Incremental Yield of Whole-Genome Sequencing Over Chromosomal Microarray Analysis and Exome Sequencing for Congenital Anomalies in Prenatal Period and Infancy: Systematic Review and Meta-analysis

Congenital anomalies can be diagnosed prenatally through genetic testing, including exome sequencing (ES), quantitative fluorescence polymerase chain reaction (QF-PCR), and chromosomal microarray analysis (CMA), in addition to whole-genome sequencing (WGS). Each method has anomalies it can better detect, with WGS having the greatest diagnostic capability; Concerns in the field include questions regarding the cost-effectiveness of WGS, along with the interpretation of findings; much of the evidence on effectiveness of WGS originates from pediatric samples, with this approach showing only slightly increased utility over ES, which is much more cost-effective. This study was designed to investigate the incremental yield of WGS over QF-PCR/CMA with or without ES for fetuses, neonates, and infants up to 1 year of age with congenital anomalies, as well as to assess the turnaround time and quantity of DNA required for testing. This study was a systematic review and meta-analysis, with studies obtained from Ovid MEDLINE, EMBASE, MEDLINE(Web of Science), The Cochrane Library, and ClinicalTrials.gov. Searches included articles published between January 2010and December 2022. Inclusion criteria were prospective or retrospective cohort studies including 3 or more cases of 1 or more congenital anomalies that would have been detectable on prenatal ultrasound and negative QF-PCR and CMA. Exclusion criteria were studies or data where CMA results were unavailable and cases of causative pathogenic copy number variants less than 50 kb or that were detectable on standard tests; articles were chosen based on analysis of 2 independent reviewers. Final analysis included a total of 18 articles including 1284 cases of congenital anomalies meeting the inclusion criteria, of which 902 were included for analysis purposes. Overall, the incremental yield of WGS over QF-PCR/CMA for combined prenatal and postnatal cohorts was 26% (95% confidence interval [CI], 18%-36%;I-2= 86%). The largest incremental yield was found for musculoskeletal anomalies (36%; 95% CI, 20%-52%;I-2= 67%) and central nervous system anomalies (30%;95% CI, 17%-42%;I-2= 65%). The most common genetic syndrome identified was Noonan syndrome, with most pathogenic variants occurring de novo and in monoallelic (autosomal dominant) inheritance genes. In the prenatal cohort, incremental yield of WGS over QF-PCR/CMA was 16% (95% CI, 9%-24%;I-2= 85%), which in-creased to 23% (95% CI, 12%-36%;I-2= 70%) for anomalies affecting multiple organ systems. In the postnatal cohort, incremental yield was 39% (95% CI, 27%-51%;I-2= 53%), increasing to 43% (95% CI, 27%-59%;I-2= 21%) for anomalies affecting multiple organ systems. Three included studies analyzed the incremental yield of WGS over QF-PCR/CMA and ES, both prenatally and postnatally. In these cases, the incremental yield was only 1% (95% CI, 0%-4%;I-2= 47%). Median turnaround time for WGS was 18 days, with 1 study reporting turnaround time for QF-PCR/CMA and ES at 31 +/- 8 days. Mean quantity of DNA required for WGS versus QF-PCR/CMA and ES was 100 +/- 0 versus 350 +/- 50 ng (P=0.03). These results indicate a significant incremental yield of WGS over QF-PCR/CMA, with the greatest increase in the post-natal cohort in individuals with multisystem anomalies. The results, however, are insufficient to suggest the superiority of WGS over QF-PCR/CMA and ES. This analysis is consistent with the results of previous studies comparing WGS and ES in pediatric cohorts and adds evidence to the consensus that WGS is the optimal strategy for critically ill patients in this age group. Future research should focus on optimizing testing strategies for prenatal and newborn cohorts, as well as determining what methods are optimal in different settings according to affordability and accessibility.