First applications of a targeted exome sequencing approach in fetuses with ultrasound abnormalities reveals an important fraction of cases with associated gene defects

Abstract

Background. Fetal malformations and other structural abnormalities are relatively frequent findings in the course of routine prenatal ultrasonographic examination. Due to their considerable genetic and clinical heterogeneity, the underlying genetic cause is often elusive and the resulting inability to provide a precise diagnosis precludes proper reproductive and fetal risk assessment. We report the development and first applications of an expanded exome sequencing-based test, coupled to a bioinformatics-driven prioritization algorithm, targeting gene disorders presenting with abnormal prenatal ultrasound findings.Methods. We applied the testing strategy to14 euploid fetuses, from 11 on-going pregnancies and three products of abortion, all with various abnormalities or malformations detected through prenatal ultrasound examination. Whole exome sequencing (WES) was followed by variant prioritization, utilizing a custom analysis pipeline (Fetalis algorithm), targeting 758 genes associated with genetic disorders which may present with abnormal fetal ultrasound findings.Results. A definitive or highly-likely diagnosis was made in 6 of 14 cases (43%), of which 3 were abortuses (Ellis-van Creveld syndrome, Ehlers-Danlos syndrome and Nemaline myopathy 2) and 3 involved on-going pregnancies (Citrullinemia, Noonan syndrome, PROKR2-related Kallmann syndrome). In the remaining eight on-going pregnancy cases (57%), a ZIC1 variant of unknown clinical significance was detected in one case, while in seven cases testing did not reveal any pathogenic variant(s). Pregnancies were followed-up to birth, resulting in one neonate harboring the PROKR2 mutation, presenting with isolated minor structural cardiac abnormalities, and in seven apparently healthy neonates.Discussion. The expanded targeted exome sequencing-based approach described herein (Fetalis), provides strong evidence suggesting a definite and beneficial increase in our diagnostic capabilities in prenatal diagnosis of otherwise chromosomally balanced fetuses with troubling ultrasound abnormalities. Furthermore, the proposed targeted exome sequencing strategy, designed primarily as a diagnostic rather than a research discovery tool, overcomes many of the problems and limitations associated with clinical wide-scale WES testing in a prenatal setting.

Intra-familial variability associated with recessive RYR1 mutation diagnosed prenatally by exome sequencing

“…There are a few reports of whole exome or genome sequencing being used for diagnostic purposes in the prenatal setting when congenital malformations are identified during prenatal scans. [30][31][32][33] Our study confirms the value and diagnostic potential of next-generation sequencing in fetal medicine. It also demonstrates that whole exome sequencing can successfully be performed on fetal DNA (from amniotic cells) that has been whole genome amplified.…”

Exploring the Issues Surrounding Clinical Exome Sequencing in the Prenatal Setting

“…This is echoed in a study by Carss et al (2014), where exome sequencing was performed on 30 fetuses and newborns with a variety of ultrasound anomalies and determined a diagnostic yield of 10% over conventional chromosomal microarray analysis (CMA). Other studies have reported definitive or likely definitive diagnoses in approximately 20-40% of fetuses with sonographic abnormalities, with the wide range likely due to small cohorts (Drury et al 2015;Pangalos et al 2016;Vora et al 2017;Westerfield et al 2015). Laboratories in the USA performing clinical prenatal exome sequencing have also presented initial data with a comparable or higher diagnostic yield to exome sequencing performed in a postnatal setting (Alamillo et al 2015;Walkiewicz 2016).…”

“…Exome sequencing on prenatal samples from ongoing or terminated pregnancies with fetal anomalies is being conducted on both a clinical and research basis. Although these early reports include relatively small numbers of cases, typically under 30 samples, results indicate exome sequencing can improve the prenatal diagnosis rates for fetuses with ultrasound anomalies not explained by conventional karyotype or CMA (Alamillo et al 2015;Drury et al 2015;Pangalos et al 2016;Vora et al 2017;Walkiewicz 2016;Westerfield et al 2015). While the American College of Medical Genetics and Genomics (ACMG) has published guidelines addressing some of the challenges from utilizing exome sequencing such as the return of secondary findings, the authors do not address prenatal or preconception sequencing (Berg et al 2011;Kalia et al 2016).…”

Parental experiences of prenatal whole exome sequencing (WES) in cases of ultrasound diagnosed fetal structural anomaly

“…12 Research relating to the use of genetic sequencing for prenatal diagnosis in ongoing pregnancy is limited 4 ; however, the feasibility of WES in prenatal diagnostics has been demonstrated in small case series. 3,12,13 Survey data involving 186 expectant parents in the USA demonstrated that 83% thought that prenatal WES should be offered, 14 and research into the views of 15 women with noncontinuing anomalous pregnancies found that they had high hopes and expectations of WES, despite testing enabling a diagnosis in only 1 in 3 (30% of cases). 15 Successful implementation of WES for prenatal diagnosis would require rigorous health economic assessment and would be dependent upon the development of rapid analytical and interpretation pipelines.…”