Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges—Systematic Review of the Literature and Meta-Analysis

Abstract

Fetal malformations occur in 2–3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. “Structural anomalies” include non-transient anatomic alterations. “Soft markers” are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as “dynamic”. This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.

Chromosomal Microarray Analysis in Fetuses Detected with Isolated Cardiovascular Malformation: A Multicenter Study, Systematic Review of the Literature and Meta-Analysis

“…Every genetic investigation must be preceded and followed by non-directive genetic counseling with the aim of educating consultants about the possible conditions related to the malformation and the available testing, providing the basis for thoughtful decision making, according to psychological, socio-economic, cultural and religious backgrounds [ 9 ].…”

“…It can be performed in fetuses with structural anomalies after or alongside standard karyotype or as a first-tier test. Fetuses with heart diseases, as well as most structural anomalies, may benefit from this assay, whose incremental diagnostic rate over standard karyotyping ranges from 3.18% (CI 3.11–3.25) to 6.47% (CI 6.23–6.71) in this subgroup of isolated malformations [ 9 ].…”

Clinical Validation and Diagnostic Utility of Optical Genome Mapping in Prenatal Diagnostic Testing

“…In the 2000s, chromosomal microarray (CMA) demonstrated the ability to detect sub-microscopic CNVs (micro-deletions and duplications) with a resolution of approximately 50-100 kbp and was recommended by ACOG and ISUOG as the first-line test in high-risk pregnancies with an abnormal ultrasound [ 15,16 ]. Although CMAs cannot detect balanced SVs or the orientation/location of duplications/insertions, they demonstrated an incremental diagnostic yield of 2.1-8.5% in fetuses with structural anomalies [ 17 ]. Recently, with the rapid progress in next-generation sequencing, exome sequencing has been evaluated as a diagnostic test and has demonstrated an incremental diagnostic yield of 19.4-27.4% in fetuses with structural anomalies [ 17 ].…”

“…Although CMAs cannot detect balanced SVs or the orientation/location of duplications/insertions, they demonstrated an incremental diagnostic yield of 2.1-8.5% in fetuses with structural anomalies [ 17 ]. Recently, with the rapid progress in next-generation sequencing, exome sequencing has been evaluated as a diagnostic test and has demonstrated an incremental diagnostic yield of 19.4-27.4% in fetuses with structural anomalies [ 17 ]. However, because exome sequencing is limited to the detection of small variants (single nucleotide variants and small indels), cannot detect several classes of SVs, and has a large variant of unknown significance (VUS) burden, it is recommended only in select cases following a negative cytogenetic result [ 17 ].…”

“…Recently, with the rapid progress in next-generation sequencing, exome sequencing has been evaluated as a diagnostic test and has demonstrated an incremental diagnostic yield of 19.4-27.4% in fetuses with structural anomalies [ 17 ]. However, because exome sequencing is limited to the detection of small variants (single nucleotide variants and small indels), cannot detect several classes of SVs, and has a large variant of unknown significance (VUS) burden, it is recommended only in select cases following a negative cytogenetic result [ 17 ]. Overall, the current diagnostic workflow relies on multiple technologies that are performed simultaneously or in a tiered fashion, often leading to increased cost and time to reach a diagnosis when clinical decision-making is time-limited.…”