Prenatal Genetic Testing: Navigating NIPT, Microarray and Molecular Testing When Fetal Anomalies Are Identified

Advances in prenatal genetic testing are giving clinicians more opportunities to identify the cause of fetal anomalies before delivery. At the same time, expanding test options can make it challenging to determine which modality is appropriate and how much confidence to place in a result.
For obstetricians, maternal-fetal medicine (MFM) specialists and other prenatal providers, understanding the strengths and limitations of noninvasive prenatal testing (NIPT), cytogenetic testing and molecular sequencing is increasingly important when counseling families and coordinating fetal care.

NIPT remains a screening test

Traditional NIPT can screen for common trisomies. Traditional NIPT can screen for common trisomies and sex chromosome aneuploidies, but it is not diagnostic. Positive predictive value can vary with maternal and gestational age, while maternal mosaicism or malignancy may affect results. Maternal obesity may also reduce the fetal DNA fraction because of dilution.
The limitations become particularly important with expanded screening. Many microdeletions are smaller than what can be reliably detected through NIPT, and positive predictive values for microdeletions and duplications can be low.
For referring providers, an abnormal NIPT result should be interpreted in the context of the fetal phenotype and confirmed with diagnostic testing rather than considered in isolation.

When fetal abnormalities raise suspicion for a genetic disorder

The appropriate diagnostic approach depends on the clinical scenario. Chromosomal microarray provides a diagnosis in approximately 6% to 7% of fetuses with abnormalities identified on ultrasound, with a reported diagnostic yield of approximately 10% when multiple anomalies are present. Molecular testing options include next-generation sequencing panels, whole-exome sequencing and emerging approaches to single-gene NIPT.
More than half of pregnancies involving fetal anomalies may have nondiagnostic karyotype and microarray findings. In these cases, molecular testing may provide additional answers. The presentation cites diagnostic yields of 36% for exome sequencing and 41% for genome sequencing, while noting that Phoenix Children’s clinical experience has found the incremental yield of genome above exome to be approximately 1%.
Genetic panels also have limitations. Panels may be slow to incorporate newly discovered genes or genes associated with ultra-rare disorders, and selecting an appropriate panel can be difficult when the fetal phenotype continues evolving. As a result, a negative panel may lead to additional testing.

Prenatal phenotype matters

One of the fundamental challenges of prenatal genetic diagnosis is that the fetal phenotype is incomplete.
Prenatal interpretation of exome and genome sequencing depends heavily on phenotypic information obtained through ultrasound, fetal MRI and fetal echocardiography. Structural abnormalities may not yet be apparent because of gestational age, while other prenatal findings may be nonspecific or differ from the better-characterized postnatal phenotype of a disorder.
This makes coordinated evaluation important when multiple abnormalities or an unusual constellation of findings is identified.
A case presented by Rachel Lombardo, MD, a medical geneticist in the Division of Genetics and Metabolism at Phoenix Children's, illustrates this point. A fetus evaluated for suspected osteogenesis imperfecta had severely shortened and bowed long bones on ultrasound. Fetal MRI demonstrated calvarial demineralization, moderate-to-severe shortening and bowing of the long bones, a femur-length-to-abdominal-circumference ratio below 0.16 and evidence of pulmonary hypoplasia. Single-gene NIPT identified a known pathogenic COL1A2 variant.
Several prenatal findings can raise concern for a skeletal or short-stature syndrome, including bowed femurs or humeri, poor bone mineralization, a narrow thoracic cavity and low fetal lung volumes.

A negative screening result does not eliminate genetic risk

Clinicians should also be cautious about interpreting a negative carrier screen as exclusion of a rare disorder.
Expanded carrier panels differ in the genes and conditions included. In one case, a family's expanded carrier screening included some, but not all, genes associated with Joubert syndrome. Their child was subsequently diagnosed with Joubert syndrome, and the parents were found to carry a pathogenic variant in a gene that had not been included on their previous carrier panel.
The case reinforces a critical counseling point: negative carrier screening does not exclude carrier status for disorders or genes outside the panel tested.

What referring providers should consider

When prenatal imaging identifies one or more anomalies, genetic testing decisions should be guided by the evolving fetal phenotype, limitations of prior screening and the diagnostic question being asked. Collaboration among obstetric, MFM, genetics, fetal imaging and pediatric subspecialty teams can help families understand what a test result does, and just as importantly, does not establish.