Clinical significance of regions of homozygosity detection in prenatal chromosomal microarray analysis

Chromosomal microarray analysis (CMA) detects pathogenic copy-number variants (pCNVs) and regions of homozygosity (ROHs) in prenatal genetic analysis. This study evaluates the clinical significance of ROH detection in prenatal settings. We reviewed 178 fetuses with ROH detected by CMA among 20,546 fetuses from 2015 to 2023. Clinical and laboratory results, including ultrasound anomalies, cell-free DNA (cfDNA) screening, karyotyping, exome sequencing (ES), and methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), were analyzed. These 178 fetuses with ROH accounted for 0.87% of prenatal cases. Among them, 24.2% had positive cfDNA screening results, and 52.8% underwent follow-up ES, trio CMA, and MS-MLPA. Follow-up studies detected pathogenic homozygous variants within ROH in two fetuses and uniparental disomy (UPD)-related diseases in five fetuses. Our results and findings from the other five large prenatal case series from literature indicated that ROH detection in prenatal CMA has a baseline positive predictive value of 2.7% for autosomal-recessive disorders, 9.6% for UPD-related diseases, and 0.04% overall additive diagnostic yield. These findings support the use of ES and MS-MLPA for follow-up testing and provide guidance for genetic counseling in fetuses with ROH.