Objective To systematically explore the association between pathogenic/likely pathogenic copy number variations (pCNV) and ultrasonographic anomalies and soft markers. Design Retrospective cohort study. Setting Data were obtained from multiple centers in china. Population or Sample Fetuses performed low-pass genome sequencing and ultrasonography between 2016 and 2020. Method The yields of pCNV under various ultrasonographic indications were compared with that of fetuses with no identifiable anomalies. In addition, the ultrasonographic characteristics of aneuploidy and pCNV were described in comparison with those of fetuses without chromosomal aberrations. Main Outcome Measures Yields of aneuploidy and pCNV in different ultrasonographic indications. Results Ten of the 12 ultrasonographic anomalies had significantly higher yield of pCNV, except for fetal hydrops and abnormal amniotic fluid, of which the gastrointestinal, facial, respiratory systems, and abdominal wall defect were rarely reported. Similarly, five of the 12 soft markers had significantly higher yield of pCNV, with single umbilical artery being rarely reported. Furthermore, this study reported that four duplications/deletions were associated with novel ultrasonographic findings. Conclusions Based on specific ultrasonographic phenotypes, prenatal genetic testing could be considered in a tailored fashion. Keywords Low-pass genome sequencing; ultrasonographic anomaly; soft marker; copy number variations; aneuploidy; prenatal diagnosis Tweetable abstract Fetuses with structural anomalies and specific soft markers are recommended for copy number variations analysis

Genome sequencing(GS) has been applied in the diagnosis of global developmental delay(GDD)/intellectual disability(ID). However, the performance in those with inconclusive results from chromosomal microarray analysis(CMA) and exome sequencing(ES) is unknown. We recruited 100 pediatric GDD/ID patients from multiple sites in China from February 2018 to August 2020 for GS. Patients have received at least one genomic diagnostic test prior to enrollment. Reanalysis of CMA/ES data was performed. The yield of GS was calculated and explanations for missed diagnoses by CMA/ES were investigated. Clinical utility was assessed by interviewing the parents by phone. The overall diagnostic yield of GS was 23%. Seven families could have been solved with reanalysis of ES data. 13 families were missed by previous CMA/ES due to improper method. Three remained unsolved after ES reanalysis due to allele dropout, complex variants missed by ES, and a CNV in untranslated regions. Follow-up of the diagnosed families revealed that nine families experienced changes in clinical management, including identification of targeted treatments, cessation of unnecessary treatment, and considerations for family planning. GS demonstrated high diagnostic yield and clinical utility in this cohort of undiagnosed GDD/ID patients, detecting a wide range of variant types of different sizes in a single workflow.