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Liu Y, Liu S, Liu J, Bai T, Jing X, Deng C, Xia T, Cheng J, Xing L, Wei X, Luo Y, Zhou Q, Xie D, Xiong Y, Liu L, Zhu Q, Liu H. Identification of copy number variations among fetuses with isolated ultrasound soft markers in pregnant women not of advanced maternal age. Orphanet J Rare Dis 2024; 19:56. [PMID: 38336695 PMCID: PMC10858470 DOI: 10.1186/s13023-024-03066-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/03/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Pathogenic (P) copy number variants (CNVs) may be associated with second-trimester ultrasound soft markers (USMs), and noninvasive prenatal screening (NIPS) can enable interrogate the entire fetal genome to screening of fetal CNVs. This study evaluated the clinical application of NIPS for detecting CNVs among fetuses with USMs in pregnant women not of advanced maternal age (AMA). RESULTS Fetal aneuploidies and CNVs were identified in 6647 pregnant women using the Berry Genomics NIPS algorithm.Those with positive NIPS results underwent amniocentesis for prenatal diagnosis. The NIPS and prenatal diagnosis results were analyzed and compared among different USMs. A total of 96 pregnancies were scored positive for fetal chromosome anomalies, comprising 37 aneuploidies and 59 CNVs. Positive predictive values (PPVs) for trisomy 21, trisomy 18, trisomy 13, and sex chromosome aneuploidies were 66.67%, 80.00%, 0%, and 30.43%, respectively. NIPS sensitivity for aneuploidies was 100%. For CNVs, the PPVs were calculated as 35.59% and false positive rate of 0.57%. There were six P CNVs, two successfully identified by NIPS and four missed, of which three were below the NIPS resolution limit and one false negative. The incidence of aneuploidies was significantly higher in fetuses with absent or hypoplastic nasal bone, while that of P CNVs was significantly higher in fetuses with aberrant right subclavian artery (ARSA), compared with other groups. CONCLUSIONS NIPS yielded a moderate PPV for CNVs in non-AMA pregnant women with fetal USM. However, NIPS showed limited ability in identifying P CNVs. Positive NIPS results for CNVs emphasize the need for further prenatal diagnosis. We do not recommend the use of NIPS for CNVs screening in non-AMA pregnant women with fetal USM, especially in fetuses with ARSA.
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Affiliation(s)
- Yunyun Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Sha Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Jianlong Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Ting Bai
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xiaosha Jing
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Cechuan Deng
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Tianyu Xia
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Jing Cheng
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Lingling Xing
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xiang Wei
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yuan Luo
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Quanfang Zhou
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Dan Xie
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yueyue Xiong
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Ling Liu
- Prenatal Diagnostic Center, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Qian Zhu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China.
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.
| | - Hongqian Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China.
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.
- Prenatal Diagnostic Center, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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Hu X, Hu Y, Wang H, Yu C, Zheng J, Zhang H, Zheng J. Comparison of Chromosomal Microarray Analysis and Noninvasive Prenatal Testing in Pregnant Women with Fetal Ultrasonic Soft Markers. Risk Manag Healthc Policy 2024; 17:29-40. [PMID: 38196919 PMCID: PMC10775152 DOI: 10.2147/rmhp.s437441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/20/2023] [Indexed: 01/11/2024] Open
Abstract
Objective This study aimed to assess the utility of chromosomal microarray analysis (CMA) and noninvasive prenatal testing (NIPT) in detecting clinically significant chromosomal abnormalities among fetuses presenting ultrasonic soft markers (USMs). Methods A retrospective observational study, spanning from January 1, 2019, to September 30, 2022, enrolled 539 singleton pregnant women with fetal USMs at our center. Of these, 418 cases (77.6%) underwent NIPT, while 121 cases (22.4%) opted for invasive prenatal diagnosis post-appropriate genetic counseling. Cases with high-risk NIPT results proceeded to invasive prenatal diagnosis, where conventional karyotyping and CMA were concurrently performed. Further stratification was done based on the number of USMs, classifying cases into single-USM and multiple-USM groups. Results Of the 24 cases (4.5%) exhibiting abnormal findings, 17 presented numerical chromosomal abnormalities, 2 featured clinically significant copy number variations (CNVs), 3 showed variants of unknown significance (VOUS), 1 displayed LOH, and 1 exhibited chromosome nine inversion. Notably, 18 cases (75%) theoretically detectable by karyotyping (eg, sizes above 10Mb) and 16 cases (66.7%) detectable by NIPT for five common aneuploidies were identified. Six submicroscopic findings (25%) were exclusively detectable by CMA. The predominant clinically relevant aberrations were observed in the thickened nuchal-translucency (TNT) group (9/35, 25.7%), followed by the multiple soft markers group (3/32, 9.3%). In the NIPT group, the false positive rate was 1.22%, and the false negative rate was 0%. Conclusion The prevalence of chromosome aneuploidy exceeded that of submicroscopic chromosomal imbalance in pregnant women with fetal USMs. NIPT demonstrated efficacy, particularly for soft markers like echogenic intracardiac focus. However, for those with TNT and multiple soft markers, invasive prenatal diagnosis, including CMA testing, is recommended as the primary investigative approach.
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Affiliation(s)
- Xianqing Hu
- Department of Obstetrics and Gynecology, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou People’s Hospital, Wenzhou Maternal and Child Health Care Hospital, Wenzhou, People’s Republic of China
| | - Yanjun Hu
- Department of Obstetrics and Gynecology, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou People’s Hospital, Wenzhou Maternal and Child Health Care Hospital, Wenzhou, People’s Republic of China
| | - Hai Wang
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou People’s Hospital, Wenzhou Maternal and Child Health Care Hospital, Wenzhou, People’s Republic of China
| | - Caicha Yu
- Department of Ultrasonography, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou People’s Hospital, Wenzhou Maternal and Child Health Care Hospital, Wenzhou, People’s Republic of China
| | - Jiayong Zheng
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou People’s Hospital, Wenzhou Maternal and Child Health Care Hospital, Wenzhou, People’s Republic of China
| | - Hongping Zhang
- Department of Obstetrics and Gynecology, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou People’s Hospital, Wenzhou Maternal and Child Health Care Hospital, Wenzhou, People’s Republic of China
| | - Jianqiong Zheng
- Department of Obstetrics and Gynecology, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou People’s Hospital, Wenzhou Maternal and Child Health Care Hospital, Wenzhou, People’s Republic of China
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Bussolaro S, Raymond YC, Acreman ML, Guido M, Da Silva Costa F, Rolnik DL, Fantasia I. The accuracy of prenatal cell-free DNA screening for sex chromosome abnormalities: A systematic review and meta-analysis. Am J Obstet Gynecol MFM 2023; 5:100844. [PMID: 36572107 DOI: 10.1016/j.ajogmf.2022.100844] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/26/2022] [Accepted: 12/20/2022] [Indexed: 12/26/2022]
Abstract
OBJECTIVE Although cell-free DNA screening for sex chromosome abnormalities is increasingly used in clinical practice, its diagnostic accuracy and clinical utility remain unclear. This systematic review and meta-analysis aimed to determine the performance of cell-free DNA in the detection of sex chromosome abnormalities. DATA SOURCES Medline and PubMed, Embase, and Web of Science were searched from inception to January 2022 for articles relating to cell-free DNA screening for sex chromosome abnormalities. STUDY ELIGIBILITY CRITERIA Original articles, randomized control trials, conference abstracts, cohort and case-control studies, and case series with more than 10 cases with diagnostic confirmation were considered for inclusion. METHODS Quality assessment of each included publication was performed using the Quality Assessment of Diagnostic Accuracy Studies 2 tool. The positive predictive value was calculated as the proportion of true positive cases among those who tested positive and underwent diagnostic testing. Sensitivity and specificity were pooled, and a summary receiver operating characteristic curve was produced using bivariate models that included studies that had diagnostic confirmation for high- and low-risk women. RESULTS The search identified 7553 results. Of these, 380 proceeded to the full-text screening, of which 94 articles were included in the meta-analysis with a total of 1,531,240 women tested. All studies reported a confirmatory genetic test. The pooled positive predictive value was 49.4% (95% confidence interval, 45.8-53.1). The pooled positive predictive value was 32.0% (95% confidence interval, 27.0%-37.3%) for monosomy X, 67.6% (95% confidence interval, 62.5%-72.5%) for XXY, 57.5% (95% confidence interval, 51.7%-63.1%) for XXX, and 70.9% (95% confidence interval, 63.9%-77.1%) for XYY. The pooled sensitivity and specificity of cell-free DNA for sex chromosome abnormalities were 94.1% (95% confidence interval, 90.8%-96.3%) and 99.5% (95% confidence interval, 99.0%-99.7%), respectively, with an area under the summary receiver operating characteristic curve of 0.934 (95% confidence interval, 0.907-0.989). CONCLUSION Although the sensitivity and specificity of cell-free DNA for sex chromosome abnormalities are high, the positive predictive value was approximately 50%. The positive predictive value was higher for sex chromosome abnormalities with a supernumerary Y chromosome and lower for monosomy X. Clinicians should inform couples about these findings when offering cell-free DNA for sex chromosome abnormalities.
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Affiliation(s)
- Sofia Bussolaro
- Department of Medicine, Surgery, and Health Sciences, University of Trieste, Trieste, Italy (Dr Bussolaro)
| | - Yvette C Raymond
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Australia (Ms Raymond and Dr Rolnik)
| | - Melissa L Acreman
- Department of Obstetrics and Gynaecology, Ipswich Hospital, Queensland, Australia (Dr Acreman)
| | - Maurizio Guido
- Obstetrics and Gynaecology Unit, San Salvatore Hospital, L'Aquila, Italy (XX Guido and Dr Fantasia); Department of Life, Health, and Environmental Sciences, University of L'Aquila, L'Aquila, Italy (XX Guido)
| | - Fabricio Da Silva Costa
- Maternal Fetal Medicine Unit, Gold Coast University Hospital, Gold Coast, Queensland, Australia (Dr Da Silva Costa); School of Medicine, Griffith University, Gold Coast, Queensland, Australia (Dr Da Silva Costa)
| | - Daniel L Rolnik
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Australia (Ms Raymond and Dr Rolnik); Monash Women's, Monash Health, Clayton, Australia (Dr Rolnik)
| | - Ilaria Fantasia
- Obstetrics and Gynaecology Unit, San Salvatore Hospital, L'Aquila, Italy (XX Guido and Dr Fantasia).
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