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Duan H, Wang W, Zhang Y, Chen X, Jiang Z, Li J. Accuracy of expanded noninvasive prenatal testing for maternal copy number variations: A comparative study with CNV-seq of maternal lymphocyte DNA. Taiwan J Obstet Gynecol 2024; 63:536-539. [PMID: 39004482 DOI: 10.1016/j.tjog.2024.02.006] [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] [Accepted: 02/20/2024] [Indexed: 07/16/2024] Open
Abstract
OBJECTIVE To evaluate the accuracy of expanded noninvasive prenatal testing (NIPT) for maternal copy number variations. MATERIALS AND METHODS Expanded NIPT was used to detect CNVs ≥2 Mb at a whole-genome scale. The threshold of maternal deletion was copy numbers (CN) ≤ 1.6, and the threshold of maternal duplication was CN ≥ 2.4. RESULTS Of the 5440 pregnant women with successful expanded NIPT results, 28 maternal CNVs ≥2 Mb were detected in 27 pregnant women. Except for five cases reported as test failure, 23 CNVs ≥2 Mb were confirmed among the remaining 22 pregnant women by CNV-seq of maternal lymphocyte DNA. The genomic location, copy numbers and fragment size of maternal CNVs reported by expanded NIPT were consistent with the results of CNV-seq of maternal lymphocyte DNA. CONCLUSIONS Maternal CNVs ≥2 Mb can be accurately evaluated according to the CN indicated by expanded NIPT results.
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Affiliation(s)
- Honglei Duan
- Center for Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Wanjun Wang
- Center for Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Ying Zhang
- Center for Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Xuemei Chen
- Center for Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Zihan Jiang
- Center for Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Jie Li
- Center for Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
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Gabrielli F, Papa FT, Di Pietro F, Paytuví-Gallart A, Julian D, Sanseverino W, Alfonsi C. MaterniCode: New Bioinformatic Pipeline to Detect Fetal Aneuploidies and Rearrangements Using Next-Generation Sequencing. Int J Genomics 2024; 2024:8859058. [PMID: 38962150 PMCID: PMC11221998 DOI: 10.1155/2024/8859058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 05/16/2024] [Accepted: 05/23/2024] [Indexed: 07/05/2024] Open
Abstract
Objective: The present study is aimed at introducing and evaluating MaterniCode, a state-of-the-art bioinformatic pipeline for noninvasive prenatal testing (NIPT) that leverages the Ion Torrent semiconductor sequencing platform. The initiative strives to revolutionize prenatal diagnostics by offering a rapid and cost-effective method without sacrificing accuracy. Methods: Two distinct bioinformatic strategies were employed for fetal sex determination, one of which achieved 100% accuracy. We analyzed 1225 maternal blood samples for fetal aneuploidies, benchmarking against the industry standard Illumina VeriSeq™ NIPT Solution v2. The capability of MaterniCode to detect and characterize complex chromosomal anomalies was also assessed. Results: MaterniCode achieved near-perfect accuracy in fetal sex determination through chromosome Y (chrY )-specific gene analysis, whereas the alternative method, employing the ratio of high-quality mapped reads on chrY relative to all reads, delivered 100% accuracy. For fetal aneuploidy detection, both the integrated WisecondorX and NIPTeR algorithms demonstrated a 100% sensitivity and specificity rate, consistent with Illumina VeriSeq™ NIPT Solution v2. The pipeline also successfully identified and precisely mapped significant chromosomal abnormalities, exemplified by a 2.4 Mb deletion on chromosome 13 and a 3 Mb duplication on chromosome 2. Conclusion: MaterniCode has proven to be an innovative and highly efficient tool in the domain of NIPT, demonstrating excellent sensitivity and specificity. Its robust capability to effectively detect a wide range of complex chromosomal aberrations, including rare and subtle variations, positions it as a promising and valuable addition to prenatal diagnostic technologies. This enhancement to diagnostic precision significantly aids clinicians in making informed decisions during pregnancy management.
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Affiliation(s)
- Federico Gabrielli
- Biolab srl, Laboratorio di Genetica molecolare e Genomica 63100, Ascoli Piceno, Italy
| | - Filomena Tiziana Papa
- Biolab srl, Laboratorio di Genetica molecolare e Genomica 63100, Ascoli Piceno, Italy
| | - Fabio Di Pietro
- Biolab srl, Laboratorio di Genetica molecolare e Genomica 63100, Ascoli Piceno, Italy
| | | | - Daniel Julian
- Sequentia Biotech SL, C/del Dr. Trueta, 179 08005, Barcelona, Spain
| | | | - Cinzia Alfonsi
- Biolab srl, Laboratorio di Genetica molecolare e Genomica 63100, Ascoli Piceno, Italy
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Xu Y, Lou J, Qian Y, Jin P, Qian Y, Hong J, Xu Y, Yin Y, Yi S, Dong M. Performance of noninvasive prenatal screening for fetal sex chromosome aneuploidies in a cohort of 116,862 pregnancies. Expert Rev Mol Diagn 2024; 24:467-472. [PMID: 38526221 DOI: 10.1080/14737159.2024.2333951] [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: 08/29/2023] [Accepted: 02/20/2024] [Indexed: 03/26/2024]
Abstract
BACKGROUND Noninvasive prenatal screening (NIPS) has shown good performance in screening common aneuploidies. However, its performance in detecting fetal sex chromosome aneuploidies (SCAs) needs to be evaluated in a large cohort. RESEARCH DESIGN AND METHODS In this retrospective observation, a total of 116,862 women underwent NIPS based on DNA nanoball sequencing from 2015 to 2022. SCAs were diagnosed based on karyotyping or chromosomal microarray analysis (CMA). Among them, 2,084 singleton pregnancies received karyotyping and/or CMA. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of NIPS for fetal SCAs were evaluated. RESULTS The sensitivity was 97.7% (95%CI, 87.7-99.9), 87.3% (95% CI, 76.5-94.4), 96.1% (95%CI, 86.5-99.5), and 95.7% (95% CI, 78.1-99.9), the PPV was 25.8% (95%CI, 19.2-33.2), 80.9% (95%CI, 69.5-89.4), 79.0% (95%CI, 66.8-88.3), and 53.7% (95%CI, 37.4-69.3) for 45,X, 47,XXY, 47,XXX, and 47,XYY, respectively. The specificity was 94.1% (95%CI, 93.0-95.1) for 45,X, and more than 99.0% for sex chromosome trisomy (SCT). The NPV was over 99.0% for all. CONCLUSIONS NIPS screening for fetal SCAs has high sensitivity, specificity and NPV. The PPV of SCAs was moderate, but that of 45,X was lower than that of SCTs. Invasive prenatal diagnosis should be recommended for high-risk patients.
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Affiliation(s)
- Yanfei Xu
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jianbo Lou
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Department of Obstetrics and Gynecology, Shaoxing Maternal and Child Health Care Hospital, Shaoxing, China
| | - Yeqing Qian
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Pengzhen Jin
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yangwen Qian
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiawei Hong
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yuqing Xu
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yixuan Yin
- Hangzhou Women's Hospital, Prenatal Diagnosis Center, Hangzhou, China
| | - Songjia Yi
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Minyue Dong
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
- Department of Reproductive Medicine, Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, China
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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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5
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Zhang J, Wu Y, Chen S, Luo Q, Xi H, Li J, Qin X, Peng Y, Ma N, Yang B, Qiu X, Lu W, Chen Y, Jiang Y, Chen P, Liu Y, Zhang C, Zhang Z, Xiong Y, Shen J, Liang H, Ren Y, Ying C, Dong M, Li X, Xu C, Wang H, Zhang D, Xu C, Huang H. Prospective prenatal cell-free DNA screening for genetic conditions of heterogenous etiologies. Nat Med 2024; 30:470-479. [PMID: 38253798 DOI: 10.1038/s41591-023-02774-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024]
Abstract
Prenatal cell-free DNA (cfDNA) screening uses extracellular fetal DNA circulating in the peripheral blood of pregnant women to detect prevalent fetal chromosomal anomalies. However, numerous severe conditions with underlying single-gene defects are not included in current prenatal cfDNA screening. In this prospective, multicenter and observational study, pregnant women at elevated risk for fetal genetic conditions were enrolled for a cfDNA screening test based on coordinative allele-aware target enrichment sequencing. This test encompasses the following three of the most frequent pathogenic genetic variations: aneuploidies, microdeletions and monogenic variants. The cfDNA screening results were compared to invasive prenatal or postnatal diagnostic test results for 1,090 qualified participants. The comprehensive cfDNA screening detected a genetic alteration in 135 pregnancies with 98.5% sensitivity and 99.3% specificity relative to standard diagnostics. Of 876 fetuses with suspected structural anomalies on ultrasound examination, comprehensive cfDNA screening identified 55 (56.1%) aneuploidies, 6 (6.1%) microdeletions and 37 (37.8%) single-gene pathogenic variants. The inclusion of targeted monogenic conditions alongside chromosomal aberrations led to a 60.7% increase (from 61 to 98) in the detection rate. Overall, these data provide preliminary evidence that a comprehensive cfDNA screening test can accurately identify fetal pathogenic variants at both the chromosome and single-gene levels in high-risk pregnancies through a noninvasive approach, which has the potential to improve prenatal evaluation of fetal risks for severe genetic conditions arising from heterogenous molecular etiologies. ClinicalTrials.gov registration: ChiCTR2100045739 .
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Affiliation(s)
- Jinglan Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Beijing BioBiggen Technology Co., Ltd, Beijing, China.
| | - Yanting Wu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Songchang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Qiong Luo
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Hui Xi
- National Health Commission (NHC) Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Jianli Li
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiaomei Qin
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Ying Peng
- National Health Commission (NHC) Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Na Ma
- National Health Commission (NHC) Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Bingxin Yang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Qiu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Weiliang Lu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yuan Chen
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Jiang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Panpan Chen
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Yifeng Liu
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Chen Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Zhiwei Zhang
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Yu Xiong
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Jie Shen
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Huan Liang
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yunyun Ren
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chunmei Ying
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Minyue Dong
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaotian Li
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Congjian Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Hua Wang
- National Health Commission (NHC) Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China.
- NHC Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China.
| | - Dan Zhang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China.
| | - Chenming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China.
| | - Hefeng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China.
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China.
- Shanghai Frontiers Science Research Center of Reproduction and Development, Shanghai, China.
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6
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Ma L, Li Y, Li L, Wu H, Liu Y, Yang X, Lin A. A high Z-score might increase the positive predictive value of cell-free noninvasive prenatal testing for singleton-pregnant women. J Matern Fetal Neonatal Med 2023; 36:2233662. [PMID: 37433666 DOI: 10.1080/14767058.2023.2233662] [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: 03/09/2023] [Revised: 05/19/2023] [Accepted: 07/01/2023] [Indexed: 07/13/2023]
Abstract
OBJECTIVE To explore the positive predictive value (PPV) in noninvasive prenatal testing (NIPT)-positive cases and analyze the effect of the Z-score intervals on PPV performance. METHODS In this retrospective study, 26,667 pregnant women underwent NIPT from November 2014 to August 2022, of which 169 were NIPT-positive cases. NIPT-positive cases were divided into three groups according to the Z-score: 3 ≤ Z < 6, 6 ≤ Z < 10, and Z ≥ 10. RESULTS The PPVs of NIPT were 91.26% (94/103) for trisomy (T) 21, 80.65% (25/31) for T18, and 36.84% (7/19) for T13. The PPVs for the 3 ≤ Z < 6, 6 ≤ Z < 10, and Z ≥ 10 groups were 50%, 84.62%, and 87.95%, respectively. A higher PPV was found in the NIPT results when the Z-score was larger, with significant differences. The PPVs for T21/T18/T13 were 71.43%/42.86%/25% for 3 ≤ Z < 6, 90.32%/85.71%/57.14% for 6 ≤ Z < 10, and 93.85%/100%/25% for Z ≥ 10. For T21, T18, and T13, the correlations between the Z-score and fetal fraction concentration in true positives were r = 0.85, r = 0.59, and r = 0.71 (all p < .001), respectively. CONCLUSION Z-score is associated with the PPV performance of NIPT in fetal T13, T18, and T21. The possibility of false positives caused by placental chimerism should be considered when determining whether high Z-values lead to high PPVs.
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Affiliation(s)
- Li Ma
- Center for Laboratory Diagnosis, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
| | - Yulan Li
- Center for Laboratory Diagnosis, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
| | - Lei Li
- Department of Obstetrics, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
| | - Hong Wu
- Center for Laboratory Diagnosis, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
| | - Yongming Liu
- Center for Laboratory Diagnosis, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
| | - Xin Yang
- Center for Laboratory Diagnosis, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
| | - Aimin Lin
- Department of Gynaecology, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
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7
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Norton ME. Cell-free DNA Screening for Aneuploidy. Clin Obstet Gynecol 2023; 66:557-567. [PMID: 37650668 DOI: 10.1097/grf.0000000000000796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Cell-free DNA (cfDNA) screening has high detection for the common fetal autosomal aneuploidies, but is not diagnostic. The positive predictive value should be utilized in counseling after a positive cell-free DNA screen, and diagnostic testing should be offered for confirmation. cfDNA screening does not report a result in ~3% of cases; nonreportable results indicate an increased risk for aneuploidy and some adverse perinatal outcomes. False-positive cfDNA screening occurs due to confined placental mosaicism, maternal copy number variants, mosaicism, and cancer. Pretest education and counseling should be provided with emphasis on the potential benefits, risks, and limitations before cfDNA screening.
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Affiliation(s)
- Mary E Norton
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California
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8
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Cai M, Lin N, Chen X, Li Y, Lin M, Fu X, Huang H, He S, Xu L. Non-invasive prenatal testing for the diagnosis of congenital abnormalities: Insights from a large multicenter study in southern China. Braz J Med Biol Res 2023; 56:e12506. [PMID: 37377305 DOI: 10.1590/1414-431x2023e12506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/04/2023] [Indexed: 06/29/2023] Open
Abstract
Although non-invasive prenatal testing (NIPT) is widely used to detect fetal abnormalities, the results of NIPT vary by population, and data for the screening efficiency of NIPT positive predictive value (PPV) from different populations is limited. Herein, we retrospectively analyzed the NIPT results in a large multicenter study involving 52,855 pregnant women. Depending on gestational age, amniotic fluid or umbilical cord blood was extracted for karyotype and/or chromosome microarray analysis (CMA) in NIPT-positive patients, and the PPV and follow-up data were evaluated to determine its clinical value. Among the 52,855 cases, 754 were NIPT-positive, with a positivity rate of 1.4%. Karyotype analysis and/or CMA confirmed 323 chromosomal abnormalities, with a PPV of 45.1%. PPV for trisomy 21 (T21), trisomy 18 (T18), trisomy 13 (T13), sex chromosomal aneuploidies (SCAs), and copy number variations (CNVs) were 78.9, 35.3, 22.2, 36.9, and 32.9%, respectively. The PPVs for T21, T18, and T13 increased with age, whereas the PPVs for SCAs and CNVs had little correlation with age. The PPV was significantly higher in patients with advanced age and abnormal ultrasound. The NIPT results are affected by population characteristics. NIPT had a high PPV for T21 and a low PPV for T13 and T18, and screening for SCAs and CNVs showed clinical significance in southern China.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Ying Li
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Min Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xianguo Fu
- Department of Prenatal Diagnosis, Ningde Municipal Hospital, Ningde Normal University, Ningde, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Shuqiong He
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
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Haggerty A, Spaulding J, Fisher S, Byers B, Mahoney N, Nelson M, Althof P, Dave B. Patient with Mosaic Turner Syndrome and a Derivative X Chromosome with a Variant Triple X Diagnosis in Fetus: A Case Report. Cytogenet Genome Res 2023; 162:609-616. [PMID: 36787703 DOI: 10.1159/000529619] [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: 08/05/2022] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
Although Turner syndrome is most often sporadic, multigenerational recurrence has been reported more often in the offspring of women with mosaic or variant forms of Turner syndrome. We present a case in which natural conception in a woman with identified 45,X/46,XX mosaicism resulted in a fetus with a gain of a derivative X chromosome. The unexpected fetal finding prompted further cytogenetic evaluation of the patient and subsequent identification of an additional cell line with the same derivative X chromosome, not observed in the initial study. To our knowledge, this is the first case in which further investigation of an abnormal noninvasive prenatal screen resulted in the identification of both maternal and fetal sex chromosome abnormality. We discuss the discordant finding, similar cases, and potential phenotype with respect to skewed X inactivation. We also highlight the use of multiple testing methodologies to characterize the serendipitous identification of a derivative X chromosome.
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Affiliation(s)
- Abigail Haggerty
- Warren G. Sanger Human Genetics Laboratory, University of Nebraska Medical Center/Nebraska Medicine, Omaha, Nebraska, USA,
| | - Joanna Spaulding
- Warren G. Sanger Human Genetics Laboratory, University of Nebraska Medical Center/Nebraska Medicine, Omaha, Nebraska, USA
- Department of Genetic Medicine, Munroe Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Sara Fisher
- Department of Medical Sciences, College of Allied Health Professions, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Benjamin Byers
- Department of Obstetrics and Gynecology, Bryan Health, Lincoln, Nebraska, USA
| | - Nicolle Mahoney
- Gynecology & Fertility, Gynecology & Fertility P.C., Lincoln, Nebraska, USA
| | - Marilu Nelson
- Warren G. Sanger Human Genetics Laboratory, University of Nebraska Medical Center/Nebraska Medicine, Omaha, Nebraska, USA
| | - Pamela Althof
- Warren G. Sanger Human Genetics Laboratory, University of Nebraska Medical Center/Nebraska Medicine, Omaha, Nebraska, USA
| | - Bhavana Dave
- Warren G. Sanger Human Genetics Laboratory, University of Nebraska Medical Center/Nebraska Medicine, Omaha, Nebraska, USA
- Department of Genetic Medicine, Munroe Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, USA
- Department of Pathology/Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
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10
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Tian M, Feng L, Li J, Zhang R. Focus on the frontier issue: progress in noninvasive prenatal screening for fetal trisomy from clinical perspectives. Crit Rev Clin Lab Sci 2023; 60:248-269. [PMID: 36647189 DOI: 10.1080/10408363.2022.2162843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The discovery of cell-free fetal DNA (cffDNA) in maternal blood and the rapid development of massively parallel sequencing have revolutionized prenatal testing from invasive to noninvasive. Noninvasive prenatal screening (NIPS) based on cffDNA enables the detection of fetal trisomy through sequencing, comparison, and bioassays. Its accuracy is better than that of traditional screening methods, and it is the most advanced clinical application of high-throughput sequencing technologies. However, the existing sequencing methods are limited by high costs and complex sequencing procedures. These limitations restrict the availability of NIPS for pregnant women. Many amplification methods have been developed to overcome the limitations of sequencing methods. The rapid development of non-sequencing methods has not been accompanied by reviews to summarize them. In this review, we initially describe the detection principles for sequencing-based NIPS. We summarize the rapidly evolving amplification technologies, focusing on the need to reduce costs and simplify the procedures. To ensure that the testing systems are feasible and that the testing processes are reliable, we expand our vision to the clinic. We evaluate the clinical validity of NIPS in terms of sensitivity, specificity, and positive predictive value. Finally, we summarize the application guidelines and discuss the corresponding quality control methods for NIPS. In addition to cffDNA, extracellular vesicle DNA, RNA, protein/peptide, and fetal cells can also be detected as biomarkers of NIPS. With the development of prenatal testing, NIPS has become increasingly important. Notably, NIPS is a screening test instead of a diagnostic test. The testing methods and procedures used in the NIPS process require standardization.
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Affiliation(s)
- Meng Tian
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Peking University Fifth School of Clinical Medicine, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Lei Feng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Peking University Fifth School of Clinical Medicine, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Peking University Fifth School of Clinical Medicine, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China
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11
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Xiang L, Zhu J, Deng K, Li Q, Tao J, Li M, Wang Y, Yuan X, Yao Y, Li X. Non-invasive prenatal testing for the detection of trisomies 21, 18, and 13 in pregnant women with various clinical indications: A multicenter observational study of 1,854,148 women in China. Prenat Diagn 2023. [PMID: 36639250 DOI: 10.1002/pd.6312] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/29/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
OBJECTIVE This study aimed to evaluate the performance of noninvasive prenatal testing (NIPT) for detecting three common trisomies (T21, T18, and T13) in pregnant women with diverse clinical indications. METHODS Frequencies of NIPT, of high chance of having one of the three trisomies, and of confirmed trisomies were determined for women with each of seven clinical indications in a national cross-sectional survey of approximately 300 prenatal diagnosis centers. Data were collected for the period from October 1, 2016 to September 30, 2018 using the Prenatal Diagnosis Technology Management On-line Information System. The performance of NIPT for detecting the three trisomies in pregnant women with different clinical indications was assessed in terms of sensitivity, specificity, positive predictive value (PPV), negative predictive value, and the corresponding 95% confidence intervals. RESULTS A total of 5766 true positive cases for T21, T18, and T13 were detected among 1,854,148 samples, giving an overall detection rate of 0.31% (95% CI: 0.30%-0.32%). Most positive cases were associated with "NT thickening" (1.18%) and "advanced maternal age" (0.51%). The detection sensitivities of NIPT were 99.60% for T21, 99.14% for T18, and 100% for T13, while the corresponding specificities were 99.90%, 99.94%, and 99.95%. The corresponding PPVs were 69.77%, 47.24%, and 22.36%. NIPT showed high sensitivity and specificity, regardless of clinical indication. In contrast, PPV for three trisomies varied widely between 9.09% and 66.46% depending on the clinical indication. Across seven clinical indications, PPV ranged from 50.62% to 73.09% for T21, 20.00%-58.33% for T18, and 4.17%-47.37% for T13. The highest PPVs were 73.09% for T21 in pregnancies involving "advanced maternal age", 58.33% for T18 in pregnancies with "NT thickening", and 47.37% for T13 in pregnancies with "NT thickening". CONCLUSIONS NIPT shows high sensitivity and specificity for detecting T21, T18, and T13 in pregnant women with different clinical indications. However, PPV depends strongly on clinical indication, highlighting the need to strengthen education and genetic counseling about prenatal screening.
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Affiliation(s)
- Liangcheng Xiang
- National Office for Maternal and Child Health Surveillance of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jun Zhu
- National Center for Birth Defect Monitoring of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Kui Deng
- National Office for Maternal and Child Health Surveillance of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Qi Li
- National Office for Maternal and Child Health Surveillance of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jing Tao
- National Office for Maternal and Child Health Surveillance of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mingrong Li
- National Office for Maternal and Child Health Surveillance of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yanping Wang
- National Center for Birth Defect Monitoring of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xuelian Yuan
- National Office for Maternal and Child Health Surveillance of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yongna Yao
- National Center for Birth Defect Monitoring of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiaohong Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China.,Sichuan Birth Defects Clinical Research Center, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
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12
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Xue H, Yu A, Lin M, Chen X, Guo Q, Xu L, Huang H. Efficiency of expanded noninvasive prenatal testing in the detection of fetal subchromosomal microdeletion and microduplication in a cohort of 31,256 single pregnancies. Sci Rep 2022; 12:19750. [PMID: 36396840 PMCID: PMC9672043 DOI: 10.1038/s41598-022-24337-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
Noninvasive prenatal testing (NIPT) is widely used to screen for common fetal chromosomal aneuploidies. However, the ability of NIPT-Plus to detect copy number variation (CNV) is debatable. Accordingly, we assessed the efficiency of NIPT-Plus to detect clinically significant fetal CNV. We performed a prospective analysis of 31,260 singleton pregnancies, included from June 2017 to December 2020. Cell-free fetal DNA was directly sequenced using the semiconductor sequencing platform for women with high-risk CNV with clinically significant results. Fetal karyotyping and chromosomal microarray analysis (or next-generation sequencing) are recommended for invasive diagnostic procedures. Women at low risk with no other abnormal results continued their pregnancies. We analyzed the expanded NIPT results, diagnostic test results, and follow-up information to evaluate its performance in detecting fetal CNV. Of the 31,260 pregnant women who received NIPT-Plus, 31,256 cases were tested successfully, a high risk of clinically significant CNV was detected in 221 cases (0.71%); 18 women refused further diagnosis; 203 women underwent invasive prenatal diagnosis; and 78 true positive cases and 125 false positive cases, with an overall positive predictive value (PPV) of 38.42% and a false positive rate of 0.40%. For known microdeletion/microduplication syndromes (n = 27), the PPVs were 75% DiGeorge syndrome (DGS), 80% 22q11.22 microduplication, 50% Prader-Willi syndrome, and 50% cri-du-chat. For the remaining clinically significant fetal CNVs (n = 175), the combined PPVs were 46.5% (CNVs > 10 Mb) and 28.57% (CNVs ≤ 10 Mb). NIPT-Plus screening for CNV has certain clinical value. NIPT-Plus yielded relatively high PPVs for 22q11.2 microduplication syndrome and DGS, and low to moderate PPVs for other CNVs.
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Affiliation(s)
- Huili Xue
- grid.256112.30000 0004 1797 9307Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| | - Aili Yu
- grid.256112.30000 0004 1797 9307Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| | - Min Lin
- grid.256112.30000 0004 1797 9307Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| | - Xuemei Chen
- grid.256112.30000 0004 1797 9307Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| | - Qun Guo
- grid.256112.30000 0004 1797 9307Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| | - Liangpu Xu
- grid.256112.30000 0004 1797 9307Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| | - Hailong Huang
- grid.256112.30000 0004 1797 9307Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
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13
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Xu C, Li J, Chen S, Cai X, Jing R, Qin X, Pan D, Zhao X, Ma D, Xu X, Liu X, Wang C, Yang B, Zhang L, Li S, Chen Y, Pan N, Tang P, Song J, Liu N, Zhang C, Zhang Z, Qiu X, Lu W, Ying C, Li X, Xu C, Wang Y, Wu Y, Huang HF, Zhang J. Genetic deconvolution of fetal and maternal cell-free DNA in maternal plasma enables next-generation non-invasive prenatal screening. Cell Discov 2022; 8:109. [PMID: 36229437 PMCID: PMC9562363 DOI: 10.1038/s41421-022-00457-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/09/2022] [Indexed: 11/09/2022] Open
Abstract
Current non-invasive prenatal screening (NIPS) analyzes circulating fetal cell-free DNA (cfDNA) in maternal peripheral blood for selected aneuploidies or microdeletion/duplication syndromes. Many genetic disorders are refractory to NIPS largely because the maternal genetic material constitutes most of the total cfDNA present in the maternal plasma, which hinders the detection of fetus-specific genetic variants. Here, we developed an innovative sequencing method, termed coordinative allele-aware target enrichment sequencing (COATE-seq), followed by multidimensional genomic analyses of sequencing read depth, allelic fraction, and linked single nucleotide polymorphisms, to accurately separate the fetal genome from the maternal background. Analytical confounders including multiple gestations, maternal copy number variations, and absence of heterozygosity were successfully recognized and precluded for fetal variant analyses. In addition, fetus-specific genomic characteristics, including the cfDNA fragment length, meiotic error origins, meiotic recombination, and recombination breakpoints were identified which reinforced the fetal variant assessment. In 1129 qualified pregnancies tested, 54 fetal aneuploidies, 8 microdeletions/microduplications, and 8 monogenic variants were detected with 100% sensitivity and 99.3% specificity. Using the comprehensive cfDNA genomic analysis tools developed, we found that 60.3% of aneuploidy samples had aberrant meiotic recombination providing important insights into the mechanism underlying meiotic nondisjunctions. Altogether, we show that the genetic deconvolution of the fetal and maternal cfDNA enables thorough and accurate delineation of fetal genome which paves the way for the next-generation prenatal screening of essentially all types of human genetic disorders.
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Affiliation(s)
- Chenming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Jianli Li
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Songchang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaoqiang Cai
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Ruilin Jing
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiaomei Qin
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Dong Pan
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xin Zhao
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Dongyang Ma
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiufeng Xu
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiaojun Liu
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Can Wang
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Bingxin Yang
- International Peace Maternity and Child Health Hospital, 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
| | - Shuyuan Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yiyao Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Nina Pan
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Tang
- Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang, China
| | - Jieping Song
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Nian Liu
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Chen Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiwei Zhang
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiang Qiu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Weiliang Lu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chunmei Ying
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xiaotian Li
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Congjian Xu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yanlin Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanting Wu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.
| | - He-Feng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,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. .,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China.
| | - Jinglan Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,Beijing BioBiggen Technology Co., Ltd, Beijing, China.
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14
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Moellgaard MH, Lund ICB, Becher N, Skytte A, Andreasen L, Srebniak MI, Vogel I. Incidental finding of maternal malignancy in an unusual non-invasive prenatal test and a review of similar cases. Clin Case Rep 2022; 10:e6280. [PMID: 36245448 PMCID: PMC9552546 DOI: 10.1002/ccr3.6280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/07/2022] [Indexed: 11/11/2022] Open
Abstract
We present a clinical case where a complex abnormal non‐invasive prenatal test (NIPT) result in a research project revealed carcinoma of the breast in the pregnant woman. Furthermore, the NIPT result did not demonstrate the same fetal chromosomal aberration as the chorion villus sample. A literature search for similar cases was performed identifying 43 unique cases, where abnormal NIPT results were related to maternal malignancy. Malignancy is a rare but important cause of complex abnormal non‐invasive prenatal test (NIPT) results and should be considered when fetal karyotype and abnormal NIPT results are discordant. Furthermore, a follow‐up invasive sample is essential for correct fetal diagnosis when abnormal NIPT results are found.
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Affiliation(s)
| | - Ida Charlotte Bay Lund
- Center for Fetal diagnosticsAarhus University/Aarhus University HospitalAarhusDenmark,Department of Clinical GeneticsAarhus University/Aarhus University HospitalAarhusDenmark
| | - Naja Becher
- Department of Clinical GeneticsAarhus University/Aarhus University HospitalAarhusDenmark
| | - Anne‐Bine Skytte
- Department of Clinical GeneticsAarhus University/Aarhus University HospitalAarhusDenmark,Cryos InternationalAarhusDenmark
| | - Lotte Andreasen
- Department of Clinical GeneticsAarhus University/Aarhus University HospitalAarhusDenmark
| | | | - Ida Vogel
- Center for Fetal diagnosticsAarhus University/Aarhus University HospitalAarhusDenmark,Department of Clinical GeneticsAarhus University/Aarhus University HospitalAarhusDenmark
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15
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Li J, Lu J, Su F, Yang J, Ju J, Lin Y, Xu J, Qi Y, Hou Y, Wu J, He W, Yang Z, Wu Y, Tang Z, Huang Y, Zhang G, Yang Y, Long Z, Cheng X, Liu P, Xia J, Zhang Y, Wang Y, Chen F, Zhang J, Zhao L, Jin X, Gao Y, Yin A. Non-Invasive Prenatal Diagnosis of Monogenic Disorders Through Bayesian- and Haplotype-Based Prediction of Fetal Genotype. Front Genet 2022; 13:911369. [PMID: 35846127 PMCID: PMC9283829 DOI: 10.3389/fgene.2022.911369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 06/13/2022] [Indexed: 12/02/2022] Open
Abstract
Background: Non-invasive prenatal diagnosis (NIPD) can identify monogenic diseases early during pregnancy with negligible risk to fetus or mother, but the haplotyping methods involved sometimes cannot infer parental inheritance at heterozygous maternal or paternal loci or at loci for which haplotype or genome phasing data are missing. This study was performed to establish a method that can effectively recover the whole fetal genome using maternal plasma cell-free DNA (cfDNA) and parental genomic DNA sequencing data, and validate the method’s effectiveness in noninvasively detecting single nucleotide variations (SNVs), insertions and deletions (indels). Methods: A Bayesian model was developed to determine fetal genotypes using the plasma cfDNA and parental genomic DNA from five couples of healthy pregnancy. The Bayesian model was further integrated with a haplotype-based method to improve the inference accuracy of fetal genome and prediction outcomes of fetal genotypes. Five pregnancies with high risks of monogenic diseases were used to validate the effectiveness of this haplotype-assisted Bayesian approach for noninvasively detecting indels and pathogenic SNVs in fetus. Results: Analysis of healthy fetuses led to the following accuracies of prediction: maternal homozygous and paternal heterozygous loci, 96.2 ± 5.8%; maternal heterozygous and paternal homozygous loci, 96.2 ± 1.4%; and maternal heterozygous and paternal heterozygous loci, 87.2 ± 4.7%. The respective accuracies of predicting insertions and deletions at these types of loci were 94.6 ± 1.9%, 80.2 ± 4.3%, and 79.3 ± 3.3%. This approach detected pathogenic single nucleotide variations and deletions with an accuracy of 87.5% in five fetuses with monogenic diseases. Conclusions: This approach was more accurate than methods based only on Bayesian inference. Our method may pave the way to accurate and reliable NIPD.
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Affiliation(s)
- Jia Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Shijiazhuang BGI Genomics, Shijiazhuang, China
| | - Jiaqi Lu
- Medical Genetics Centre, Guangdong Women and Children’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Fengxia Su
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
| | - Jiexia Yang
- Prenatal Diagnosis Centre, Guangdong Women and Children’s Hospital, Guangzhou, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children’s Hospital, Guangzhou, China
| | - Jia Ju
- BGI-Shenzhen, Shenzhen, China
| | - Yu Lin
- BGI-Shenzhen, Shenzhen, China
| | | | - Yiming Qi
- Prenatal Diagnosis Centre, Guangdong Women and Children’s Hospital, Guangzhou, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children’s Hospital, Guangzhou, China
| | - Yaping Hou
- Prenatal Diagnosis Centre, Guangdong Women and Children’s Hospital, Guangzhou, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children’s Hospital, Guangzhou, China
| | - Jing Wu
- Prenatal Diagnosis Centre, Guangdong Women and Children’s Hospital, Guangzhou, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children’s Hospital, Guangzhou, China
| | - Wei He
- Prenatal Diagnosis Centre, Guangdong Women and Children’s Hospital, Guangzhou, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children’s Hospital, Guangzhou, China
| | - Zhengtao Yang
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Yujing Wu
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
| | - Zhuangyuan Tang
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
| | - Yingping Huang
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
| | - Guohong Zhang
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
| | - Ying Yang
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
| | | | | | | | - Jun Xia
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | - Jianguo Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Shijiazhuang BGI Genomics, Shijiazhuang, China
| | - Lijian Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Shijiazhuang BGI Genomics, Shijiazhuang, China
- College of Medical Technology, Hebei Medical University, Shijiazhuang, China
- *Correspondence: Lijian Zhao, ; Xin Jin, ; Ya Gao, ; Aihua Yin,
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, China
- *Correspondence: Lijian Zhao, ; Xin Jin, ; Ya Gao, ; Aihua Yin,
| | - Ya Gao
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
- *Correspondence: Lijian Zhao, ; Xin Jin, ; Ya Gao, ; Aihua Yin,
| | - Aihua Yin
- Prenatal Diagnosis Centre, Guangdong Women and Children’s Hospital, Guangzhou, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children’s Hospital, Guangzhou, China
- *Correspondence: Lijian Zhao, ; Xin Jin, ; Ya Gao, ; Aihua Yin,
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16
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Chen L, Wang L, Hu Z, Tao Y, Song W, An Y, Li X. Combining Z-Score and Maternal Copy Number Variation Analysis Increases the Positive Rate and Accuracy in Non-Invasive Prenatal Testing. Front Genet 2022; 13:887176. [PMID: 35719402 PMCID: PMC9201951 DOI: 10.3389/fgene.2022.887176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: To evaluate positive rate and accuracy of non-invasive prenatal testing (NIPT) combining Z-score and maternal copy number variation (CNV) analysis. To assess the relationship between Z-score and positive predictive value (PPV). Methods: This prospective study included 61525 pregnancies to determine the correlation between Z-scores and PPV in NIPT, and 3184 pregnancies to perform maternal CNVs analysis. Positive results of NIPT were verified by prenatal diagnosis and/or following-up after birth. Z-score grouping, logistic regression analysis, receiver operating characteristic (ROC) curves, and S-curve trends were applied to correlation analysis of Z-scores and PPV. The maternal CNVs were classified according to the technical standard for the interpretation of ACMG. Through genetic counseling, fetal and maternal phenotypes and family histories were collected. Results: Of the 3184 pregnant women, 22 pregnancies were positive for outlier Z-scores, suggesting fetal aneuploidy. 12 out of 22 pregnancies were true positive (PPV = 54.5%). 17 pregnancies were found maternal pathogenic or likely pathogenic CNVs (> 0.5 Mb) through maternal CNV analysis. Prenatal diagnosis revealed that 7 out of 11 fetuses carried the same CNVs as the mother. Considering the abnormal biochemical indicators during pregnancy and CNV-related clinical phenotypes after birth, two male fetuses without prenatal diagnosis were suspected to carry the maternally-derived CNVs. Further, we identified three CNV-related family histories with variable phenotypes. Statistical analysis of the 61525 pregnancies revealed that Z-scores of chromosomes 21 and 18 were significantly associated with PPV at 3 ≤ Z ≤ 40. Notably, three pregnancies with Z > 40 were both maternal full aneuploidy. At Z < -3, fetuses carried microdeletions instead of monosomies. Sex chromosome trisomy was significantly higher PPV than monosomy. Conclusion: The positive rate of the NIPT screening model combining Z-score and maternal CNV analysis increased from 6.91‰ (22/3184) to 12.25‰ (39/3184) and true positives increased from 12 to 21 pregnancies. We found that this method could improve the positive rate and accuracy of NIPT for aneuploidies and CNVs without increasing testing costs. It provides an early warning for the inheritance of pathogenic CNVs to the next generation.
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Affiliation(s)
- Liheng Chen
- Department of Medical Genetics, Changzhi Maternal and Child Health Care Hospital, Changzhi, China
- School of Life Sciences, Fudan University, Shanghai, China
| | - Lihong Wang
- Department of Pediatrics, Changzhi Maternal and Child Health Care Hospital, Changzhi, China
| | - Zhipeng Hu
- Department of Medical Genetics, Changzhi Maternal and Child Health Care Hospital, Changzhi, China
| | - Yilun Tao
- Department of Medical Genetics, Changzhi Maternal and Child Health Care Hospital, Changzhi, China
| | - Wenxia Song
- Obstetrics Department, Changzhi Maternal and Child Health Care Hospital, Changzhi, China
| | - Yu An
- School of Life Sciences, Fudan University, Shanghai, China
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China
| | - Xiaoze Li
- Department of Medical Genetics, Changzhi Maternal and Child Health Care Hospital, Changzhi, China
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17
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Chen CP, Chen SW, Wu PS, Wu FT, Wang W. A false-positive result at non-invasive prenatal testing due to maternal 17p12 microduplication. Taiwan J Obstet Gynecol 2022; 61:532-534. [PMID: 35595453 DOI: 10.1016/j.tjog.2022.03.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2022] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVE We present a false-positive result at non-invasive prenatal testing (NIPT) due to maternal 17p12 microduplication. CASE REPORT A 37-year-old, gravida 2, para 1, woman underwent amniocentesis at 19 weeks of gestation because of advanced maternal age. Amniocentesis revealed a karyotype of 46,XY. Simultaneous array comparative genomic hybridization (aCGH) revealed the result of a 1.3-Mb duplication of 17p12 or arr [GRCh37] 17p12 (14,111,772-15,442,066) × 3 encompassing four Online Mendelian Inheritance in Man (OMIM) genes of COX10, HS3ST3B1, PMP22 and TEKT3. The mother did not have any neurologic problems. The parents were phenotypically normal. aCGH analysis of maternal blood revealed that the mother carried the same 17p12 microduplication. Two years ago, NIPT analysis during her first pregnancy revealed abnormality of chromosome 17 with 17p11.2p12 duplication. However, subsequent aCGH analysis at amniocentesis revealed no genomic imbalance in the fetus, and no further examination of the parental bloods was made. During this pregnancy, prenatal ultrasound was unremarkable, and the parents decided to continue the pregnancy. CONCLUSION A false-positive result at NIPT should raise a suspicion of maternal genomic imbalance.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan
| | | | - Fang-Tzu Wu
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
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18
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Lyu Z, Huang C. Systematic analysis of the causes of NIPS sex chromosome aneuploidy false-positive results. Mol Genet Genomic Med 2022; 10:e1963. [PMID: 35535634 PMCID: PMC9266605 DOI: 10.1002/mgg3.1963] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 04/01/2022] [Accepted: 04/18/2022] [Indexed: 11/11/2022] Open
Abstract
OBJECTIVE To investigate the underlying causes of false positives in NIPT of fetal sex chromosomal aneuploidies using fetal cell-free DNA from maternal plasma. METHODS In the present study, we focus on a cohort of 23,984 pregnancy cases with NIPT. Karyotyping and FISH analysis were employed to verify the NIPT detected false-positive results of fetal sex chromosomal aneuploidies, and a comparative CNV sequencing on positive and negative NIPT cases was uniquely performed to elucidate the underlying causes. RESULTS A total of 166 cases (0.69%) were identified as fetal sex chromosomal abnormalities, while 84 cases were found to be false-positive results possibly associated with maternal X chromosomal aneuploidies (n = 8), maternal X chromosomal structural abnormalities (n = 1), maternal CNVs (n = 4) as well as known placental mosaicism (n = 1). Furthermore, our study showed that the maternal chromosome CNV between 1-1.6 Mb was associated with false-positive NIPT results in sex chromosomal abnormalities. CONCLUSION Our research demonstrated the spectrum of factors causing false positives in NIPT of fetal sex chromosomal abnormalities based on a large cohort. The effective maternal CNV size cut-off identified in our study could integrate into bioinformatics algorithms for reducing the false-positive rate, however, further investigation is necessary to confirm this.
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Affiliation(s)
- Zhaoru Lyu
- Queen Mary College, Nanchang University, Nanchang, China
| | - Chunhong Huang
- School of Basic Medical Sciences, Nanchang University, Nanchang, China
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19
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Zhou J, Ouyang G, Wu L, Zhang M, Weng R, Lin S, Wang Y, Li K, Yang X, Wu Y, Liang Z, Li F, Qu S, Yang X. Simulated confined placental mosaicism proportion (SCPMP) based on cell-free fetal DNA fraction enrichment can reduce false-positive results in non-invasive prenatal testing. Prenat Diagn 2022; 42:1008-1014. [PMID: 35441712 DOI: 10.1002/pd.6150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 01/25/2022] [Accepted: 04/14/2022] [Indexed: 11/11/2022]
Abstract
OBJECTIVE To decrease the false-positive rate of NIPT using cell-free fetal DNA (cffDNA) fraction enrichment and the simulated confined placental mosaicism proportion (SCPMP) threshold application via cffDNA quantification. METHOD Using a cffDNA enrichment method, 303 plasma samples with positive NIPT results (Z-score > 3.0; 200 true-positive and 103 false-positive cases) were re-sequenced. A method to calculate the SCPMP based on the quantified cffDNA fraction was developed; the SCPMP threshold between true- and false-positive NIPT results was determined and used for re-analyses. RESULTS With enrichment, the fetal fraction of the 303 samples was 26.9 ± 8.4%, compared to 11.0 ± 3.2% without enrichment. The optimized threshold method with double determination using the Z-value-defined SCPMP can reduce the false-positive rates for trisomies 21, 18, and 13 by 87%, 80%, and 88.9%, respectively. CONCLUSION Our optimized method can decrease the false-positive rate of NIPT results. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Junhua Zhou
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Guojun Ouyang
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, 510665, P.R. China
| | - Long Wu
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, 510665, P.R. China
| | - Min Zhang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Rongtao Weng
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, 510665, P.R. China
| | - Shuman Lin
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, 510665, P.R. China
| | - Yuanli Wang
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, 510665, P.R. China
| | - Kun Li
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Xu Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Yingsong Wu
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Zhikun Liang
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, 510665, P.R. China
| | - Fenxia Li
- Department of obstetrics and Gynecology, Nanfang Hospital, Southern Medical university, Guangzhou, Guangdong, China
| | - Shoufang Qu
- National Institutes for Food and Drug Control, Beijing, 100050
| | - Xuexi Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
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20
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Liu C, Zhou Y, Liu P, Geng Y, Zhang H, Dun Y, Zhen M, Zhao Z, Zhu M, Huang Q, Liu R, Wang X. Application of ultrasound combined with noninvasive prenatal testing in prenatal testing. Transl Pediatr 2022; 11:85-98. [PMID: 35242654 PMCID: PMC8825935 DOI: 10.21037/tp-21-617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/14/2022] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Both noninvasive prenatal testing (NIPT) and prenatal ultrasound are widely used in clinical settings due to their safety, noninvasiveness, and accuracy, showing high detection rates for fetal chromosomal aneuploidies and structural abnormalities. However, whether the combined application of these two techniques has higher clinical applicability remains to be demonstrated. METHODS The clinical and laboratory data of 3,050 pregnant women who underwent NIPT were collected. The clinical feasibility and health economics of NIPT were investigated by analyzing the accuracy, postnatal follow-up results, and population applicability of NIPT. In addition, an analysis ultrasonography, NIPT, and karyotyping results were performed to evaluate the combined application of ultrasonography and NIPT in screening fetal chromosomal abnormalities. RESULTS NIPT could accurately detect trisomies 21, 18, and 13, and was highly sensitive and specific in detecting other autosomal and sex chromosomal aneuploidies. The positive rates of chromosomal abnormalities in the presence of 1 or 2 or more ultrasound markers were 7.5% and 29.2%, respectively, indicating that ultrasonography combined with NIPT should be preferred for the detection of fetal chromosomal abnormalities. CONCLUSIONS Health economic analysis revealed NIPT to be superior to conventional serologic screening in terms of accuracy and socioeconomics. Ultrasound and NIPT are complementary to each other and the combined techniques can improve the screening ability of fetal chromosomal abnormalities and provide clinicians with more diagnostic information.
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Affiliation(s)
- Ci Liu
- Seven Section of Department of Gynaecology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yingjie Zhou
- Seven Section of Department of Gynaecology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Peng Liu
- Seven Section of Department of Gynaecology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yue Geng
- Seven Section of Department of Gynaecology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Heng Zhang
- Seven Section of Department of Gynaecology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yajing Dun
- Seven Section of Department of Gynaecology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Menglei Zhen
- Seven Section of Department of Gynaecology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhiyu Zhao
- Department of Gynecology, Zhengding Maternal and Child Health Hospital, Zhengding, China
| | - Mingju Zhu
- Department of Ultrasound, Lingshou County Maternal and Child Health Care Hospital, Lingshou County, China
| | - Qingzhi Huang
- Department of Obstetrics and Gynecology, Fuping County Hospital, Fuping County, China
| | - Ruicen Liu
- Seven Section of Department of Gynaecology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xiuli Wang
- Department of Clinical Laboratory, The Second Hospital of Hebei Medical University, Shijiazhuang, China
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21
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Liu Y, Jing X, Xing L, Liu S, Liu J, Cheng J, Deng C, Bai T, Xia T, Wei X, Luo Y, Zhou Q, Zhu Q, Liu H. Noninvasive Prenatal Screening Based on Second-Trimester Ultrasonographic Soft Markers in Low-Risk Pregnant Women. Front Genet 2021; 12:793894. [PMID: 35003226 PMCID: PMC8733646 DOI: 10.3389/fgene.2021.793894] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/25/2021] [Indexed: 11/18/2022] Open
Abstract
Background: We aimed to assess the clinical application of noninvasive prenatal screening (NIPS) based on second-trimester ultrasonographic soft markers (USMs) in low-risk pregnant women. Methods: Data of pregnant women between April 2015 and December 2019 were retrospectively analyzed. Pregnant women [age at expected date of confinement (EDC) of <35 years; low risks for trisomy 21 (T21) and trisomy 18 (T18) based on maternal serum screening; presenting second-trimester USMs (7 types)] who successfully underwent NIPS and had available follow-up information were included in our study. Cases with positive NIPS results were prenatally diagnosed. All patients were followed up for 6 months to 2 years after NIPS, and their clinical outcomes were obtained. Subgroup analyses were performed according to the different USMs. Results: NIPS suggested that among a total of 10,023 cases, 37 (0.37%) were at high risk of aneuploidy, including 4 T21, 6 trisomy 13 (T13), and 27 sex chromosome abnormalities (SCA). Ten cases with aneuploidy (0.10%) were confirmed by prenatal diagnosis, consisting of two T21 and eight SCA. The eight fetuses with SCA consisted of one monosomy X, two XXY, one XXXY, one XXX, one XYY, and two mosaicisms. T21 was detected in one fetus with absent or hypoplastic nasal bone and one fetus with echogenic intracardiac focus (EICF). SCA was detected in five fetuses with EICF, two fetuses with multiple soft markers, and one fetus with echogenic bowel. The positive rate of chromosomal aneuploidy was significantly higher in fetuses with absent or hypoplastic nasal bone (6.25 vs. 0.10%, p = 0.017), echogenic bowel (3.7 vs. 0.10%, p = 0.029), and multiple soft markers (0.678 vs. 0.10%, p = 0.045) than in the total fetuses. The positive predictive values (PPVs) of NIPS in these three groups were 100%, 50%, and 100%, respectively. EICF accounted for 93.25% (9,346/10,023) of the study population, whereas the PPV of NIPS was only 20%. Conclusion: NIPS is an advanced screening test for low-risk pregnant women. In the 10,023 pregnant women sampled, SCA were more common than autosomal trisomy, and EICF was the most frequent USM but the least predictive aneuploidy. Further aneuploidy evaluation is suggested for low-risk pregnant women whose ultrasound indicates absent or hypoplastic nasal bone, echogenic bowel, or multiple soft markers. NIPS can serve as a second-line complementary screening for these women.
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Affiliation(s)
- Yunyun Liu
- Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Xiaosha Jing
- Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Lingling Xing
- Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Sha Liu
- Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Jianlong Liu
- Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Jing Cheng
- Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Cechuan Deng
- Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Ting Bai
- Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Tianyu Xia
- Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Xiang Wei
- Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Yuan Luo
- Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Quanfang Zhou
- Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Qian Zhu
- Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Hongqian Liu
- Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
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22
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Clinical Validation of Fetal cfDNA Analysis Using Rolling-Circle-Replication and Imaging Technology in Osaka (CRITO Study). Diagnostics (Basel) 2021; 11:diagnostics11101837. [PMID: 34679535 PMCID: PMC8534576 DOI: 10.3390/diagnostics11101837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/29/2021] [Accepted: 09/29/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Noninvasive prenatal genetic testing (NIPT) has been adopted as the first choice for aneuploidy screening. The purposes of this study were to investigate the accuracy of Vanadis® NIPT (hereafter CRITO-NIPT) in order to gain a deeper insight into the reasons for discrepancies, as well as to discuss the role of fetal ultrasound. METHODS Between 2019 and 2020, CRITO-NIPT was performed in 1218 cases of patients who underwent CVS or amniocentesis after a detailed fetal ultrasound exam and genetic counseling. The CRITO-NIPT results were compared with the genetic results. In cases of test discrepancies, the placentae were collected for detailed genetic research, and the pre-procedure fetal ultrasound findings were referred to. RESULTS The positive predictive value of T21, T18, and T13 was 93.55%, 88.46%, and 100%, respectively. In 90% of the of false positive (FP) cases, the placentae were examined. In 75% of the CRITO FP-T21 cases, placental mosaicism, or a demised twin's T21, were confirmed. There were complicated mosaic cases, including tetrasomy 21/trisomy7 and monosomy 21/trisomy21 cases. In one of three no-call cases, an intermediate deletion of chromosome 13 was detected. CONCLUSIONS The CRITO study investigated the mechanism of false positives, and the detailed mechanisms in mosaic and no-call cases. There have hitherto been no reports that have provided insight by partitioning the placenta to compare the NIPT and invasive test results, nor that have provided detailed ultrasound findings in the cases of discordant results, revealing the demonstrated importance of, and necessity for, detailed ultrasonography. This article describes the potential of rolling-circle replication as a powerful biosensing platform, as well as the importance of examining the fetus in detail with ultrasound. However, we should remember that the potential applications raise ethical and social concerns that go beyond aneuploidy and its methodology.
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Yoshizato T, Kozuma Y, Horinouchi T, Shinagawa T, Yokomine M, Ushijima K. Diagnosis of Fetal Abnormalities during the First Trimester. Kurume Med J 2021; 66:85-92. [PMID: 34135197 DOI: 10.2739/kurumemedj.ms662002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The quality of prenatal diagnosis of fetal abnormalities has advanced with improved resolution of ultrasound imaging and cytogenetic/molecular analysis. In this article, we briefly review the history of diagnosing fetal abnormalities and the current status of prenatal diagnosis during the first trimester (up to the first 14 weeks' gestation), focusing especially on fetal malformations and chromosomal abnormalities. As for detectable morphological abnormalities, roughly half of all major structural anomalies including those in the central nervous system, cardiovascular system and gastrointestinal system can be detected, if not definitely diagnosed. For screening of chromosomal abnormalities, especially for trisomy 21, ultrasound soft markers such as increased nuchal translucency, maternal serum markers and their combinations have been implemented. More recently, non-invasive prenatal testing, by analyzing cell-free DNA in maternal serum, is now available to detect chromosomal abnormalities with higher predictability. Although invasive chorionic villus sampling offers definite diagnosis for chromosomal abnormalities during the first trimester, non-invasive diagnostic techniques are patient-friendly and promising in the future perspectives on prenatal diagnosis for chromosomal abnormalities.
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Affiliation(s)
- Toshiyuki Yoshizato
- Department of Obstetrics and Gynecology, Kurume University School of Medicine
| | - Yutaka Kozuma
- Department of Obstetrics and Gynecology, Kurume University School of Medicine
| | - Takashi Horinouchi
- Department of Obstetrics and Gynecology, Kurume University School of Medicine
| | - Takaaki Shinagawa
- Department of Obstetrics and Gynecology, Kurume University School of Medicine
| | - Masato Yokomine
- Department of Obstetrics and Gynecology, Kurume University School of Medicine
| | - Kimio Ushijima
- Department of Obstetrics and Gynecology, Kurume University School of Medicine
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Davies RW, Kucka M, Su D, Shi S, Flanagan M, Cunniff CM, Chan YF, Myers S. Rapid genotype imputation from sequence with reference panels. Nat Genet 2021; 53:1104-1111. [PMID: 34083788 PMCID: PMC7611184 DOI: 10.1038/s41588-021-00877-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 04/23/2021] [Indexed: 12/30/2022]
Abstract
Inexpensive genotyping methods are essential to modern genomics. Here we present QUILT, which performs diploid genotype imputation using low-coverage whole genome sequence data. QUILT employs Gibbs sampling to partition reads into maternal and paternal sets, facilitating rapid haploid imputation using large reference panels. We show this partitioning to be accurate over many megabases, enabling highly accurate imputation close to theoretical limits and outperforming existing methods. Moreover, QUILT can impute accurately using diverse technologies, including using long reads from Oxford Nanopore Technologies, and a novel form of low-cost barcoded Illumina sequencing called haplotagging, with the latter showing improved accuracy at low coverages. Relative to DNA genotyping microarrays, QUILT offers improved accuracy at reduced cost, particularly for diverse populations that are traditionally underserved in modern genomic analyses, with accuracy nearly doubling at rare SNPs. Finally, QUILT can accurately impute (4-digit) HLA types, the first such method from low-coverage sequence data.
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Affiliation(s)
| | - Marek Kucka
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Dingwen Su
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Sinan Shi
- Department of Statistics, University of Oxford, Oxford, UK
| | - Maeve Flanagan
- Department of Pediatrics, Weill Cornell Medical College, New York, NY, USA
| | | | | | - Simon Myers
- Department of Statistics, University of Oxford, Oxford, UK.,The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
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Ge Y, Li J, Zhuang J, Zhang J, Huang Y, Tan M, Li W, Chen J, Zhou Y. Expanded noninvasive prenatal testing for fetal aneuploidy and copy number variations and parental willingness for invasive diagnosis in a cohort of 18,516 cases. BMC Med Genomics 2021; 14:106. [PMID: 33853619 PMCID: PMC8045328 DOI: 10.1186/s12920-021-00955-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/01/2021] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Noninvasive prenatal testing (NIPT) has been wildly used to screen for common aneuplodies. In recent years, the test has been expanded to detect rare autosomal aneuploidies (RATs) and copy number variations (CNVs). This study was performed to investigate the performance of expanded noninvasive prenatal testing (expanded NIPT) in screening for common trisomies, sex chromosomal aneuploidies (SCAs), rare autosomal aneuploidies (RATs), and copy number variations (CNVs) and parental willingness for invasive prenatal diagnosis in a Chinese prenatal diagnosis center. METHODS A total of 24,702 pregnant women were retrospectively analyzed at the Women and Children's Hospital from January 2013 to April 2019, among which expanded NIPT had been successfully conducted in 24,702 pregnant women. The high-risk expanded NIPT results were validated by karyotype analysis and chromosomal microarray analysis. All the tested pregnant women were followed up for pregnancy outcomes. RESULTS Of the 24,702 cases, successful follow-up was conducted in 98.77% (401/446) of cases with common trisomies and SCAs, 91.95% (80/87) of RAT and CNV cases, and 76.25% (18,429/24,169) of cases with low-risk screening results. The sensitivity of expanded NIPT was 100% (95% confidence interval[CI], 97.38-100%), 96.67%(95%CI, 82.78-99.92%), and 100%(95%CI, 66.37-100.00%), and the specificity was 99.92%(95%CI, 99.87-99.96%), 99.96%(95%CI, 99.91-99.98%), and 99.88% (95%CI, 99.82-99.93%) for the detection of trisomies 21, 18, and 13, respectively. Expanded NIPT detected 45,X, 47,XXX, 47,XXY, XYY syndrome, RATs, and CNVs with positive predictive values of 25.49%, 75%, 94.12%, 76.19%, 6.45%, and 50%, respectively. The women carrying fetuses with Trisomy 21/Trisomy 18/Trisomy 13 underwent invasive prenatal diagnosis and terminated their pregnancies at higher rates than those at high risk for SCAs, RATs, and CNVs. CONCLUSIONS Our study demonstrates that the expanded NIPT detects fetal trisomies 21, 18, and 13 with high sensitivity and specificity. The accuracy of detecting SCAs, RATs, and CNVs is still relatively poor and needs to be improved. With a high-risk expanded NIPT result, the women at high risk for common trisomies are more likely to undergo invasive prenatal diagnosis procedures and terminate their pregnancies than those with unusual chromosome abnormalities.
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Affiliation(s)
- Yunsheng Ge
- Prenatal Diagnosis Center, Women and Children's Hospital, School of Medicine, Xiamen University, 10 Zhenhai Road, Xiamen, 361003, Fujian Province, China
| | - Jia Li
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong Province, China
| | - Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian Province, China
| | - Jian Zhang
- Prenatal Diagnosis Center, Women and Children's Hospital, School of Medicine, Xiamen University, 10 Zhenhai Road, Xiamen, 361003, Fujian Province, China
| | - Yanru Huang
- Prenatal Diagnosis Center, Women and Children's Hospital, School of Medicine, Xiamen University, 10 Zhenhai Road, Xiamen, 361003, Fujian Province, China
| | - Meihua Tan
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong Province, China
| | - Wei Li
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong Province, China
| | - Jiayan Chen
- Prenatal Diagnosis Center, Women and Children's Hospital, School of Medicine, Xiamen University, 10 Zhenhai Road, Xiamen, 361003, Fujian Province, China
| | - Yulin Zhou
- Prenatal Diagnosis Center, Women and Children's Hospital, School of Medicine, Xiamen University, 10 Zhenhai Road, Xiamen, 361003, Fujian Province, China.
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Utility of noninvasive genome-wide screening: a prospective cohort of obstetric patients undergoing diagnostic testing. Genet Med 2021; 23:1341-1348. [PMID: 33782554 DOI: 10.1038/s41436-021-01147-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 11/08/2022] Open
Abstract
PURPOSE Copy-number variant (CNV) assessment is recommended for patients undergoing prenatal diagnostic testing. Noninvasive screening tests have not been extensively validated for CNV detection. The objective of this study was to compare the ability of genome-wide noninvasive prenatal screening (NIPS) to chromosomal microarray to detect clinically significant findings. METHODS We prospectively enrolled 198 subjects at the time of consent for diagnostic prenatal testing. Genome-wide NIPS results were compared with diagnostic testing results to assess NIPS test performance (n = 160, 38 subjects without microarray results excluded). Cohen's kappa statistic was used to assess test agreement. RESULTS Genome-wide NIPS did not detect clinically significant chromosomal abnormalities at the same rate as diagnostic testing, κ = 0.75 (95% confidence interval [CI], 0.62-0.87). When excluding CNVs <7 Mb and findings outside the limits of genome-wide NIPS, test agreement improved, κ = 0.88 (0.79-0.97) driven by agreement for common aneuploidies (κ = 1.0). However, among patients with an abnormal fetal survey, agreement was only fair, κ = 0.38 (0.08-0.67). CONCLUSION While NIPS is an excellent screening test for common aneuploidies, genome-wide NIPS misses clinically significant findings detected on routine diagnostic testing. False positive and false negative cases highlight the importance of pretest counseling regarding NIPS limitations, especially in the setting of fetal anomalies.
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Juvale IIA, Che Has AT. The Potential Role of miRNAs as Predictive Biomarkers in Neurodevelopmental Disorders. J Mol Neurosci 2021; 71:1338-1355. [PMID: 33774758 DOI: 10.1007/s12031-021-01825-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/02/2021] [Indexed: 12/22/2022]
Abstract
Neurodevelopmental disorders are defined as a set of abnormal brain developmental conditions marked by the early childhood onset of cognitive, behavioral, and functional deficits leading to memory and learning problems, emotional instability, and impulsivity. Autism spectrum disorder, attention-deficit/hyperactivity disorder, Tourette syndrome, fragile X syndrome, and Down's syndrome are a few known examples of neurodevelopmental disorders. Although they are relatively common in both developed and developing countries, very little is currently known about their underlying molecular mechanisms. Both genetic and environmental factors are known to increase the risk of neurodevelopmental disorders. Current diagnostic and screening tests for neurodevelopmental disorders are not reliable; hence, individuals with neurodevelopmental disorders are often diagnosed in the later stages. This negatively affects their prognosis and quality of life, prompting the need for a better diagnostic biomarker. Recent studies on microRNAs and their altered regulation in diseases have shed some light on the possible role they could play in the development of the central nervous system. This review attempts to elucidate our current understanding of the role that microRNAs play in neurodevelopmental disorders with the hope of utilizing them as potential biomarkers in the future.
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Affiliation(s)
- Iman Imtiyaz Ahmed Juvale
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Ahmad Tarmizi Che Has
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia.
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Domaradzka J, Deperas M, Obersztyn E, Kucińska-Chahwan A, Brison N, Van Den Bogaert K, Roszkowski T, Kędzior M, Bartnik-Głaska M, Łuszczek A, Jakubów-Durska K, Vermeesch JR, Nowakowska BA. A placental trisomy 2 detected by NIPT evolved in a fetal small Supernumerary Marker Chromosome (sSMC). Mol Cytogenet 2021; 14:18. [PMID: 33722255 PMCID: PMC7962352 DOI: 10.1186/s13039-021-00535-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Non-invasive prenatal testing (NIPT) is a rapidly developing and widely used method in the prenatal screening. Recently, the widespread use of the NIPT caused a neglecting of the limitations of this technology. CASE PRESENTATION The 38-year-old woman underwent amniocentesis because of a high risk of trisomy 2 revealed by the genome-wide Non-Invasive Prenatal Test (NIPT). The invasive prenatal diagnosis revealed the mosaicism for a small supernumerary marker chromosome sSMC derived from chromosome 2. Interphase fluorescence in situ hybridization (FISH) on uncultured amniocytes revealed three signals of centromere 2 in 30% of the cells. GTG-banded metaphases revealed abnormal karyotype (47,XX,+mar[21]/46,XX[19]) and was confirmed by array comparative genomic hybridization (aCGH). Cytogenetic analyses (FISH, aCGH, karyotype) on fetal skin biopsies were performed and confirmed the genomic gain of the centromeric region of chromosome 2. In the placenta, three cell lines were detected: a normal cell line, a cell line with trisomy 2 and a third one with only the sSMC. CONCLUSION Whole-genome Non-Invasive Prenatal Testing allows not only the identification of common fetal trisomies but also diagnosis of rare chromosomal abnormalities. Especially in such cases, it is extremely important to perform not only NIPT verification on a sample of material other than trophoblast, but also to apply appropriate research methods. Such conduct allows detailed analysis of the detected aberration, thus appropriate clinical validity.
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Affiliation(s)
- Justyna Domaradzka
- Medical Genetics Department, The Institute of Mother and Child, Kasprzaka 17A, 01-211, Warsaw, Poland.
| | - Marta Deperas
- Medical Genetics Department, The Institute of Mother and Child, Kasprzaka 17A, 01-211, Warsaw, Poland
| | - Ewa Obersztyn
- Medical Genetics Department, The Institute of Mother and Child, Kasprzaka 17A, 01-211, Warsaw, Poland
| | - Anna Kucińska-Chahwan
- Department of Obstetrics and Gynecology, Centre of Postgraduate Medical Education, Czerniakowska 231, 00-416, Warsaw, Poland
| | - Nathalie Brison
- Centre for Human Genetics, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | | | - Tomasz Roszkowski
- Department of Obstetrics and Gynecology, Centre of Postgraduate Medical Education, Czerniakowska 231, 00-416, Warsaw, Poland
| | - Marta Kędzior
- Medical Genetics Department, The Institute of Mother and Child, Kasprzaka 17A, 01-211, Warsaw, Poland
| | - Magdalena Bartnik-Głaska
- Medical Genetics Department, The Institute of Mother and Child, Kasprzaka 17A, 01-211, Warsaw, Poland
| | - Alicja Łuszczek
- Medical Genetics Department, The Institute of Mother and Child, Kasprzaka 17A, 01-211, Warsaw, Poland
| | - Krystyna Jakubów-Durska
- Medical Genetics Department, The Institute of Mother and Child, Kasprzaka 17A, 01-211, Warsaw, Poland
| | | | - Beata Anna Nowakowska
- Medical Genetics Department, The Institute of Mother and Child, Kasprzaka 17A, 01-211, Warsaw, Poland
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Dai R, Yu Y, Zhang H, Li L, Jiang Y, Liu R, Zhang H. Analysis of 17,428 pregnant women undergoing non-invasive prenatal testing for fetal chromosome in Northeast China. Medicine (Baltimore) 2021; 100:e24740. [PMID: 33578623 PMCID: PMC10545248 DOI: 10.1097/md.0000000000024740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 11/13/2020] [Accepted: 01/16/2021] [Indexed: 11/26/2022] Open
Abstract
ABSTRACT Non-invasive prenatal testing (NIPT) is an incomparable prenatal screening technology, but we should undergo amniocentesis to confirm fetal chromosome when pregnancies receive a positive result via NIPT. We aimed to investigate the detection rate and positive predictive value of NIPT results in pregnancies from Northeast China, and to determine the reasons for false positive and false negative NIPT results.This study evaluates 17,428 singleton pregnancies had undergone NIPT detection. 202 samples were NIPT positive with the detection rate was 1.16% (202/17,428). Among all the positive samples, 160 samples (79.21%) were referred for an amniocentesis procedure to investigate the fetal chromosome. The positive predictive value of T21, T18, and T13 was found to be 75% with a 0.07% false positive rate. Positive predictive value from high to low was as follows: trisomy 21 (84.38%), followed by trisomy 18 (61.54%), autosomal abnormalities (52.94%), sex chromosomal abnormalities (38.46%), and trisomy 13 (33.33%). The positive predictive values for sex chromosome abnormalities turned out to be mosaic sex chromosome aneuploidies (83.33%), followed by XYY (57.14%), XXY (37.50%), XXX (36.36%), and Monosomy X (28.95%). Out of the 160 samples had amniocentesis, the true positive cases in trisomy 21 had a higher percentage of Z-scores compared with the false positive cases in trisomy 21 (P < .05). And the true positive cases in trisomy 18 had a significantly higher percentage of Z-scores compared with the false positive cases in trisomy 18 (P < .01).These findings indicate that the positive predictive value of T21, T18, and T13 was found to be 75% with a 0.07% false positive rate. It is worth noting that the positive predictive value of NIPT for autosomes and sex chromosomes. Moreover, if women receive a positive result via NIPT, they should pay attention to the results with undergoing further prenatal diagnosis.
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Lu W, Huang T, Wang XR, Zhou JH, Yuan HZ, Yang Y, Huang TT, Liu DP, Liu YQ. Next-generation sequencing: a follow-up of 36,913 singleton pregnancies with noninvasive prenatal testing in central China. J Assist Reprod Genet 2020; 37:3143-3150. [PMID: 33094428 PMCID: PMC7714822 DOI: 10.1007/s10815-020-01977-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/12/2020] [Indexed: 12/18/2022] Open
Abstract
PURPOSE To evaluate the noninvasive prenatal testing (NIPT) results of 36,913 cases in Jiangxi province of central China and explore its application value in prenatal screening and diagnosis. METHODS This retrospective analysis included 36,913 singleton pregnant women who underwent NIPT because of moderate-/high-risk pregnancy or voluntary requirements between January 2017 and December 2019 in our hospital. Chromosomal abnormalities such as trisomies 21, 18, and 13 (T21, T18, T13) and sex chromosome aneuploidies (SCAs) were judged by standard Z-score analysis. Positive NIPT results were confirmed by amniocentesis and karyotyping. Pregnancy outcomes were followed up via telephone interview. RESULTS A total of 1.01% (371/36,913) positive cases were detected by NIPT, comprising 137, 46, 31, and 157 cases of T21, T18, T13, and SCAs, respectively. A total of 116 of T21, 27 of T18, 13 of T13, and 51 of SCAs were confirmed to be true positive; all normal cases that had been followed up were verified to be true negative. The NIPT sensitivity in T21, T18, T13, and SCAs was 100.00% individually, whereas the specificity was 99.94% (36,488/36,509), 99.95% (36,579/36,598), 99.95% (36,594/36,612), and 99.72% (36,472/36,574), respectively. Furthermore, the negative predictive values of T21, T18, T13, and SCAs were all 100%, while the positive predictive values were 84.67%, 58.70%, 41.94%, and 33.33%, respectively. CONCLUSION NIPT is highly sensitive and has a low false positive rate in testing clinically significant fetal aneuploidies of general reproductive women. However, this technique cannot substitute for amniocentesis and karyotyping, and detailed genetic counseling is also essential for the high-risk group of NIPT.
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Affiliation(s)
- Wan Lu
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Ting Huang
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Xin-Rong Wang
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Ji-Hui Zhou
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Hui-Zhen Yuan
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Yan Yang
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Ting-Ting Huang
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Dan-Ping Liu
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Yan-Qiu Liu
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China.
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Albertini RJ, Kaden DA. Mutagenicity monitoring in humans: Global versus specific origin of mutations. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 786:108341. [PMID: 33339577 DOI: 10.1016/j.mrrev.2020.108341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 10/08/2020] [Accepted: 10/14/2020] [Indexed: 01/19/2023]
Abstract
An underappreciated aspect of human mutagenicity biomonitoring is tissue specificity reflected in different assays, especially those that measure events that can only occur in developing bone marrow (BM) cells. Reviewed here are 9 currently-employed human mutagenicity biomonitoring assays. Several assays measure chromosome-level events in circulating T-lymphocytes (T-cells), i.e., traditional analyses of aberrations, translocation studies involving chromosome painting and fluorescence in situ hybridization (FISH) and determinations of micronuclei (MN). Other T-cell assays measure gene mutations. i.e., hypoxanthine-guanine phosphoriboslytransferase (HPRT) and phosphoribosylinositol glycan class A (PIGA). In addition to the T-cell assays, also reviewed are those assays that measure events in peripheral blood cells that necessarily arose in BM cells, i.e., MN in reticulocytes; glycophorin A (GPA) gene mutations in red blood cells (RBCs), and PIGA gene mutations in RBC or granulocytes. This review considers only cell culture- or cytometry-based assays to describe endpoints measured, methods, optimal sampling times, and sample summaries of typical quantitative and qualitative results. However, to achieve its intended focus on the target cells where events occur, kinetics of the cells of peripheral blood that derive at some point from precursor cells are reviewed to identify body sites and tissues where the genotoxic events originate. Kinetics indicate that in normal adults, measured events in T-cells afford global assessments of in vivo mutagenicity but are not specific for BM effects. Therefore, an agent's capacity for inducing mutations in BM cells cannot be reliably inferred from T-cell assays as the magnitude of effect in BM, if any, is unknown. By contrast, chromosome or gene level mutations measured in RBCs/reticulocytes or granulocytes must originate in BM cells, i.e. in RBC or granulocyte precursors, thereby making them specific indicators for effects in BM. Assays of mutations arising directly in BM cells may quantitatively reflect the mutagenicity of potential leukemogenic agents.
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Affiliation(s)
- Richard J Albertini
- University of Vermont, 111 Colchester Avenue, Burlington, VT 05401, United States
| | - Debra A Kaden
- Ramboll US Consulting, Inc., 101 Federal Street, Suite 1900, Boston, MA 02110, United States.
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Zheng Y, Wang G, Li J, Wan S, Dang Y, Tang M, Zhang J, Yang H. Non-invasive prenatal testing detects duplication abnormalities of fetal chromosome 12. Eur J Obstet Gynecol Reprod Biol 2020; 253:278-284. [PMID: 32898774 DOI: 10.1016/j.ejogrb.2020.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 11/24/2022]
Abstract
PURPOSE The 12q terminal duplication is a chromosomal structural abnormality that has been rarely reported. The common clinical manifestations include intellectual disability and speech delay. We report two cases of patients with a duplication of chromosome 12q which was discovered incidentally during non-invasive prenatal genetic testing (NIPT). METHODS Next generation sequencing-based NIPT and karyotype analysis confirmed the type and inheritance of the rearrangement, and chromosomal microarray-based analysis also confirmed the end replication. RESULTS One patient had a 18Mb 12q24.21q24.33 duplication. The other patient had a12.04Mb12.q24.31q24.33 duplication and a 9.56Mb deletion in 18p11.32p11.22. The duplicated regions on chromosome 12 and the deletion on chromosome 18 in the patients were pathogenic, and the fetuses may have clinical characteristics, such as mental retardation, facial deformities, and psychomotor retardation. Ultimately, both pregnant women chose to terminate their pregnancy. CONCLUSION The cases we reported show that NIPT cannot only detect conventional chromosomes, but can also detect microdeletions and microduplications, which broadens the scope of clinical application for NIPT and provides genetic information for high-risk pregnant women as early as possible.
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Affiliation(s)
- Yunyun Zheng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of AFMU (Air Force Medical University), Xi'an, 710032, Shaanxi, China
| | - Guihu Wang
- National-Local Joint Engineering Research Center of Biodiagnostics and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jia Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of AFMU (Air Force Medical University), Xi'an, 710032, Shaanxi, China
| | - Shanning Wan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of AFMU (Air Force Medical University), Xi'an, 710032, Shaanxi, China
| | - Yinghui Dang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of AFMU (Air Force Medical University), Xi'an, 710032, Shaanxi, China
| | - Miaomiao Tang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of AFMU (Air Force Medical University), Xi'an, 710032, Shaanxi, China
| | - Jianfang Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of AFMU (Air Force Medical University), Xi'an, 710032, Shaanxi, China
| | - Hong Yang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of AFMU (Air Force Medical University), Xi'an, 710032, Shaanxi, China.
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A retrospective analysis the clinic data and follow-up of non-invasive prenatal test in detection of fetal chromosomal aneuploidy in more than 40,000 cases in a single prenatal diagnosis center. Eur J Med Genet 2020; 63:104001. [PMID: 32622960 DOI: 10.1016/j.ejmg.2020.104001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/22/2020] [Accepted: 06/28/2020] [Indexed: 01/07/2023]
Abstract
OBJECTIVE To evaluate the efficacy of non-invasive prenatal test (NIPT) in the detection of chromosomal aneuploidy according to the follow-up information from a single prenatal diagnosis center. METHODS A total of 40,311 cases were retrospectively reviewed. The screening was performed using a BGI protocol, pre-test and post-test genetic counseling was provided, and the pregnancy outcomes were recorded. The results of NIPT and clinical follow-up data were analyzed together with the pregnancy outcomes, confirmatory testing results, and ultrasound findings. RESULTS Of the 40,311cases were includes in the study, successful follow-up was conducted in 468 (1.16%) cases with high risk, 225 (0.56%) cases with rare autosomal trisomy (RAT) and copy number variation (CNV). 39,572 (98.17%) cases with low risk and 623 (1.57%) cases of which were confirmed with adverse pregnancy outcomes. 46 (0.1%) cases with failed tests. Among them, 398 (84.7%) cases with high-risk results chose invasive testing, revealing 198 true positive cases. In cases with RAT and CNV results, 189 cases underwent invasive testing, revealing 5 cases RAT and 4 pathogenic CNVs. CONCLUSIONS NIPT appears to be effective in detecting the fetal chromosomal aneuploidies T21, T18 and SCAs, but it exist false positive/negative cases, unconfirmed high-risk cfDNA results, and the high false positive rate in cases with RAT and CNV results implied the limitations of this screening method. Our study showed the importance to associate cfDNA screening results with clinical follow-up data and provided information that may help with result interpretation, genetic counseling and the decision making in clinic.
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Martin KA, Samango-Sprouse CA, Kantor V, Dhamankar R, Valenti E, Trefogli MT, Balosbalos I, Lagrave D, Lyons D, Kao C, Hakonarson H, Billings PR. Detection of maternal X chromosome abnormalities using single nucleotide polymorphism-based noninvasive prenatal testing. Am J Obstet Gynecol MFM 2020; 2:100152. [PMID: 33345882 DOI: 10.1016/j.ajogmf.2020.100152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 02/03/2023]
Abstract
BACKGROUND Maternal X chromosome abnormalities may cause discordant results between noninvasive prenatal screening tests and diagnostic evaluation of the fetus/newborn, leading to unnecessary invasive testing. Women with X chromosome abnormalities are at increased risk for reproductive, pregnancy, or other health complications, which may be reduced or ameliorated by early diagnosis, monitoring, and intervention. OBJECTIVE This study aimed to validate a single nucleotide polymorphism-based noninvasive prenatal test to identify X chromosome abnormalities of maternal origin. STUDY DESIGN All tests unable to evaluate fetal risk for aneuploidy because of uninformative algorithm results were eligible for inclusion. Two groups of cases were prospectively identified: Group A (n=106) where a maternal X chromosome abnormality was suspected and Group B (control group, n=107) where a fetal chromosome abnormality involving chromosome 13, 18, 21, or X was suspected but did not meet criteria for reporting. Maternal DNA was isolated from the plasma-depleted cellular pellet and sent to a reference laboratory for blinded analysis using chromosomal microarray. A chromosome abnormality involving chromosomes 13, 18, 21, or X was reported by the reference laboratory if ≥5 Mb in size and present in ≥20% of the DNA. RESULTS A maternal X chromosome abnormality was suspected in 1/1305 tests (149/194,385; 0.08%). In Group A, a maternal X chromosome abnormality was confirmed in 100/106 cases (94.3% positive predictive value, 1-sided 97.5% confidence interval, 88.1%-100.0%). Turner syndrome was the most commonly suspected maternal abnormality (58/106, 54.7%), with confirmation of mosaic or nonmosaic 45,X by microarray in 38/58 (65.5%) cases. Noninvasive prenatal screening tests suspected the presence of maternal 47,XXX with or without mosaicism in 40/106 (37.7%) cases, confirmed by microarray in 38/40 (95.0%). In Group B (n=107), no maternal microarray abnormalities were reported, providing a negative predictive value of 100% (1-sided 97.5% confidence interval, 96.6%-100.0%). CONCLUSION When noninvasive prenatal testing suspected a maternal X chromosome abnormality, maternal microarray confirmed an X chromosome abnormality with 94.3% positive predictive value. Of the maternal X chromosome abnormalities detected by array, >50% were 45,X. When fetal chromosome abnormalities involving chromosomes 13, 18, 21, or X were suspected, no maternal chromosome abnormalities were reported, yielding a negative predictive value of 100%. Women with maternal X abnormalities suspected with noninvasive prenatal testing may be at increased risk for reproductive and health complications; early evaluation and treatment may prevent long-term consequences or disability.
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Affiliation(s)
| | - Carole A Samango-Sprouse
- Department of Pediatrics, George Washington University of Health Sciences, Washington, DC; The Focus Foundation, Davidsonville, MD; Department of Human and Molecular Genetics, Florida International University, Miami, FL
| | | | | | | | | | | | | | | | - Charlly Kao
- Center for Advanced Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hakon Hakonarson
- Center for Advanced Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
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Non-invasive prenatal testing leading to a maternal diagnosis of Charcot-Marie-Tooth neuropathy. J Hum Genet 2020; 65:1035-1038. [PMID: 32555312 DOI: 10.1038/s10038-020-0789-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/20/2020] [Accepted: 06/03/2020] [Indexed: 11/08/2022]
Abstract
Non-invasive prenatal testing (NIPT) is increasingly used in routine practice due to its high sensitivity and specificity in detecting fetal chromosomal anomalies. Several reports have highlighted that NIPT can diagnose previously unsuspected malignancy or benign copy number variation in the expectant mother. We report a case in which NIPT detected a duplication involving the 17p11.2-17p12 region with possible Potocki-Lupski syndrome in the fetus. However, on further questioning, the mother revealed that she had Charcot-Marie-Tooth neuropathy type IA (CMT1A) and thus using array CGH, we were able to confirm that the 17p duplication was maternal in origin, included only the typical CMT1A region and that the fetus had a normal chromosome complement. Although it may be rare for a mother to have a pathogenic chromosome duplication/deletion, with the expansion in scope of NIPT from classic trisomies to global chromosome coverage and monogenic conditions, more examples of fortuitous maternal diagnosis will certainly be forthcoming and this should be taken into account during pre-test genetic counseling.
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Budis J, Gazdarica J, Radvanszky J, Szucs G, Kucharik M, Strieskova L, Gazdaricova I, Harsanyova M, Duris F, Minarik G, Sekelska M, Nagy B, Turna J, Szemes T. Combining count- and length-based z-scores leads to improved predictions in non-invasive prenatal testing. Bioinformatics 2020; 35:1284-1291. [PMID: 30219853 DOI: 10.1093/bioinformatics/bty806] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/16/2018] [Accepted: 09/13/2018] [Indexed: 02/06/2023] Open
Abstract
MOTIVATION Non-invasive prenatal testing or NIPT is currently among the top researched topic in obstetric care. While the performance of the current state-of-the-art NIPT solutions achieve high sensitivity and specificity, they still struggle with a considerable number of samples that cannot be concluded with certainty. Such uninformative results are often subject to repeated blood sampling and re-analysis, usually after two weeks, and this period may cause a stress to the future mothers as well as increase the overall cost of the test. RESULTS We propose a supplementary method to traditional z-scores to reduce the number of such uninformative calls. The method is based on a novel analysis of the length profile of circulating cell free DNA which compares the change in such profiles when random-based and length-based elimination of some fragments is performed. The proposed method is not as accurate as the standard z-score; however, our results suggest that combination of these two independent methods correctly resolves a substantial portion of healthy samples with an uninformative result. Additionally, we discuss how the proposed method can be used to identify maternal aberrations, thus reducing the risk of false positive and false negative calls. AVAILABILITY AND IMPLEMENTATION The open-source code of the proposed methods, together with test data, is freely available for non-commercial users at github web page https://github.com/jbudis/lambda. SUPPLEMENTARY INFORMATION Supplementary materials are available at Bioinformatics online.
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Affiliation(s)
- Jaroslav Budis
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia.,Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia
| | - Juraj Gazdarica
- Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Jan Radvanszky
- Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Gabor Szucs
- Department of Applied Mathematics and Statistics, Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia
| | | | - Lucia Strieskova
- Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Iveta Gazdaricova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Maria Harsanyova
- Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Frantisek Duris
- Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia
| | | | | | - Balint Nagy
- Department of Human Genetics, University of Debrecen, Debrecen, Hungary
| | - Jan Turna
- Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia.,Comenius University Science Park, Bratislava, Slovakia
| | - Tomas Szemes
- Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia.,Comenius University Science Park, Bratislava, Slovakia
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Chau MHK, Cao Y, Kwok YKY, Chan S, Chan YM, Wang H, Yang Z, Wong HK, Leung TY, Choy KW. Characteristics and mode of inheritance of pathogenic copy number variants in prenatal diagnosis. Am J Obstet Gynecol 2019; 221:493.e1-493.e11. [PMID: 31207233 DOI: 10.1016/j.ajog.2019.06.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/05/2019] [Accepted: 06/07/2019] [Indexed: 12/01/2022]
Abstract
BACKGROUND Microdeletions and microduplications can occur in any pregnancy independent of maternal age. The spectrum and features of pathogenic copy number variants including the size, genomic distribution, and mode of inheritance are not well studied. These characteristics have important clinical implications regarding expanding noninvasive prenatal screening for microdeletions and microduplications. OBJECTIVES The aim was to investigate the spectrum and characteristics of pathogenic copy number variants in prenatal genetic diagnosis and to provide recommendations for expanding the scope of noninvasive prenatal screening for microdeletions and microduplications. STUDY DESIGN This was a retrospective study of 1510 pregnant women who underwent invasive prenatal diagnostic testing by chromosomal microarray analysis. Prenatal samples were retrieved by amniocentesis or chorionic villus sampling and sent to our prenatal genetic diagnosis laboratory for chromosomal microarray analysis. The risk of carrying a fetus with pathogenic copy number variants is stratified by the patients' primary indication for invasive testing. We searched the literature for published prenatal chromosomal microarray data to generate a large cohort of 23,865 fetuses. The characteristics and spectrum of pathogenic copy number variants including the type of aberrations (gains or losses), genomic loci, sizes, and the mode of inheritance were studied. RESULTS Overall, 375 of 23,865 fetuses (1.6%) carried pathogenic copy number variants for any indication for invasive testing, and 44 of them (11.7%) involve 2 or more pathogenic copy number variants. A total of 428 pathogenic copy number variants were detected in these fetuses, of which 280 were deletions and 148 were duplications. Three hundred sixty (84.1%) were less than 5 Mb in size and 68 (15.9%) were between 5 and 10 Mb. The incidence of carrying a pathogenic copy number variant in the high-risk group is 1 in 36 and the low-risk group is 1 in 125. Parental inheritance study results were available for 311 pathogenic copy number variants, 71 (22.8%) were maternally inherited, 36 (11.6%) were paternally inherited, and 204 (65.6%) occurred de novo. CONCLUSION Collectively, pathogenic copy number variants are common in pregnancies. High-risk pregnancies should be offered invasive testing with chromosomal microarray analysis for the most comprehensive investigation. Detection limits on size, parental inheritance, and genomic distribution should be carefully considered before implementing copy number variant screening in expanded noninvasive prenatal screening.
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Affiliation(s)
- Matthew Hoi Kin Chau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ye Cao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yvonne Ka Yin Kwok
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Samantha Chan
- Warwick Medical School at the University of Warwick, Coventry, United Kingdom
| | - Yiu Man Chan
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Huilin Wang
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; Department of Central Laboratory, Bao'an Maternity and Child Healthcare Hospital, Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research, and Transformation Team, Shenzhen, China; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Zhenjun Yang
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Hoi Kin Wong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China; The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China.
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Krstić N, Običan SG. Current landscape of prenatal genetic screening and testing. Birth Defects Res 2019; 112:321-331. [PMID: 31633301 DOI: 10.1002/bdr2.1598] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 09/17/2019] [Indexed: 12/25/2022]
Abstract
Pregnant patients should be offered the option of prenatal genetic screening and diagnostic testing. The type of screening and testing offered to a patient may depend on various factors including but not limited to age, family history, fetal findings, exposures, and patient preferences. Prenatal screening is available for a variety of genetic conditions including aneuploidy, congenital abnormalities, and carrier status. Diagnostic testing options include karyotype, prenatal microarray, as well as next-generation sequencing. The various options differ in methodology, accuracy, timing and indication for testing, and information they provide. Given that the technologies related to prenatal testing are rapidly evolving and improving, the array of available screening and testing modalities are increasing. This article reviews the current offerings in prenatal screening and diagnosis.
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Affiliation(s)
- Nevena Krstić
- Department of Obstetrics and Gynecology, University of South Florida, Morsani College of Medicine, Tampa, Florida
| | - Sarah G Običan
- Department of Obstetrics and Gynecology, University of South Florida, Morsani College of Medicine, Tampa, Florida
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Guseh SH. Noninvasive prenatal testing: from aneuploidy to single genes. Hum Genet 2019; 139:1141-1148. [PMID: 31555907 DOI: 10.1007/s00439-019-02061-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/04/2019] [Indexed: 12/16/2022]
Abstract
Noninvasive prenatal testing has undergone rapid advances in the last few years. Although researchers have long known about circulating pregnancy-based cell-free fragments of DNA in maternal plasma, it was the introduction of massively parallel sequencing that allowed noninvasive prenatal testing to become a widely used clinical test. This review will begin with an in-depth analysis of the use of noninvasive prenatal testing for aneuploidy, including common causes for inaccurate and/or discordant results. It will also review the ongoing expansion of noninvasive prenatal testing to include copy number variants and select single-gene disorders. Finally, integrated throughout the review is a comparison of noninvasive prenatal testing to more traditional screening methods along with some medical and ethical implications of the widespread use of this new technology.
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Affiliation(s)
- Stephanie H Guseh
- Division of Maternal-Fetal Medicine, Obstetrics and Gynecology, Harvard Medical School, Brigham and Women's Hospital, 75 Francis St, Boston, MA, USA.
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Audibert F, De Bie I, Johnson JA, Okun N, Wilson RD, Armour C, Chitayat D, Kim R. No. 348-Joint SOGC-CCMG Guideline: Update on Prenatal Screening for Fetal Aneuploidy, Fetal Anomalies, and Adverse Pregnancy Outcomes. JOURNAL OF OBSTETRICS AND GYNAECOLOGY CANADA 2019; 39:805-817. [PMID: 28859766 DOI: 10.1016/j.jogc.2017.01.032] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
OBJECTIVE To review the available prenatal screening options in light of the recent technical advances and to provide an update of previous guidelines in the field of prenatal screening. INTENDED USERS Health care providers involved in prenatal screening, including general practitioners, obstetricians, midwives, maternal fetal medicine specialists, geneticists, and radiologists. TARGET POPULATION All pregnant women receiving counselling and providing informed consent for prenatal screening. EVIDENCE Published literature was retrieved through searches of Medline, PubMed, and the Cochrane Library in and prior to March 2016 using an appropriate controlled vocabulary (prenatal diagnosis, amniocentesis, chorionic villi sampling, non-invasive prenatal screening) and key words (prenatal screening, prenatal genetic counselling). Results were restricted to systematic reviews, randomized control trials/controlled clinical trials, and observational studies written in English and published from January 1985 to May 2016. Searches were updated on a regular basis and incorporated in the guideline. Grey (unpublished) literature was identified through searching the websites of health technology assessment and health technology-related agencies, clinical practice guideline collections, clinical trial registries, and national and international medical speciality societies. GUIDELINE UPDATE Evidence will be reviewed 5 years after publication to determine whether all or part of the guideline should be updated. However, if important new evidence is published prior to the 5-year cycle, the review process may be accelerated for a more rapid update of some recommendations.
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Zhu J, Qi H, Cao S, Cai L, Wen X, Tang G, Wan Q, Chen C, Wang J, Zeng W, Luo Y. Detection of a rare de novo 18p terminal deletion with inverted duplication in a Chinese pregnant woman. Mol Genet Genomic Med 2019; 7:e868. [PMID: 31317671 PMCID: PMC6732341 DOI: 10.1002/mgg3.868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/16/2019] [Accepted: 07/07/2019] [Indexed: 01/07/2023] Open
Abstract
Background The 18p terminal deletion with inverted duplication is an extremely rare chromosome structure abnormality and the common clinical manifestations include intellectual disability and speech delay, etc. Up to now, only three confirmed cases were reported in Europe, and here, for the first time in the Asian population, we report a case of de novo 18p inv‐dup‐del in a Chinese pregnant woman. This structural variation was accidentally discovered by the noninvasive prenatal testing (NIPT) during her prenatal examination. Methods Next generation sequencing (NGS) based copy number variations (CNVs) screening and karyotype analysis were performed to verify the type and heredity of the rearrangement, and the fluorescent in situ hybridization (FISH) analysis was also used to confirm the terminal deletion and inverted duplication. Results The patient has a de novo 18p11.31‐18p11.1 inverted duplication with a 6.2 Mb 18p terminal deletion. This rare chromosome imbalance, most likely caused by the U‐type exchange mechanism, resulted in the aberrant phenotype of mental disability, speech delay, seizure, and strabismus. However, the rearrangement was not inherited by her unborn child. Conclusion This report added a new type of variation to the spectrum of 18p terminal deletion with inverted duplication, and demonstrated that the maternal chromosome rearrangement discovered in NIPT should not just be consider as an interference factor but also a potential indicator of previously undiscovered pathogenic chromosome structure variations in pregnant women.
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Affiliation(s)
- Jianjiang Zhu
- Prenatal Diagnosis Center, Beijing Haidian Maternal and Child Health Hospital, Beijing, P. R. China
| | - Hong Qi
- Prenatal Diagnosis Center, Beijing Haidian Maternal and Child Health Hospital, Beijing, P. R. China
| | - Sha Cao
- Annoroad Gene Technology Co. Ltd, Beijing, P. R. China
| | - Lirong Cai
- Prenatal Diagnosis Center, Beijing Haidian Maternal and Child Health Hospital, Beijing, P. R. China
| | - Xiaohui Wen
- Prenatal Diagnosis Center, Beijing Haidian Maternal and Child Health Hospital, Beijing, P. R. China
| | - Guodong Tang
- Prenatal Diagnosis Center, Beijing Haidian Maternal and Child Health Hospital, Beijing, P. R. China
| | - Qian Wan
- Annoroad Gene Technology Co. Ltd, Beijing, P. R. China
| | - Chen Chen
- Annoroad Gene Technology Co. Ltd, Beijing, P. R. China
| | - Juan Wang
- Annoroad Gene Technology Co. Ltd, Beijing, P. R. China
| | - Wen Zeng
- Prenatal Diagnosis Center, Beijing Haidian Maternal and Child Health Hospital, Beijing, P. R. China
| | - Yao Luo
- Prenatal Diagnosis Center, Beijing Haidian Maternal and Child Health Hospital, Beijing, P. R. China
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Kypri E, Ioannides M, Touvana E, Neophytou I, Mina P, Velissariou V, Vittas S, Santana A, Alexidis F, Tsangaras K, Achilleos A, Patsalis P, Koumbaris G. Non-invasive prenatal testing of fetal chromosomal aneuploidies: validation and clinical performance of the veracity test. Mol Cytogenet 2019; 12:34. [PMID: 31338126 PMCID: PMC6628499 DOI: 10.1186/s13039-019-0446-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/30/2019] [Indexed: 02/05/2023] Open
Abstract
Introduction Non-Invasive Prenatal Testing (NIPT) for fetal aneuploidies using cell-free DNA (cfDNA) has been widely adopted in clinical practice due to its improved accuracy. A number of NIPT tests have been developed and validated. The purpose of this study is to evaluate the performance of the Veracity NIPT test for sex chromosome aneuploidy (SCA) detection in singleton pregnancies, autosomal aneuploidy detection in twin pregnancies and evaluation of Veracity clinical performance under routine NIPT conditions in a diverse cohort. Methods Blinded retrospective study in singleton pregnancies (n = 305); blinded retrospective and prospective study in twin pregnancies (n = 306) and prospective evaluation of clinical performance in singleton and twin pregnancies (n = 10564). Results Validation study results for the detection of SCAs in singleton pregnancies exhibited 100% sensitivity and specificity and correctly classified 7 (45,X), 4 (47,XXY), 2 (47,XXX) and 1 (47,XYY) cases. Validation study results for autosomal aneuploidy detection in twin pregnancies exhibited 100% sensitivity and specificity and correctly classified 3 trisomy 21, 1 trisomy 18 and 1 trisomy 13 samples. Clinical performance evaluation of Veracity was performed in 10564 pregnancies with median gestational age of 13 weeks, median maternal age 35 years and median gestational weight of 64 kg. Based on confirmation feedback the PPV for trisomies 21, 18 and 13 was estimated at 100% (95% CI, 92–100%), 100% (95% CI, 69–100%) and 71% (95% CI, 29–96%), respectively. Estimated PPV for Monosomy X was 57% (95%CI, 18–90%), while the NPV for SCA detection was estimated at 100% (95% CI, 99.94–100%). Conclusion Veracity NIPT test is based on a very powerful, highly accurate methodology that can be safely applied in the clinical setting. Electronic supplementary material The online version of this article (10.1186/s13039-019-0446-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elena Kypri
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus
| | - Marios Ioannides
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus
| | - Evi Touvana
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus
| | - Ioanna Neophytou
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus
| | - Petros Mina
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus
| | - Voula Velissariou
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus.,DNA Diagnosis N Analysis, Adrianoupoleos 1, 55133 Kalamaria, Thessaloniki, Greece
| | - Spiros Vittas
- DNA Diagnosis N Analysis, Adrianoupoleos 1, 55133 Kalamaria, Thessaloniki, Greece
| | - Alfredo Santana
- Clinical Genetics Unit, Childhood Hospital Materno-Infantil, Childhood Hospital Materno-Infantil, Las Palmas, GC, Canary Islands Spain
| | - Filippos Alexidis
- Eurogenetica, Adrianoupoleos 7, 55133 Kalamaria, Thessaloniki, Greece
| | - Kyriakos Tsangaras
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus
| | - Achilleas Achilleos
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus
| | - Philippos Patsalis
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus
| | - George Koumbaris
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Engomi, 2409 Nicosia, Cyprus
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Shi J, Zhang R, Li J, Zhang R. Novel perspectives in fetal biomarker implementation for the noninvasive prenatal testing. Crit Rev Clin Lab Sci 2019; 56:374-392. [PMID: 31290367 DOI: 10.1080/10408363.2019.1631749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Noninvasive prenatal testing (NIPT) utilizes cell-free fetal DNA (cffDNA) present in maternal peripheral blood to detect chromosomal abnormalities. The detection of 21-trisomy, 18-trisomy, and 13-trisomy in the fetus has become a common screening method during pregnancy and has been widely applied in routine clinical testing because of its analytical and clinical validity. Currently, noninvasive prenatal testing involving copy number variations (CNVs) and other frequent single-gene disorders is being widely studied, and it plays an important and indispensable role in prenatal detection. The multiple approaches that have been reported and validated by various laboratories have different merits and limitations. Their clinical validity, utility, and application vary with different diseases. This review summarizes the principles, methods, advantages, and limitations of noninvasive prenatal testing for the detection of aneuploidy, CNVs and single-gene disorders. Before implementation of NIPT into clinical practice, a list of criteria that the application must meet is crucial. Essential parameters such as clinical sensitivity, clinical specificity, positive predictive value (PPV) and negative predictive value (NPV) are required to properly evaluate the clinical validity and utility of NIPT. We then discuss and analyze these clinical parameters and clinical application guidelines, providing physicians and scientists with feasible strategies and the latest research information.
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Affiliation(s)
- Jiping Shi
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| | - Runling Zhang
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College , Beijing , China
| | - Jinming Li
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| | - Rui Zhang
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
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Villela D, Che H, Van Ghelue M, Dehaspe L, Brison N, Van Den Bogaert K, Devriendt K, Lewi L, Bayindir B, Vermeesch JR. Fetal sex determination in twin pregnancies using non-invasive prenatal testing. NPJ Genom Med 2019; 4:15. [PMID: 31285848 PMCID: PMC6609680 DOI: 10.1038/s41525-019-0089-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 05/31/2019] [Indexed: 01/23/2023] Open
Abstract
Non-invasive prenatal testing (NIPT) is accurate for fetal sex determination in singleton pregnancies, but its accuracy is not well established in twin pregnancies. Here, we present an accurate sex prediction model to discriminate fetal sex in both dichorionic diamniotic (DCDA) and monochorionic diamniotic/monochorionic monoamniotic (MCDA/MCMA) twin pregnancies. A retrospective analysis was performed using a total of 198 twin pregnancies with documented sex. The prediction was based on a multinomial logistic regression using the normalized frequency of X and Y chromosomes, and fetal fraction estimation. A second-step regression analysis was applied when one or both twins were predicted to be male. The model determines fetal sex with 100% sensitivity and specificity when both twins are female, and with 98% sensitivity and 95% specificity when a male is present. Since sex determination can be clinically important, implementing fetal sex determination in twins will improve overall twin pregnancies management.
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Affiliation(s)
- Darine Villela
- 1Department of Human Genetics, KU Leuven, Leuven, Belgium.,2Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Huiwen Che
- 1Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Marijke Van Ghelue
- 1Department of Human Genetics, KU Leuven, Leuven, Belgium.,3Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway.,4Department of Clinical Medicine, University of Tromsø, Tromsø, Norway
| | - Luc Dehaspe
- 1Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | | | - Koen Devriendt
- 1Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Liesbeth Lewi
- 5Clinical Department of Obstetrics and Gynecology, University Hospitals Leuven, Leuven, Belgium.,6Department of Development and Regeneration, Cluster Woman and Child, Group Biomedical Sciences, KU Leuven, Leuven, Belgium
| | - Baran Bayindir
- 1Department of Human Genetics, KU Leuven, Leuven, Belgium
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Hu H, Wang L, Wu J, Zhou P, Fu J, Sun J, Cai W, Liu H, Yang Y. Noninvasive prenatal testing for chromosome aneuploidies and subchromosomal microdeletions/microduplications in a cohort of 8141 single pregnancies. Hum Genomics 2019; 13:14. [PMID: 30871627 PMCID: PMC6419401 DOI: 10.1186/s40246-019-0198-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 02/26/2019] [Indexed: 12/28/2022] Open
Abstract
Background Noninvasive prenatal testing (NIPT) for fetal aneuploidies by scanning cell-free fetal DNA in maternal plasma is rapidly becoming a first-tier aneuploidy screening test in clinical practices. With the development of whole-genome sequencing technology, small subchromosomal deletions and duplications that could not be detected by conventional karyotyping are now able to be detected with NIPT technology. Methods In the present study, we examined 8141 single pregnancies with NIPT to calculate the positive predictive values of each of the chromosome aneuploidies and the subchromosomal microdeletions and microduplications. Results We confirmed that the positive predictive values (PPV) for trisomy 13, trisomy 18, trisomy 21, and sex chromosome aneuploidy were 14.28%, 60%, 80%, and 45.83%, respectively. At the same time, we also found 51 (0.63%) positive cases for chromosomal microdeletions or microduplications but only 13 (36.11%) true-positive cases. These results indicate that NIPT for trisomy 21 detection had the highest accuracy, while accuracy was low for chromosomal microdeletion and microduplications. Conclusions Therefore, it is very important to improve the specificity, accuracy, and sensitivity of NIPT technology for the detection of subchromosomal microdeletions and microduplications.
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Affiliation(s)
- Hua Hu
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Li Wang
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Jiayan Wu
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Peng Zhou
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Jingli Fu
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Jiuchen Sun
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Weiyi Cai
- CapitalBio Technology Inc., Beijing, 101111, China
| | - Hailiang Liu
- CapitalBio Technology Inc., Beijing, 101111, China.
| | - Ying Yang
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China.
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Zheng Y, Chen B, Wan S, Xu H, Dang Y, Song T, Li Y, Zhang J. Detection of 21q11.2-q22.11 deletions in a fetus by NIPT. J Clin Lab Anal 2019; 33:e22711. [PMID: 30666717 PMCID: PMC6818560 DOI: 10.1002/jcla.22711] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/14/2018] [Accepted: 10/15/2018] [Indexed: 01/29/2023] Open
Abstract
Background Non‐invasive prenatal testing (NIPT) is extensively used in the detection of fetal trisomies 21, 18, and 13, which is promptly becoming a common clinical practice. Concerned about the clinical application of non‐invasive detection of the fetal autosomal duplications or deletion. Case Presentation A 34‐year‐old, healthy pregnant woman was referred to the First Affiliated Hospital of the Air Force Medical University. The ultrasound examination indicates that low‐lying placenta, the fetus has a left ventricular bright spot and small amount of pericardial effusion. NIPT was chosen to further screen for fetal chromosomal abnormalities. NIPT results indicated an approximately 18 Mb deletion, which was verified by prenatal diagnosis. The chromosome microarray analysis (CMA) result showed about 19.2 Mb deletions in 21q11.2‐q22.11. The karyotype analysis result showed 46,XN,del(21)(q11.2q22.1). Prenatal diagnosis was consistent with NIPT results, and the paternal karyotype revealed no obvious abnormalities. Conclusion In this study, we successfully detected and diagnosed deletions of large fragments in chromosome 21 in a fetus using NIPT. This indicates that NIPT can provide effective genetic information for detecting fetal subchromosomal deletions/duplications.
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Affiliation(s)
- Yunyun Zheng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital Of Air Force Medical University, Xi'an, Shaanxi, China
| | - Biliang Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital Of Air Force Medical University, Xi'an, Shaanxi, China
| | - Shanning Wan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital Of Air Force Medical University, Xi'an, Shaanxi, China
| | - Hui Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital Of Air Force Medical University, Xi'an, Shaanxi, China
| | - Yinghui Dang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital Of Air Force Medical University, Xi'an, Shaanxi, China
| | - Tingting Song
- Department of Obstetrics and Gynecology, The First Affiliated Hospital Of Air Force Medical University, Xi'an, Shaanxi, China
| | - Yu Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital Of Air Force Medical University, Xi'an, Shaanxi, China
| | - Jianfang Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital Of Air Force Medical University, Xi'an, Shaanxi, China
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Wilkins-Haug L, Zhang C, Cerveira E, Ryan M, Mil-Homens A, Zhu Q, Reddi H, Lee C, Bianchi DW. Biological explanations for discordant noninvasive prenatal test results: Preliminary data and lessons learned. Prenat Diagn 2019; 38:445-458. [PMID: 29633279 DOI: 10.1002/pd.5260] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/25/2018] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Maternal plasma cell-free DNA (cfDNA) analysis is a powerful screening tool for Down syndrome. In a pilot series, we examined biologic causes of discordance between the cfDNA test results and the fetal karyotype. We also explored the feasibility of obtaining trio biospecimens by using parental engagement. METHODS A convenience sample of women with discordant cfDNA results were recruited by their care providers. We provided shipping materials and instructions for biospecimen collection. Maternal, newborn, and placental samples were examined with droplet digital PCR. RESULTS Thirteen of 15 women successfully had biospecimens obtained remotely. High-quality DNA was extracted in 12 of 13 women. Presumed biologic etiologies for discordance were identified in 7 of 12 women: 3 cases from additional clinical review (male renal transplant, vanishing twin, and colon cancer) and 4 cases from additional laboratory investigation using droplet digital PCR (3 with confined placental mosaicism and 1 with true fetal mosaicism). CONCLUSIONS Understanding the biology behind cfDNA-fetal karyotype discordancy is useful for follow-up clinical care. Our study suggests that most cases could be resolved by using a trio biospecimen protocol and parental involvement. To improve accuracy, additional sequencing of biospecimens will be required.
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Affiliation(s)
- Louise Wilkins-Haug
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Eliza Cerveira
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mallory Ryan
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Adam Mil-Homens
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Qihui Zhu
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Honey Reddi
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Charles Lee
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Diana W Bianchi
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA.,Prenatal Genomics and Therapy Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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48
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Discordant sex between fetal screening and postnatal phenotype requires evaluation. J Perinatol 2019; 39:28-33. [PMID: 30459335 PMCID: PMC6340391 DOI: 10.1038/s41372-018-0278-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 09/27/2018] [Accepted: 10/16/2018] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Non-invasive prenatal screening (NIPS) utilizes circulating cell-free DNA (cfDNA) to screen for fetal genetic abnormalities. NIPS is the first widely-available prenatal screen to assess genotypic sex. Most pediatricians have limited familiarity with NIPS technology and potential etiologies of discordant results. Increased familiarity may provide diagnostic insight and improve clinical care. STUDY DESIGN We reviewed all patients with discordant genotypic fetal sex assessed by cfDNA and neonatal phenotypic sex referred to our medical center. RESULT Four infants with discordant cfDNA result and phenotypic sex were identified. Etiologies include vanishing twin syndrome, difference of sexual development, sex chromosome aneuploidy and maternal chimerism. CONCLUSIONS We present four cases illustrating potential etiologies of discordant cfDNA result and postnatal phenotypic sex. Unanticipated cfDNA results offer the perinatologist a unique opportunity for early diagnosis and targeted treatment of various conditions, many of which may not have otherwise been detected in the perinatal period.
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Kaseniit KE, Hogan GJ, D'Auria KM, Haverty C, Muzzey D. Strategies to minimize false positives and interpret novel microdeletions based on maternal copy-number variants in 87,000 noninvasive prenatal screens. BMC Med Genomics 2018; 11:90. [PMID: 30340588 PMCID: PMC6194617 DOI: 10.1186/s12920-018-0410-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 10/01/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Noninvasive prenatal screening (NIPS) of common aneuploidies using cell-free DNA from maternal plasma is part of routine prenatal care and is widely used in both high-risk and low-risk patient populations. High specificity is needed for clinically acceptable positive predictive values. Maternal copy-number variants (mCNVs) have been reported as a source of false-positive aneuploidy results that compromises specificity. METHODS We surveyed the mCNV landscape in 87,255 patients undergoing NIPS. We evaluated both previously reported and novel algorithmic strategies for mitigating the effects of mCNVs on the screen's specificity. Further, we analyzed the frequency, length, and positional distribution of CNVs in our large dataset to investigate the curation of novel fetal microdeletions, which can be identified by NIPS but are challenging to interpret clinically. RESULTS mCNVs are common, with 65% of expecting mothers harboring an autosomal CNV spanning more than 200 kb, underscoring the need for robust NIPS analysis strategies. By analyzing empirical and simulated data, we found that general, outlier-robust strategies reduce the rate of mCNV-caused false positives but not as appreciably as algorithms specifically designed to account for mCNVs. We demonstrate that large-scale tabulation of CNVs identified via routine NIPS could be clinically useful: together with the gene density of a putative microdeletion region, we show that the region's relative tolerance to duplications versus deletions may aid the interpretation of microdeletion pathogenicity. CONCLUSIONS Our study thoroughly investigates a common source of NIPS false positives and demonstrates how to bypass its corrupting effects. Our findings offer insight into the interpretation of NIPS results and inform the design of NIPS algorithms suitable for use in screening in the general obstetric population.
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Affiliation(s)
- Kristjan Eerik Kaseniit
- Myriad Women's Health (previously Counsyl), 180 Kimball Way, South San Francisco, CA, 94080, USA
| | - Gregory J Hogan
- Myriad Women's Health (previously Counsyl), 180 Kimball Way, South San Francisco, CA, 94080, USA
| | - Kevin M D'Auria
- Myriad Women's Health (previously Counsyl), 180 Kimball Way, South San Francisco, CA, 94080, USA
| | - Carrie Haverty
- Myriad Women's Health (previously Counsyl), 180 Kimball Way, South San Francisco, CA, 94080, USA
| | - Dale Muzzey
- Myriad Women's Health (previously Counsyl), 180 Kimball Way, South San Francisco, CA, 94080, USA.
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Sato T, Samura O, Matsuoka T, Yoshida M, Aoki H, Migita O, Okamoto A, Hata K. Molecular genetic analysis reveals atypical confined placental mosaicism with a small supernumerary marker chromosome derived from chromosome 18: A clinical report of discordant results from three prenatal tests. Eur J Med Genet 2018; 62:103533. [PMID: 30171908 DOI: 10.1016/j.ejmg.2018.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/21/2018] [Accepted: 08/28/2018] [Indexed: 11/29/2022]
Abstract
We present a case with discordant results in three prenatal screening methods, with additional genetic analyses. Non-invasive prenatal testing (NIPT) was performed on a 41-year-old Japanese woman at 10 weeks of gestation, and the result was positive for trisomy 18 with high accuracy. Amniocentesis was performed at 16 weeks of gestation. However, the result showed 47,XX,+mar[16]/47,XX,+18[2]. Fetal examination by ultrasound revealed no malformations. After termination of the pregnancy, we performed additional genetic analyses, and confirmed the presence of confined placental mosaicism (CPM). Furthermore, a small supernumerary marker chromosome (sSMC) was detected in fetal cells, which was derived de novo from the centromere of chromosome 18. Single nucleotide polymorphism array analysis revealed that fetal chromosome 18 was inherited with maternal uniparental disomy, with a relatively large copy-neutral loss of heterozygosity, including its centromere. Our genetic analyses strongly indicated the cause of result discrepancy in prenatal testing as incomplete trisomy 18 rescue leading to atypical CPM with a sSMC. These findings also offer insight into the mechanisms by which chromosomal aberrations form during human oogenesis and embryogenesis.
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Affiliation(s)
- Taisuke Sato
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, 3-25-8, Nishi-Shinbashi, Minato-ku, Tokyo, 105-8461, Japan; Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1, Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Osamu Samura
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, 3-25-8, Nishi-Shinbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Tomona Matsuoka
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, 3-25-8, Nishi-Shinbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Masaki Yoshida
- GeneTech Inc., Sumitomo-Shiba Daimon Building 11th Floor, 2-5-5, Shibadaimon, Minato-ku, Tokyo, 105-0012, Japan
| | - Hiroaki Aoki
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, 3-25-8, Nishi-Shinbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Ohsuke Migita
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1, Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, 3-25-8, Nishi-Shinbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1, Okura, Setagaya-ku, Tokyo, 157-8535, Japan.
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