Exome sequencing enhances the diagnostic rate of perinatal autopsy: A prospective multicentre clinical utility trial with implications for prenatal diagnosis.

Abstract

Objectives: To determine the utility of exome sequencing as an adjunct to perinatal post mortem for congenital anomalies. To model the likely outcome of exome sequencing as a prenatal test in the same setting. Method(s): Probands with congenital anomalies were referred by perinatal pathologists. They were enrolled for sequencing if their microarray analysis was negative and their anomalies were considered to have a monogenic cause. Singleton or trio exome sequencing was performed as an adjunct to routine perinatal autopsy and the diagnostic outcomes were compared. A geneticist independently reviewed the probands' antenatal imaging findings and recommended a phenotype specific gene list to model the clinical utility of prenatal exome sequencing. Result(s): A prospective cohort of 131 probands was referred. Fortynine (37%) were unsuitable for inclusion. The parents of five (4%) declined enrolment and 10 (8%) could not be consented. Sixty-seven probands (52%) were enrolled. One proband could not be sequenced due to a degraded DNA sample. Results are available for 65 probands (32 singletons and 33 trios). Specific diagnoses were identified at autopsy in 11 cases (17%) including two cases with negative sequencing. Sequencing identified specific diagnoses ("pathogenic" or "likely pathogenic" variants) in 23 cases giving a diagnostic rate of 35%. The combined diagnostic rate of autopsy and exome was 38%. The individual autopsy and genomic diagnostic rates were highest in probands with significant skeletal findings (39% and 61% respectively, n = 18). Genomic diagnoses were obtained from 34% of singleton exomes, with segregation when required, and 36% of trio exomes. Variants of uncertain significance (VUS) were reported in 13 cases (20%). In four, a strong phenotype-genotype match together with plausible candidate variants indicated a need for additional studies. The combined rate of diagnostic or suspicious variants was 42%. The use of antenatal sequencing in this cohort using a candidate gene list approach would have identified a specific genomic diagnosis in 78% (18 of the 23 cases). Conclusion(s): Clinical exome sequencing doubles the diagnostic rate of perinatal autopsy for congenital anomalies and supports the prenatal use of genomic sequencing.