Application of exome sequencing for prenatal diagnosis of fetal structural anomalies: clinical experience and lessons learned from a cohort of 1618 fetuses

Abstract

Background Exome sequencing (ES) is becoming more widely available in prenatal diagnosis. However, data on its clinical utility and integration into clinical management remain limited in practice. Herein, we report our experience implementing prenatal ES (pES) in a large cohort of fetuses with anomalies detected by ultrasonography using a hospital-based in-house multidisciplinary team (MDT) facilitated by a three-step genotype-driven followed by phenotype-driven analysis framework. Methods We performed pES in 1618 fetal cases with positive ultrasound findings but negative for karyotyping and chromosome microarray analysis between January 2014 and October 2021, including both retrospective (n=565) and prospective (n=1053) cohorts. The diagnostic efficiency and its correlation to organ systems involved, phenotypic spectrum, and the clinical impacts of pES results on pregnancy outcomes were analyzed. Results A genotype-driven followed by phenotype-driven three-step approach was carried out in all trio pES. Step 1, a genotype-driven analysis resulted in a diagnostic rate of 11.6% (187/1618). Step 2, a phenotype-driven comprehensive analysis yielded additional diagnostic findings for another 28 cases (1.7%; 28/1618). In the final step 3, data reanalyses based on new phenotypes and/or clinical requests found molecular diagnosis in 14 additional cases (0.9%; 14/1618). Altogether, 229 fetal cases (14.2%) received a molecular diagnosis, with a higher positive rate in the retrospective than the prospective cohort (17.3% vs. 12.4%, p<0.01). The diagnostic rates were highest in fetuses with skeletal anomalies (30.4%) and multiple organ involvements (25.9%), and lowest in fetuses with chest anomalies (0%). In addition, incidental and secondary findings with childhood-onset disorders were detected in 11 (0.7%) cases. Furthermore, we described the prenatal phenotypes for the first time for 27 gene-associated conditions (20.0%, 27/135) upon a systematic analysis of the diagnosed cases and expanded the phenotype spectrum for 26 (19.3%) genes where limited fetal phenotypic information was available. In the prospective cohort, the combined prenatal ultrasound and pES results had significantly impacted the clinical decisions (61.5%, 648/1053). Conclusions The genotype-driven approach could identify about 81.7% positive cases (11.6% of the total cohort) with the initial limited fetal phenotype information considered. The following two steps of phenotype-driven analysis and data reanalyses helped us find the causative variants in an additional 2.6% of the entire cohort (18.3% of all positive findings). Our extensive phenotype analysis on a large number of molecularly confirmed prenatal cases had greatly enriched our current knowledge on fetal phenotype-genotype correlation, which may guide more focused prenatal ultrasound in the future. This is by far the largest pES cohort study that combines a robust trio sequence data analysis, systematic phenotype-genotype correlation, and well-established MDT in a single prenatal clinical setting. This work underlines the value of pES as an essential component in prenatal diagnosis in guiding medical management and parental decision making.

Predicting the functional effect of compound heterozygous genotypes from large scale variant effect maps

“…Given that the therapeutic potential for this medically actionable disorder is highest before patients become symptomatic, clinical sequencing coupled to informative variant interpretation can be a powerful diagnostic tool. Sequencing based diagnostics are becoming more widely applied in newborns, prenatal care [67], and as a part of clinical research efforts such as the Undiagnosed Disease Program [68,69] or Deciphering Developmental Disorders [70]. The most recent AMCG guidelines [71] recommend exome or genome sequencing as a first or second tier option for patients displaying early neonatal (<1 year) congenital abnormalities and for patients exhibiting developmental delay or intellectual disability before the age of 18.…”

“…Given that the therapeutic potential for this medically actionable disorder is highest before patients become symptomatic, clinical sequencing can be a strong diagnostic tool if variant interpretation is also informative. Sequencing based diagnostics are becoming more widely applied in newborns, prenatally [58], and as a part of programs like Undiagnosed Disease…”

Association of prenatal thoracic ultrasound abnormalities with copy number variants at a single Chinese tertiary center

“…Prenatal thoracic abnormalities are relatively rare compared with other structural abnormalities such as cardiovascular or central nervous system anomalies. 11 The genetic etiology for thoracic abnormalities is limited and remains to be elucidated. In the present…”

Access to prenatal exome sequencing for fetal malformations: A qualitative landscape analysis in the US

“…Framing the utility of ES as guiding care before, during, and after a pregnancy is in contrast with the perspective that the main goal of prenatal diagnostic testing is for decision making about termination. Terminating a pregnancy based on prenatal testing is a utility in and of itself, and a negative as well as a positive ES result may guide families to decide to continue with their pregnancy 3,33 . Providers described the utility of ES among patient populations where termination is not an option due to cultural or religious reasons, as well as those living in states where abortion is restricted.…”