TY - JOUR
T1 - Validation and depth evaluation of low-pass genome sequencing in prenatal diagnosis using 387 amniotic fluid samples
AU - Qian, Yeqing
AU - Sun, Yan
AU - Guo, Xueqin
AU - Song, Lijie
AU - Sun, Yixi
AU - Gao, Xiaoyang
AU - Liu, Bei
AU - Xu, Yuqing
AU - Chen, Na
AU - Chen, Min
AU - Luo, Yuqin
AU - Qiao, Zhihong
AU - Fan, Linlin
AU - Man, Jianfen
AU - Zhang, Kang
AU - Wang, Xiaoli
AU - Rong, Tingting
AU - Wang, Zhonghua
AU - Liu, Fengxia
AU - Zhao, Jing
AU - Wei, Xiaoming
AU - Chen, Minfeng
AU - Peng, Zhiyu
AU - Peng, Huanhuan
AU - Sun, Jun
AU - Dong, Minyue
PY - 2023
Y1 - 2023
N2 - 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.
AB - 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.
U2 - 10.1136/jmg-2022-109112
DO - 10.1136/jmg-2022-109112
M3 - Journal article
C2 - 37012053
SN - 0022-2593
VL - 60
SP - 933
EP - 938
JO - Journal of Medical Genetics
JF - Journal of Medical Genetics
ER -