Prenatal Exome Sequencing Analysis in Fetal Structural Anomalies Detected by Ultrasonography (PAGE): A Cohort Study

Abstract

Background Fetal structural anomalies, which are detected by ultrasonography, have a range of genetic causes, including chromosomal aneuploidy, copy number variations (CNVs; which are detectable by chromosomal microarrays), and pathogenic sequence variants in developmental genes. Testing for aneuploidy and CNVs is routine during the investigation of fetal structural anomalies, but there is little information on the clinical usefulness of genome-wide next-generation sequencing in the prenatal setting. We therefore aimed to evaluate the proportion of fetuses with structural abnormalities that had identifiable variants in genes associated with developmental disorders when assessed with whole-exome sequencing (WES).Methods In this prospective cohort study, two groups in Birmingham and London recruited patients from 34 fetal medicine units in England and Scotland. We used whole-exome sequencing (WES) to evaluate the presence of genetic variants in developmental disorder genes (diagnostic genetic variants) in a cohort of fetuses with structural anomalies and samples from their parents, after exclusion of aneuploidy and large CNVs. Women were eligible for inclusion if they were undergoing invasive testing for identified nuchal translucency or structural anomalies in their fetus, as detected by ultrasound after 11 weeks of gestation. The partners of these women also had to consent to participate. Sequencing results were interpreted with a targeted virtual gene panel for developmental disorders that comprised 1628 genes. Genetic results related to fetal structural anomaly phenotypes were then validated and reported postnatally. The primary endpoint, which was assessed in all fetuses, was the detection of diagnostic genetic variants considered to have caused the fetal developmental anomaly.

Exome sequencing in the assessment of congenital malformations in the fetus and neonate

“…The PAGE study is the largest prospective, prenatal study to date (Lancet 2019, in press), assessing the clinical utility of ES in investigation of the malformed fetus. So far, 610 trios (fetus and both parents) have been analysed in cases where fetal structural anomalies have been identified using ultrasound and where autosomal/sex aneuploidy and large copy number variants have been excluded 6. This prospective study demonstrated that prenatal ES provides up to a 8.5% additional diagnostic yield of pathological variants when compared with conventional genetic testing 6.…”

“…NGS can interrogate the human genome down to the level of one base pair through either: (1) exome sequencing assessing all 20 000 gene coding regions (responsible for 85% of disease-causing variants), or by (2) WGS assessing the entire genome including introns, non-coding RNA and mitochondrial DNA in addition to assessment of copy number variation and structural rearrangements 5. In perinatology, there is growing evidence from several ‘proof of concept’ studies (eg, Prenatal Assessment of Genomes and Exomes (PAGE) study and the UK Nationwide 100,000 Genomes Project), suggesting that there is a significant additional molecular diagnostic rate through introducing NGS into mainstream clinical practice while simultaneously serving as translational studies with a proposed up and running framework for ES 6 7. It is anticipated that through NGS, the rate of diagnosis of monogenic disorders presenting with congenital anomalies will increase, as will our understanding as to why such anomalies arise during development, bringing us a step further to possible prevention 8…”

“…So far, 610 trios (fetus and both parents) have been analysed in cases where fetal structural anomalies have been identified using ultrasound and where autosomal/sex aneuploidy and large copy number variants have been excluded 6. This prospective study demonstrated that prenatal ES provides up to a 8.5% additional diagnostic yield of pathological variants when compared with conventional genetic testing 6. Another smaller prospective prenatal series conducted by Columbia University (Lancet 2019, in press) demonstrated similar findings with a diagnostic yield of 10.3% (n=234 trios) 9.…”

“…The PAGE study also noted that the pathological variant rate altered according to the anatomical anomaly identified and whether these were isolated or multiple (figure 1). A relatively low rate (4%) of variants of uncertain significance (VUS) was described 6. Only if the ‘variant’ was considered causative was it fed back to parents after the end of the pregnancy.…”

Évaluation fœtale prénatale : 75 ans plus tard (1945-2019)

“…Le rendement diagnostique pour la dysplasie squelettique etait de > 80 %, avec des taux de 33 a 50 % avec la consanguinit e parentale, d'importantes r egions d'homozygosit e sur une puce de polymorphisme mononucl eotidique, malformations multiples ou des fausses couches ou une mort n eonatale inexpliqu ees. L' etude britannique sur l' evaluation pr enatale des g enomes et des exomes (PAGE) a r ev el e que le rendement diagnostique etait le plus elev e chez les foetus atteints d'anomalies multisyst emes (15 %), du squelette (15 %) et cardiaques (11 %)24 . Petrovski et coll.…”