Exome Sequencing May Enable Prenatal Diagnosis, Management

Clinical whole-exome sequencing (WES) has been utilized for both pediatric and adult patients with complex, clinical presentations (like developmental disabilities) and typically yields a molecular diagnosis rate of about 30 percent. In these cases clinical WES is effective from both a cost and time perspective in ending long diagnostic odysseys. With shortening turnaround times, experts say that WES will soon be applicable in other patient populations, including critically ill neonates and even prenatally.

Two presentations at the American College of Medical Genetics and Genomics annual meeting (March 8-12; Tampa, Florida) demonstrate the potential for WES to diagnose genetic disorders prenatally, including aneuploidies, large chromosomal deletion and duplication syndromes, as well as single-gene disorders. Timely WES results can inform developmental prognosis, pregnancy management, and recurrence risk for subsequent reproductive planning.

Researchers from Baylor University (Houston) reported results from their first 43 consecutive prenatal cases. Fetal samples were obtained through either an invasive procedure or a product of conception.

In 34 cases, WES was performed for the proband only (proband WES) followed by Sanger sequencing studies of both parental samples. In nine cases, the trio all underwent WES. For the final report, Sanger sequencing was used to confirm all contributing changes for trio cases. WES was performed on the Illumina HiSeq2500 (average 11.4 Gb data per exome) with more than 97 percent of the targeted exome regions sequenced at a depth of 20X.

The researchers found that the proband WES yielded a diagnosis of 32 percent (11 of 34) versus 33 percent in trio WES (three of nine). The turnaround time (TAT) was dramatically different for the two methods (average TAT for proband WES of 12 weeks versus one to three weeks for prenatal trio WES). When patients were classified by anomaly, diagnostic yields included:

• three of five cases of brain anomaly detected by ultrasound,
• six of 16 cases of brain anomaly and other organ system anomaly detected by ultrasound, and
• five of 22 cases of ultrasound anomaly not including the brain (e.g., cardiac, kidney, limb, and bladder anomalies, diaphragmatic hernia, heterotaxy, cystic hygroma, and edema).

Diagnosis was made for three of seven individuals with brain, cardiac defect, and other organ system anomaly. For 24 of the 43 cases this patient was the first presentation in the family and diagnosis was made for nine of these cases (38 percent). Of the 19 patients in which two or more family members had a similar phenotype, diagnosis was made for five cases (26 percent).

In a second presentation, researchers from GeneDx (Gaithersburg, Md.) shared WES results from 61 fetal samples. Twenty-six samples were from second trimester fetal terminations and demises and 16 samples were from third trimester demises.

Clinical indications for testing included fetal anomalies, fetal hydrops, intrauterine growth restriction, and discordant genetic and phenotypic fetal gender. The most common anomalies were seen in the central nervous system (22 cases), congenital heart disease (13 cases), cystic hygroma or hydrops (16 cases), facial anomalies (14 cases), and rocker bottom feet (nine cases). WES analysis was predominantly performed in fetus-parent trios (52 percent) or singleton cases (33 percent), with the remainder including fetus-parent duos or siblings.

The GeneDx researchers found that more than half of cases had prior reported normal karyotype (56 percent) or normal chromosomal microarray (69 percent).

Prior negative genetic testing was performed in five cases, including panel testing for Noonan syndrome, fetal akinesia deformation, lysosomal storage disease, and single gene testing for LAMB2, NPHS2, PLCE1, NPHS1, or FGFR3. Overall, 21 percent (n=13) of cases yielded a definitive molecular diagnosis, 34 percent (n=21) had reportable variants associated with a probable diagnosis, and 30 percent (n=18) tested negative. Similar numbers of cases had one variant (n=20) and two or more variants (n=23) identified. FGFR2 was the only gene with pathogenic variants in more than one case (two fetuses with features of skeletal dysplasia).

Novel molecular diagnoses were made including MYH3-related distal arthrogryposis, PIK3CA-related megalencephaly-capillary malformation-polymicrogyria syndrome, L1CAM-related hydrocephalus, RIPK4-related Bartsocas-Papas syndrome, MRPS22-related mitochondrial dysfunction, PKHD1-related polycystic kidney disease, and CYP11A1-related adrenal insufficiency.

Takeaway: Emerging research shows that WES performed prenatally yields similar diagnostic results as WES performed clinically in children and adults.