Validation and depth evaluation of low-pass genome sequencing in prenatal diagnosis using 387 amniotic fluid samples

Yeqing Qian, Yan Sun, Xueqin Guo, Lijie Song, Yixi Sun, Xiaoyang Gao, Bei Liu, Yuqing Xu, Na Chen, Min Chen, Yuqin Luo, Zhihong Qiao, Linlin Fan, Jianfen Man, Kang Zhang, Xiaoli Wang, Tingting Rong, Zhonghua Wang, Fengxia Liu, Jing ZhaoXiaoming Wei, Minfeng Chen, Zhiyu Peng, Huanhuan Peng, Jun Sun*, Minyue Dong*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review


Background Low-pass genome sequencing (LP GS) is an alternative to chromosomal microarray analysis (CMA). However, validations of LP GS as a prenatal diagnostic test for amniotic fluid are rare. Moreover, sequencing depth of LP GS in prenatal diagnosis has not been evaluated.Objective The diagnostic performance of LP GS was compared with CMA using 375 amniotic fluid samples. Then, sequencing depth was evaluated by downsampling.Results CMA and LP GS had the same diagnostic yield (8.3%, 31/375). LP GS showed all copy number variations (CNVs) detected by CMA and six additional variant of uncertain significance CNVs (>100 kb) in samples with negative CMA results; CNV size influenced LP GS detection sensitivity. CNV detection was greatly influenced by sequencing depth when the CNV size was small or the CNV was located in the azoospermia factor c (AZFc) region of the Y chromosome. Large CNVs were less affected by sequencing depth and more stably detected. There were 155 CNVs detected by LP GS with at least a 50% reciprocal overlap with CNVs detected by CMA. With 25 M uniquely aligned high-quality reads (UAHRs), the detection sensitivity for the 155 CNVs was 99.14%. LP GS using samples with 25 M UAHRs showed the same performance as LP GS using total UAHRs. Considering the detection sensitivity, cost and interpretation workload, 25 M UAHRs are optimal for detecting most aneuploidies and microdeletions/microduplications.Conclusion LP GS is a promising, robust alternative to CMA in clinical settings. A total of 25 M UAHRs are sufficient for detecting aneuploidies and most microdeletions/microduplications.
Original languageEnglish
JournalJournal of Medical Genetics
Pages (from-to)933-938
Number of pages6
Publication statusPublished - 2023


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