Clinical Utility of Prenatal Whole Exome Sequencing

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.

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