Diagnostic Yield of Exome Sequencing in Fetuses With Multisystem Malformations: Systematic Review and Meta-analysis

Fetal structural anomalies occur in approximately 2.5% of pregnancies, and many of these are identified via ultrasound examination. Following detection of a fetal structural anomaly, chromosomal microarray analysis (CMA) is offered. This process will uncover pathogenic copy number variants in approximately 6% to 10% of cases, on top of the 14% of chromosomal anomalies identified via karyotyping. Exome-sequencing (ES) also allows assessment of over 20,000 genes' coding regions. Although covering just 1% to 2% of the genome, ES can assess 85% of known disease-causing variants. The use of prenatal ES is rapidly emerging, and this study performed a systematic review of literature, as well as a meta-analysis for assessing diagnostic yield of ES in fetuses with negative results on CMA or karyotyping and multisystem malformations. PubMed, theWeb of Knowledge, and Cochran database were all used for the identification of relevant published manuscripts. No time limits for publication dates were applied. The following data were extracted: country and site of the study, inclusion criteria within study, study period, sample size, number of fetuses presentmultisystemmalformations, Sanger sequencing validation, interpretation approach, criteria for variant classification, and ES results and positive diagnoses. The primary outcome of the study was the diagnostic yield of ES in fetuses with at least 2 major anomalies (multisystem malformations), along with a normal chromosome as determined by karyotyping and/or CMA. A total of 17 studies focusing on ES were identified for review, with 6 from the United States, 4 from the Netherlands, 2 in the United Kingdom, and 1 each in Switzerland, China, Israel, and Denmark. These studies included 694 total cases, 213 (33%) of which were positively diagnosed by ES. Among these positive cases, 223 genes were found to be involved (in 10 cases, more than 1 gene was involved). The most frequently affected genes were as follows: KMT2D gene (Kabuki syndrome, n = 11), CHD7 gene (CHARGE syndrome, n = 7), FGFR2-related disorders gene (n = 5), and DHCR7 gene (Smith-Lemli-Opitz syndrome, n = 5). Additional findings included 22 positive cases exhibiting a gene involved in RASopathy syndromes, specifically the following genes: PTPN11 (n = 5), RIT1 (n = 4), HRAS (n = 4), KRAS (n = 2), SOS1 (n = 2), RAF1 (n = 2), BRAF (n = 2), and NRAS (n = 1). Further findings indicated 12 cases with a gene associated with formation of collagen structures (4 associated with COL1A1 gene). A main drawback of prenatal ES is the difference of prenatal phenotypes from postnatal descriptions of the same syndrome. ES is currently expanding the knowledge of various prenatal disorder presentations. Common syndromes detected by ES in fetuses with multisystem anomalies were Kabuki and CHARGE syndromes. In this analysis, all prenatal cases of Kabuki syndrome presented with cardiac defects associated with other anomalies, such as fetal hydrops, renal anomalies, or growth restriction. A potential limitation of systematic reviews is the discrepancy in eligibility criteria among publications and varying phenotypes of affected fetuses. The review process also had some limitations, as studies included not onlymultisystem multiple anomalies, which rendered data collection more complex. In addition, methods for ES were not clearly defined in some of the series. Notably, solo samples were sequenced in 2, whereas 13 studies used the trio approach. However, a meta-analysis found diagnostic yields not significantly different between the 2 approaches. Overall, this meta-analysis and systematic review showed that, in a third of cases, ES applied in fetuses with multisystem structural anomalies enables causative gene identification. It thereby seems reasonable to create policy ES in such cases following CMA results. Solo and trio approaches to ES showed no differences. To further increase the diagnostic yield of next-generation sequencing, additional studies are exploring whole-genome sequencing.