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Chen Y, Han X, Hua R, Li N, Zhang L, Hu W, Wang Y, Qian Z, Li S. Copy number variation sequencing for the products of conception: What is the optimal testing strategy. Clin Chim Acta 2024; 557:117884. [PMID: 38522821 DOI: 10.1016/j.cca.2024.117884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/01/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
BACKGROUND Copy number variation sequencing (CNV-seq) is crucial in prenatal diagnosis, but its limitations in detecting polyploidy, maternal cell contamination (MCC), and uniparental disomy (UPD) restrict its application in the analysis of products of conception (POCs). This study aimed to investigate an optimal genetic testing strategy for POCs in the era of CNV-seq. METHODS CNV-seq and quantitative fluorescent polymerase chain reaction (QF-PCR) were performed in all 4,211 spontaneous miscarriage cases. Different testing strategies were compared and the optimal testing strategies were proposed. RESULTS Of the 4,211 cases, 2561 (60.82%) exhibited clinically significant chromosomal abnormalities. CNV-seq alone, without QF-PCR, might misdiagnose 311 (7.39%) cases, including 278 polyploidy, 13 UPD, and 20 MCC. In 20 MCC cases identified by QF-PCR, CNV-seq successfully pinpointed the cause of miscarriage in 13 cases. Furthermore, in cases where QF-PCR suggested polyploidy, CNV-seq improved the diagnostic accuracy in 54 (1.28%) hypo/hypertriploidy cases. After comparing four different strategies, the sequential approach (initiating with CNV-seq followed by QF-PCR if necessary) emerged as advantageous, reducing approximately 70% of the cost associated with QF-PCR while maintaining result accuracy. CONCLUSIONS We propose an initial CNV-seq followed by QF-PCR if needed-an efficient and cost-effective strategy for the genetic analysis of POCs.
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Affiliation(s)
- Yiyao Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xu Han
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Renyi Hua
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Niu Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lanlan Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenjing Hu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanlin Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Zhida Qian
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Shuyuan Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Zhang J, Mu F, Guo Z, Cai Z, Zeng X, Du L, Wang F. Chromosome analysis of foetal tissue from 1903 spontaneous abortion patients in 5 regions of China: a retrospective multicentre study. BMC Pregnancy Childbirth 2023; 23:818. [PMID: 38007414 PMCID: PMC10675863 DOI: 10.1186/s12884-023-06108-0] [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: 08/09/2023] [Accepted: 11/04/2023] [Indexed: 11/27/2023] Open
Abstract
BACKGROUND Abnormal foetal tissue chromosome karyotypes are one of the important pathogenic factors for spontaneous abortion (SA). To investigate the age and abnormal foetal karyotypes of 1903 couples who experienced SA. METHODS A retrospective multicentre study collected age and foetal tissue karyotypes CNV-seq data of 1903 SA couples from 6 hospitals in 5 regions from January 2017 to March 2022. The distribution and correlation of abnormal foetal tissue karyotypes were evaluated by using regions and age. RESULTS In our study, 1140 couples (60.5% of the total) had abnormal foetal tissue chromosome karyotypes in all regions. We found that there were differences in the number of abnormal foetal tissue chromosome karyotypes, of which the incidence of trisomy was higher. At the same time, the populations situated in the eastern region had a more triploid (15.5%) distribution, trisomy (58.1%) in the southern region, mosaicism (14.8%) and microduplication (31.7%) in the southwestern region, microdeletion (16.7%) in the northern region. There are variances across areas, and it is more common in the north. The incidence risk of prenatal chromosomal abnormalities varied according to age group. CONCLUSION The findings of this study suggest that the karyotypes of patients with abnormal foetal tissue chromosome abortion in different regions were different. Meanwhile, patients ≥ 35 years old had a higher risk of abnormal foetal tissue chromosome abortion.
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Affiliation(s)
- Jian Zhang
- Department of Reproductive Medicine, Lanzhou University Second Hospital, Lanzhou, 730030, China
| | - Fangxiang Mu
- Department of Reproductive Medicine, Lanzhou University Second Hospital, Lanzhou, 730030, China
- Obstetrics Department, First Affiliated Hospital of Chongqing Medical University, Chongqing, 400042, China
| | - Zhongjie Guo
- Obstetrics Department, Third Hospital Affiliated to Guangdong Pharmaceutical University, Guangdong, 510410, China
| | - Zhuhua Cai
- Gynaecology Department, Rui'an People's Hospital, Wenzhou, 325207, China
| | - Xianghui Zeng
- Department of Reproductive Medicine, Lanzhou University Second Hospital, Lanzhou, 730030, China
- Department of Reproductive Medicine, Qinghai Provincial People's Hospital, Xining, 810007, China
| | - Lirong Du
- Eugenics Clinical Department, Hebei Reproductive Health Hospital, Shijiazhuang, 050090, China
| | - Fang Wang
- Department of Reproductive Medicine, Lanzhou University Second Hospital, Lanzhou, 730030, China.
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Chromosomal Copy Number Variation Analysis in Pregnancy Products from Recurrent and Sporadic Miscarriage Using Next-Generation Sequencing. Reprod Sci 2022; 29:2927-2936. [PMID: 35578104 DOI: 10.1007/s43032-022-00969-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/07/2022] [Indexed: 10/18/2022]
Abstract
Chromosomal abnormality is one of the causes of fetal miscarriage. The potential differences of fetal chromosomal abnormalities in sporadic miscarriage (SM) and recurrent miscarriage (RM) remain unclear. The purpose of this study was to investigate copy number variations (CNVs) in SM and RM to provide useful genetic guidance for pregnancy and prenatal diagnosis. Four hundred eight samples of aborted fetuses were analyzed by CNV sequencing, and further functional enrichment analysis was performed. Chromosomal abnormalities were identified in 218 (53.4%) fetuses. There were 62 cases (15.2%) with structural chromosomal abnormalities, including 41 with VUS CNVs, 8 with pathogenic CNVs (pCNVs), and 5 with likely pCNVs. Duplications or deletions of 7p22, 8p22, 8p23, and Xp22.31 were significantly more common in RM cases and therefore believed to be related to RM. A total of 289 genes were identified, and 29 different functions were enriched as potential RM candidate genes and functions, which were mainly concentrated in 4 functional categories: chemokines and chemotaxis, protease activity and protein modification, defense response to bacterial and fungal infections, and immune response. The results of this study may improve our understanding of the etiology of RM and contribute to the establishment of a population-based genetic marker information for RM.
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Zhang X, Huang Q, Yu Z, Wu H. Copy number variation characterization and possible candidate genes in miscarriage and stillbirth by next-generation sequencing analysis. J Gene Med 2021; 23:e3383. [PMID: 34342101 PMCID: PMC9285438 DOI: 10.1002/jgm.3383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/21/2021] [Accepted: 07/30/2021] [Indexed: 12/17/2022] Open
Abstract
Background The present study aimed to explore the etiological relationship between miscarriage and stillbirth and copy number variations (CNVs), as well as provide useful genetic guidance for high‐risk pregnancy. Methods In total, 659 fetal samples were recruited and subjected to DNA extraction and CNV sequencing (CNV‐seq), relevant medical records were collected. Results There were 322 cases (48.86%) with chromosomal abnormalities, including 230 with numerical abnormalities and 92 with structural abnormalities. Chromosomal monosomy variations mainly occurred on sex chromosomes and trisomy variations mainly occurred on chromosomes 16, 22, 21, 18, 13 and 15. In total, 41 pathogenic CNVs (23 microdeletions and 18 microduplications) were detected in 27 fetal tissues. The rates of numerical chromosomal abnormalities were 29.30% (109/372), 32.39% (57/176) and 57.66% (64/111) in < 30‐year‐old, 30–34‐year‐old and ≥ 35‐year‐old age pregnant women, respectively, and increased with an increasing age (p < 0.001). There was statistically significant difference (χ2 = 7.595, p = 0.022) in the rates of structural chromosomal abnormalities in these groups (13.71%, 18.75% and 7.21%, respectively). The rates of numerical chromosomal abnormalities were 45.44% (219/482), 7.80% (11/141) and 0% (0/36) in the ≤ 13 gestational weeks, 14–27 weeks and ≥ 28 weeks groups, respectively, and decreased with respect to the increasing gestational age of the fetuses (p < 0.001). Conclusions The present study has obtained useful and accurate genetic etiology information that will provide useful genetic guidance for high‐risk pregnancies.
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Affiliation(s)
- Xia Zhang
- Center for Prenatal Disgnosis, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Qingyan Huang
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Zhikang Yu
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Heming Wu
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
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