Low-pass genome sequencing (LP GS) has been widely used in CNV detection andis considered as an alternative to chromosomal microarray analysis. However, application of LP GS as a first-line prenatal diagnostic test is not ready.The increase in sequencing depth will improve detection sensitivity, followed by the increase for cost. This could greatly block the successful application of this test. In this work, we found that LP GS and CMA had the same diagnostic yield in real clinical setting. Considering detection sensitivity, cost and interpretation workload, 25 M uniquely aligned high-quality reads were recommended for detecting most aneuploidies and microdeletions/microduplications. Our study provided data quality standards and thresholds of sequencing depth for centers conducting LP GS in prenatal diagnosis in thefuture. (By Prof. Minyue Dong, https://jmg.bmj.com/content/early/2023/04/02/jmg-2022-109112 )

Prof. Minyue Dong with some co-authors at Women’s Hospital, School of Medicine, Zhejiang University (Hangzhou, Zhejiang, China)