions, since they already anticipated abnormal results.

Introducing WES into prenatal clinical care of underrepresented populations raises additional issues and considerations of payment coverage, access, and standards of care. Beyond the sheer complexity of the test and its results, clinicians and health systems must address numerous considerations, including: private and public insurance coverage; language and culture differences and their implications for genetic counseling and clinician-patient relationships; ability to access follow-up testing and clinical care; ability to access appropriate treatment and services; and particularly in the prenatal setting, local, state, and national abortion laws and decision-making about pregnancy termination. These issues and others will affect not only patients' decision-making regarding WES, but also their post-test needs for patient follow up, counseling and support. The importance of systematically assessing the clinical utility of NGS is critical for determining in which clinical and health care contexts WES will be useful and for commencing research on these considerations.

The investigator aims to examine the clinical utility of WES, including assessment of a variety of health-related and reproductive outcomes in undiagnosed prenatal cases.

Layout table for study information
Study Type : Interventional  (Clinical Trial)
Estimated Enrollment : 300 participants
Allocation: N/A
Intervention Model: Single Group Assignment
Masking: None (Open Label)
Primary Purpose: Diagnostic
Official Title: Clinical Utility of Prenatal Whole Exome Sequencing
Actual Study Start Date : August 1, 2017
Estimated Primary Completion Date : April 30, 2021
Estimated Study Completion Date : May 31, 2021

Arm Intervention/treatment
Whole exome sequencing (WES) will take place.
Device: Whole Exome Sequencing (WES)
The Investigators will enroll pregnant women with fetal anomalies detected by ultrasound. Patients will be approached by a maternal-fetal specialist, who has counseled the patient regarding the fetal anomaly that has been detected. Written informed consent will be obtained by the study prenatal genetic counselor. Many patients will have undergone prenatal diagnostic testing in an outside laboratory; in such cases, cells or extracted DNA from the original fetal sample will be used for the purpose of this study. The consent process for prenatal WES will include pre-test counseling and the option of choosing whether or not to receive uncertain results and secondary findings. After conducting whole exome sequencing, the findings will be shared with the parent(s). Routine medical care will be provided to patients. The research will study the effectiveness of sequencing as a tool for providing genetic information to parents when a prenatal study reveals a fetus with a structural anomaly.

Primary Outcome Measures :
  1. Clinical Utility (CU) of WES- a composite measure [ Time Frame: At the completion of data collection (follow-up visit at 6-12 months after return of results for WES) ]
    CU covers: a) Pregnancy termination; b) In-utero medical or surgical intervention; c) Perinatal decision making- including antepartum surveillance for fetal distress; location and mode of delivery; decisions for non-intervention or perinatal hospice care; d) Immediate neonatal management; e) Reproductive decision making and counseling subsequent to the index pregnancy.

Information from the National Library of Medicine

Choosing to participate in a study is an important personal decision. Talk with your doctor and family members or friends about deciding to join a study. To learn more about this study, you or your doctor may contact the study research staff using the contacts provided below. For general information, Learn About Clinical Studies.

Layout table for eligibility information
Ages Eligible for Study:   up to 64 Years   (Child, Adult)
Sexes Eligible for Study:   Female
Accepts Healthy Volunteers:   No

Inclusion Criteria:

  • Women carrying a pregnancy with an ultrasound diagnosis of a major structural anomaly (or multiple anomalies) in a major organ system (cardiac, central nervous system, thorax, genito-urinary, gastrointestinal/ventral wall, skeletal and or multiple anomalies )
  • Clinical concern for a potential underlying genetic condition
  • Completed or plan to complete chorionic villus sampling or amniocentesis with chromosome analysis or microarray
  • Available maternal sample

Exclusion Criteria:

  • Prior WES performed for a clinical or research indication
  • Lack of phenotypic indication of a likely underlying genetic etiology
  • Mother unwilling or unable to provide a specimen

Information from the National Library of Medicine

To learn more about this study, you or your doctor may contact the study research staff using the contact information provided by the sponsor.

Please refer to this study by its identifier (NCT number): NCT03482141

Layout table for location contacts
Contact: Mary Norton, MD 415-353-7865
Contact: Billie Lianoglou, MS 415-476-1004

Layout table for location information
United States, California
University of California San Francisco Recruiting
San Francisco, California, United States, 94143
Contact: Billie Lianoglou, MS    415-476-1004   
Sponsors and Collaborators
University of California, San Francisco
Layout table for investigator information
Principal Investigator: Mary Norton, MD University of California, San Francisco
Layout table for additonal information
Responsible Party: University of California, San Francisco Identifier: NCT03482141    
Other Study ID Numbers: 17-22420
First Posted: March 29, 2018    Key Record Dates
Last Update Posted: July 15, 2020
Last Verified: July 2020
Individual Participant Data (IPD) Sharing Statement:
Plan to Share IPD: No

Layout table for additional information
Studies a U.S. FDA-regulated Drug Product: No
Studies a U.S. FDA-regulated Device Product: Yes
Device Product Not Approved or Cleared by U.S. FDA: Yes
Additional relevant MeSH terms:
Layout table for MeSH terms
Nervous System Malformations
Urogenital Abnormalities
Heart Defects, Congenital
Congenital Abnormalities
Cardiovascular Abnormalities
Cardiovascular Diseases
Heart Diseases
Nervous System Diseases