Noninvasive Prenatal Testing For Fetal Chromosomal Copy Number Variation

Objective Chromosome karyotype analysis,chromosome microarray analysis(CMA)and noninvasive prenatal detection(NIPT)were used to investigate the performance of noninvasive prenatal testing based on low-depth whole-genome sequencing(WGS)for fetal chromosome copy number variation(CNV).Methods1.From September 2017 to May 2019,873 singleton pregnant women who were treated in the third affiliated Hospital of Guangzhou Medical University and other hospitals in Guangzhou and suggested fetal CNV by routine NIPT were selected.The gestational age was from 12 to 28 weeks.The included women were found with CNV results by routine NIPT,each having singleton fetus.The pregnant women who suffered from chromosome abnormalities,under-went transplantation or infusion of allogeneic blood products within one year,stem cell treatment or immunotherapy within 4 weeks,contraindications for invasive surgery were excluded from the study.All the subjects gave informed consent for participation in the study;2.Record the detailed clinical information about the pregnancies and the fetuses,including name,age,history of pregnancy and delivery,gestational age at collection time and clinical outcome of pregnancy;3.To detect the samples by chromosome karyotype analysis and chromosome microarray analysis;4.NIPT was performed on randomly rearranged samples using the method of low-depth whole-genome sequencing,and the algorithm of fetal copy-number analysis then identified the fetal CNV through maternal plasma sequencing(FCAPS);5.By comparing the results of chromosome karyotype analysis and CMA,to evaluate the detection efficiency and clinical significance of NIPT for fetal CNV.Results1.A total of 873 samples were collected,including 315(36.08%)high-risk pregnancies,the maternal aged ≥35 years(median age: 38 years;range: 35-51years),558(63.92%)low-risk pregnancies,the maternal aged <35 years(median age: 26 years;range: 18-34 years).The gestational age at the time of detection ranged from 11 to 28 weeks(median week: 19 weeks).Amniocentesis was performed in 658 cases and chorionic villus sampling was performed in 215 cases.2.All 873 samples were successfully detected by chromosome karyotype analysis and CMA.The results showed that there were 825 normal samples and 48 samples of CNV.Among 48 positive samples,there are 14 samples with CNV<2Mb and 34 samples with CNV ≥2Mb;3.Forty-eight samples of CNV(about 0.1-47.3Mb)were performed NIPT by the method of low-depth whole-genome sequencing(0.51-1.19X).The results suggested that there were 41 samples of CNV(85.42%),two samples with high risk of aneuploidy(4.17%)and five false-negative samples(10.42%);4.825 normal samples were detected by the same method,a total of 804 negative samples and 21 false-positive samples were detected;5.By comparison of chromosome karyotype analysis and CMA,among 14 samples with CNV<2Mb,11 were inconsistent with NIPT results,and 3 were consistent with NIPT results.Among the 34 CNV>2Mb samples,5 were inconsistent with NIPT results,and 29 were consistent with NIPT results.Among the 4 samples containing multiple CNV samples,3 were consistent with NIPT results;6.The overall sensitivity and specificity of NIPT for CNV were 66.67% and97.45%,respectively.Especially for CNV >2Mb,the sensitivity and specificity were as high as 85.29% and 98.18%.While for CNV <2Mb,the sensitivity and specificity were lower,21.43% and 99.27%,respectively.Conclusion1.It is possible to use noninvasive prenatal testing based on low-depth whole-genome sequencing to screen fetal CNV.2.NIPT based on low-depth whole-genome sequencing can not replace CMA as a routine method for fetal CNV.