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Lukacova E, Hanzlikova Z, Podlesnyi P, Sedlackova T, Szemes T, Grendar M, Samec M, Hurtova T, Malicherova B, Leskova K, Budis J, Burjanivova T. Novel liquid biopsy CNV biomarkers in malignant melanoma. Sci Rep 2024; 14:15786. [PMID: 38982214 PMCID: PMC11233564 DOI: 10.1038/s41598-024-65928-y] [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: 03/14/2024] [Accepted: 06/25/2024] [Indexed: 07/11/2024] Open
Abstract
Malignant melanoma (MM) is known for its abundance of genetic alterations and a tendency for rapid metastasizing. Identification of novel plasma biomarkers may enhance non-invasive diagnostics and disease monitoring. Initially, we examined copy number variations (CNV) in CDK genes (CDKN2A, CDKN2B, CDK4) using MLPA (gDNA) and ddPCR (ctDNA) analysis. Subsequently, low-coverage whole genome sequencing (lcWGS) was used to identify the most common CNV in plasma samples, followed by ddPCR verification of chosen biomarkers. CNV alterations in CDK genes were identified in 33.3% of FFPE samples (Clark IV, V only). Detection of the same genes in MM plasma showed no significance, neither compared to healthy plasmas nor between pre- versus post-surgery plasma. Sequencing data showed the most common CNV occurring in 6q27, 4p16.1, 10p15.3, 10q22.3, 13q34, 18q23, 20q11.21-q13.12 and 22q13.33. CNV in four chosen genes (KIF25, E2F1, DIP2C and TFG) were verified by ddPCR using 2 models of interpretation. Model 1 was concordant with lcWGS results in 54% of samples, for model 2 it was 46%. Although CDK genes have not been proven to be suitable CNV liquid biopsy biomarkers, lcWGS defined the most frequently affected chromosomal regions by CNV. Among chosen genes, DIP2C demonstrated a potential for further analysis.
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Affiliation(s)
- E Lukacova
- Department of Molecular Biology and Genomics, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia
| | | | - P Podlesnyi
- Instituto de Investigaciones Biomedicas de Barcelona (IIBB), CSIC /Centro Investigacion Biomedica en Red Enfermedades Neurodegenerativas (CiberNed), Barcelona, Spain
| | - T Sedlackova
- Geneton Ltd., Bratislava, Slovakia
- Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - T Szemes
- Geneton Ltd., Bratislava, Slovakia
- Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - M Grendar
- Laboratory of Bioinformatics and Biostatistics, Biomedical Center Martin, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia
| | - M Samec
- Department of Medical Biology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - T Hurtova
- Department of Dermatovenereology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - B Malicherova
- Department of Clinical Biochemistry, University Hospital in Martin and Jessenius Faculty of Medicine, Comenius University, Martin, Slovakia
| | - K Leskova
- Department of Pathological Anatomy, Jessenius Faculty of Medicine and University Hospital in Martin, Comenius University, Martin, Slovakia
| | - J Budis
- Geneton Ltd., Bratislava, Slovakia
- Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - T Burjanivova
- Department of Molecular Biology and Genomics, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia.
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Wang Z, Tang X, Yang S, Zhao Y, Yin T, Chen M, Zhang Y, Wang Y, Zhang F, Wang L. Noninvasive prenatal screening with conventional sequencing depth to screen fetal copy number variants: A retrospective study of 19 144 pregnant women. J Obstet Gynaecol Res 2023; 49:2825-2835. [PMID: 37806662 DOI: 10.1111/jog.15805] [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: 06/05/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023]
Abstract
AIM To investigate the detectability of noninvasive prenatal screening (NIPS) with conventional sequencing depth to detect fetal copy number variants. METHODS We performed a retrospective study in a total of 19 144 pregnant women. Their cell-free plasma DNA were assessed for trisomy 21, trisomy 18, trisomy 13, sex chromosome aneuploidies, and genome-wide copy number variants by NIPS at conventional sequencing depth. RESULTS Three hundred seventy-four cases (2.0%, 374/19 144) with abnormal results were detected, which including 84 cases (0.4%, 84/19 144) with high risk of trisomy 21, 18, and 13, 90 cases (0.5%, 90/19 144) with high risk of sex chromosome abnormalities (SCA), and 44 cases (0.2%, 44/19 144) with high risk of other chromosome aneuploidies. One hundred fifty-six cases (0.8%, 156/19 144) with high risk of copy number variations (CNVs) were also detected. In following prenatal diagnosis, composite positive predictive value (PPV) of trisomy 21, 18, and 13 was 69.6% (48/69). The PPV of SCAs was 37.3% (19/51). And the PPVs for CNVs was detected as 51.0% (<5 Mb), 71.4% (5 Mb ≤ CNV ≤10 Mb), 56.5% (>10 Mb). Finally, a follow-up about the pregnancy outcomes were conducted for all available cases. CONCLUSIONS NIPS yielded high PPVs for trisomy 21, 18, and 13 aneuploidies and moderate PPVs for SCAs and CNVs. The screening effectiveness was closely related to the size of CNV fragments. Larger CNVs, especially larger than 5 Mb, could be detected more accurately by NIPS in our analytic technique. Meanwhile, diagnostic confirmation by microarray analysis was highly recommended.
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Affiliation(s)
- Zhiwei Wang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Xinxin Tang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Shuting Yang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Yali Zhao
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Ting Yin
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Min Chen
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Yue Zhang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Yongan Wang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Fang Zhang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Leilei Wang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
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Wang D, Peng H, Wang Y, Hou Y, Guo F, Zhu J, Hu T, Yang J. Performance of noninvasive prenatal testing for twin pregnancies in South China. J Assist Reprod Genet 2023; 40:2219-2231. [PMID: 37480419 PMCID: PMC10440307 DOI: 10.1007/s10815-023-02881-1] [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: 03/01/2023] [Accepted: 07/03/2023] [Indexed: 07/24/2023] Open
Abstract
OBJECTIVE The purpose of this study was to evaluate the performance of noninvasive prenatal testing (NIPT) for the detection of chromosomal aneuploidies and copy number variations (CNVs) in twin pregnancies. METHOD A cohort of 2010 women with twin pregnancies was recruited. 1331 patients opted for NIPT, and 679 patients opted for expanded NIPT (NIPT-plus). All high-risk patients were advised to undergo invasive prenatal diagnosis. All participants were followed up until 6 months after birth. RESULTS Twenty-two cases were predicted to have a high risk of chromosome abnormalities by NIPT, of which 14 pregnant women underwent invasive prenatal diagnosis. The 14 cases included 3 cases of trisomy 21, 1 case of trisomy 18, 1 case of trisomy 7, 2 cases of sex chromosome aneuploidies (SCAs), and 7 cases of CNVs, of which the confirmed cases numbered 2, 1, 0, 1, and 0, respectively. Twenty cases were predicted to have a high risk of chromosome abnormalities by NIPT-plus, of which 16 pregnant women underwent invasive prenatal diagnosis. The 16 cases included 1 case of trisomy 21, 1 case of trisomy 7, 7 cases of SCAs, and 7 cases of CNVs, of which were confirmed in 1, 0, 3, and 2, respectively. No false-negative result was reported during the follow-up period. CONCLUSION The NIPT/NIPT-plus has excellent performance in the detection of chromosome aneuploidies in twin pregnancies. But for CNVs, the effectiveness of NIPT is poor, and the NIPT-plus have a certain detection efficiency. It is worth noting that pre- and post-genetic counseling is especially important, and the chorionicity, mode of conception, clinical indications, and fetal fraction should be considered as influencing factors.
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Affiliation(s)
- Dongmei Wang
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Haishan Peng
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Yixia Wang
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Yaping Hou
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Fangfang Guo
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Juan Zhu
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Tingting Hu
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Jiexia Yang
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China.
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Zhu S, Jia C, Hao S, Zhang Q, He J, Wang X, Lin P, Guo Y, Li Y, Feng X. Evaluation of the clinical effects of non-invasive prenatal screening for diseases associated with aneuploidy and copy number variation. Mol Genet Genomic Med 2023; 11:e2200. [PMID: 37354111 PMCID: PMC10496052 DOI: 10.1002/mgg3.2200] [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: 03/14/2022] [Revised: 11/09/2022] [Accepted: 05/04/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND To explore and compare the clinical effects of high-resolution non-invasive prenatal screening (NIPS-Plus) for common/uncommon chromosomal aneuploidy and microdeletion/microduplication syndromes (MMS). METHODS The current prospective study included a total of 25,380 pregnant women who performed NIPS-Plus, and amniocentesis was performed on women with MMS with the screening results to diagnose patients with suspected MMS. RESULTS There were 415 samples with positive results for NIPS-Plus, included 275 with aneuploidy and 140 with MMS. After diagnosis by amniocentesis, 188 cases were confirmed as true positive, included46 cases of T21, 9 cases of T18, 1 case of T13, 34 cases of SCA, 41 cases of other chromosomal euploidy and 57 cases of MMS. In addition, no false negative cases were found, MMS was classified with 5 Mb with the cutoff value, and the PPV of different fragment size was counted, respectively. CONCLUSION We found that the corresponding PPV was 44.66% with the fragment of copy number variation (CNV) being less than or equal to 5 Mb, and when it was greater than 5 Mb, the PPV was 29.73%, which suggested that NIPS-Plus was more suitable for screening the PPV of small fragment abnormalities. NIPS-Plus has a good application effect in routine aneuploidy screening and had the best detection effect for T21; moreover, it performed well in screening of MMS and had better detection effect on MMS with CNV fragment length less than 5 Mb. Based on the current results, we suggested that NIPS-Plus should be used as a comprehensive elementary prenatal screening method for all pregnant women, but for MMS caused by abnormal large fragment CNV, the detection method and efficiency still need to be improved.
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Affiliation(s)
- Shaohua Zhu
- Medical Genetic Centre, Gansu Maternity and Child‐Care HospitalLanzhouChina
- Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Chunyang Jia
- Medical Genetic Centre, Gansu Maternity and Child‐Care HospitalLanzhouChina
| | - Shengju Hao
- Medical Genetic Centre, Gansu Maternity and Child‐Care HospitalLanzhouChina
- Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Qinghua Zhang
- Medical Genetic Centre, Gansu Maternity and Child‐Care HospitalLanzhouChina
- Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Jing He
- Medical Genetic Centre, Gansu Maternity and Child‐Care HospitalLanzhouChina
| | - Xing Wang
- Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Pengwu Lin
- Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Yuanyuan Guo
- Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Yigang Li
- Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Xuan Feng
- Medical Genetic Centre, Gansu Maternity and Child‐Care HospitalLanzhouChina
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Raymond YC, Acreman ML, Bussolaro S, Mol BW, Fernando S, Menezes M, Da Silva Costa F, Fantasia I, Rolnik DL. The accuracy of cell-free DNA screening for fetal segmental copy number variants: A systematic review and meta-analysis. BJOG 2023; 130:549-559. [PMID: 36655363 DOI: 10.1111/1471-0528.17386] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/17/2022] [Accepted: 11/29/2022] [Indexed: 01/20/2023]
Abstract
BACKGROUND The performance of cell-free DNA (cfDNA) screening for microscopic copy number variants (CNVs) is unclear. OBJECTIVES This was a systematic review and meta-analysis to investigate the sensitivity, specificity and positive predictive value (PPV) of cfDNA screening for CNVs. SEARCH STRATEGY Articles published in EMBASE, PubMed or Web of Science before November 2022 were screened for inclusion. This protocol was registered with PROSPERO (23 March 2021, CRD42021250849) prior to initiation. SELECTION CRITERIA Articles published in English, detailing diagnostic outcomes for at least 10 high-risk CNV results with cfDNA were considered for inclusion. DATA COLLECTION AND ANALYSIS The PPV was calculated and pooled with random-effects models for double-arcsine transformed proportions, using cases with diagnostic confirmation. Overall sensitivity, specificity and a summary receiver-operating characteristics (ROC) curve were calculated using bivariate models. The risk of bias was assessed using QUADAS-2. MAIN RESULTS In all, 63 articles were included in the final analysis, detailing 1 591 459 cfDNA results. The pooled PPV was 37.5% (95% confidence interval [CI] 30.6-44.8), with substantial statistical heterogeneity (I2 = 93.9%). Bivariate meta-analysis estimated sensitivity and specificity to be 77.4% (95% CI 65.7-86.0) and 99.4% (95% CI 98.0-99.8), respectively, with an area under the summary ROC curve of 0.947 (95% CI 0.776-0.984). CONCLUSIONS Approximately one-third of women who screen high-risk for CNVs with cfDNA will have an affected fetus. This value is of importance for screening counselling.
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Affiliation(s)
- Yvette C Raymond
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia
| | - Melissa L Acreman
- Department of Obstetrics and Gynaecology, Ipswich Hospital, Ipswich, Queensland, Australia
| | - Sofia Bussolaro
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Ben W Mol
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia.,Aberdeen Centre for Women's Health Research, University of Aberdeen, Aberdeen, UK
| | - Shavi Fernando
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia.,Monash Women's, Monash Health, Clayton, Victoria, Australia
| | - Melody Menezes
- Monash Ultrasound for Women, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Fabricio Da Silva Costa
- Maternal Fetal Medicine Unit, Gold Coast University Hospital, Gold Coast, Queensland, Australia.,School of Medicine, Griffith University, Gold Coast, Queensland, Australia
| | - Ilaria Fantasia
- Obstetrics & Gynaecology Unit, San Salvatore Hospital, L'Aquila, Italy
| | - Daniel Lorber Rolnik
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia.,Monash Women's, Monash Health, Clayton, Victoria, Australia
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Xiang J, Peng Z. Applications of Noninvasive Prenatal Testing for Subchromosomal Copy Number Variations Using Cell-Free DNA. Clin Lab Med 2022; 42:613-625. [PMID: 36368786 DOI: 10.1016/j.cll.2022.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jiale Xiang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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Yu J, Chen N, Chen M, Shen M, Qian Y, Dong M. Case Report: Prenatal diagnosis of fetal tetrasomy 9p initially identified by non-invasive prenatal testing. Front Genet 2022; 13:1020525. [PMID: 36386834 PMCID: PMC9662610 DOI: 10.3389/fgene.2022.1020525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/10/2022] [Indexed: 12/02/2022] Open
Abstract
Tetrasomy 9p is a rare syndrome characterized by fetal growth restriction, Dandy-Walker malformation, cardiac anomalies, and facial abnormalities and is discovered by ultrasound during the prenatal examination. Herein, we report a fetus of tetrasomy 9p without obvious phenotypic manifestations during the first trimester that was identified by non-invasive prenatal testing (NIPT). NIPT revealed that the gain of 9p24.3–9p11 that was approximately 46.36 Mb in size. Karyotyping of amniocytes indicated an additional marker in all metaphase. Chromosome microarray and fluorescence in situ hybridization on uncultured amniocytes revealed tetrasomic of 9p24.3q13, and that the supernumerary chromosome is a dicentric isochromosome consisted of two copies of the 9p arm. Taken together, it was indicated that the fetal karyotype was 47,XY,+idic (9) (q13), and that multiple techniques are crucial to the prenatal diagnosis.
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Affiliation(s)
- Jialing Yu
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Na Chen
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Min Chen
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Min Shen
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yeqing Qian
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Minyue Dong
- Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics Zhejiang University, Ministry of Education, Hangzhou, Zhejiang, China
- Key Laboratory of Women’s Reproductive Health of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Minyue Dong,
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Tang X, Wang Z, Yang S, Chen M, Zhang Y, Zhang F, Tan J, Yin T, Wang L. Maternal Xp22.31 copy-number variations detected in non-invasive prenatal screening effectively guide the prenatal diagnosis of X-linked ichthyosis. Front Genet 2022; 13:934952. [PMID: 36118896 PMCID: PMC9471005 DOI: 10.3389/fgene.2022.934952] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/01/2022] [Indexed: 11/22/2022] Open
Abstract
Background and aims: X-linked ichthyosis (XLI) is a common recessive genetic disease caused by the deletion of steroid sulfatase (STS) in Xp22.31. Maternal copy-number deletions in Xp22.31 (covering STS) can be considered an incidental benefit of genome-wide cell-free DNA profiling. Here, we explored the accuracy and clinical value of maternal deletions in Xp22.31 during non-invasive prenatal screening (NIPS). Materials and methods: We evaluated 13,156 pregnant women who completed NIPS. The maternal deletions in Xp22.31 revealed by NIPS were confirmed with maternal white blood cells by chromosome microarray analysis (CMA) or copy-number variation sequencing (CNV-seq). Suspected positive women pregnant with male fetuses were informed and provided with prenatal genetic counseling. Results: Nineteen maternal deletions in Xp22.31 covering STS were detected by NIPS, which were all confirmed, ranging in size from 0.61 to 1.77 Mb. Among them, eleven women with deletions in male fetuses accepted prenatal diagnoses, and finally nine cases of XLI were diagnosed. The nine XLI males had differing degrees of skin abnormalities, and of them, some male members of ten families had symptoms associated with XLI. Conclusion: NIPS has the potential to detect clinically significant maternal X chromosomal CNVs causing XLI, which can guide the prenatal diagnosis of X-linked ichthyosis and reflect the family history, so as to enhance pregnancy management as well as children and family members’ health management.
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Baranova EE, Sagaydak OV, Galaktionova AM, Kuznetsova ES, Kaplanova MT, Makarova MV, Belenikin MS, Olenev AS, Songolova EN. Whole genome non-invasive prenatal testing in prenatal screening algorithm: clinical experience from 12,700 pregnancies. BMC Pregnancy Childbirth 2022; 22:633. [PMID: 35945516 PMCID: PMC9364619 DOI: 10.1186/s12884-022-04966-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 08/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A fast adoption of a non-invasive prenatal testing (NIPT) in clinical practice is a global tendency last years. Firstly, in Russia according a new regulation it was possible to perform a widescale testing of pregnant women in chromosomal abnormality risk. The aim of the study-to assess efficiency of using NIPT as a second-line first trimester screening test in Moscow. METHODS Based on the first trimester combined prenatal screening results 12,700 pregnant women were classified as a high-risk (cut-off ≥ 1:100) and an intermediate-risk (cut-off 1:101 - 1:2500) groups followed by whole genome NIPT. Women from high-risk group and those who had positive NIPT results from intermediate-risk group were considered for invasive prenatal diagnostic. RESULTS 258 (2.0%) samples with positive NIPT results were detected including 126 cases of trisomy 21 (T21), 40 cases of T18, 12 cases of T13, 41 cases of sex chromosome aneuploidies (SCAs) and 39 cases of rare autosomal aneuploidies (RAAs) and significant copy number variations (CNVs). Statistically significant associations (p < 0.05) were revealed for fetal fraction (FF) and both for some patient's (body mass index and weight) and fetus's (sex and high risk of aneuploidies) characteristics. NIPT showed as a high sensitivity as specificity for common trisomies and SCAs with an overall false positive rate 0.3%. CONCLUSIONS NIPT demonstrated high sensitivity and specificity. As a second-line screening test it has shown a high efficiency in detecting fetus chromosomal anomalies as well as it could potentially lower the number of invasive procedures in pregnant women.
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Affiliation(s)
- Elena E Baranova
- LLC "Evogen", Moscow, Russian Federation.,Federal State Budgetary Educational Institution of Further Professional Education "Russian Medical Academy of Continuous Professional Education" of the Ministry of Healthcare of the Russian Federation, Moscow, Russian Federation
| | | | | | | | | | | | | | - Anton S Olenev
- Moscow City Health Department, City clinical hospital №24, Moscow, Russian Federation
| | - Ekaterina N Songolova
- Moscow City Health Department, City clinical hospital №67 named after L.A. Vorokhobova, Moscow, Russian Federation
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Zhang C, He Q, Qiao L, Li H, Wang T. The performance of grey zone in common foetal aneuploidy screening by semiconductor sequencing. J OBSTET GYNAECOL 2022; 42:1782-1787. [PMID: 35465819 DOI: 10.1080/01443615.2022.2039902] [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] [Indexed: 10/18/2022]
Abstract
A total of 15,267 pregnancies were tested by NIPT in this study. Grey zone (z score: 2.58 ∼ 4 and -4∼-2.58) was set for screening out aneuploidy 21, 18 and 13. Cases with z score located in the grey zone were retested starting from DNA extraction. The chi-squared test and/or the Fisher's exact test were used to compare variables. One hundred and eight screening-positive samples in the first run of NIPT were common trisomies 21 (N = 83), trisomies18 (N = 13) or trisomies 13 (N = 12), with PPVs of 87.18%, 76.92%, and 30% respectively. For the cases in the grey zone, most of them (67.15%, 184/274) were reported with Z score of Chromosome 21 in the grey zone and 176 were reclassified as negative by the second run of NIPT; while 3 cases reclassified as trisomy 21 and 1 case reclassified as trisomy 13 were finally confirmed by karyotyping analysis, with PPV 25% and 20% respectively. The grey zone and the second run of NIPT in this study showed that the grey zone and second run NIPT approach was able to accurately help categorise cases as negative and positive. Invasive diagnosis is recommended to prevent false negative aneuploidies for samples located in the special z score scope of 2.58-3 for two runs of NIPT. IMPACT STATEMENTWhat is already known on this subject? Grey zone was widely used in NIPT. The performance of grey zone of clinical samples on Illumina HiSeq 2000 instrument has been reported, and the performance of grey zone on some mainstream sequencers with simulated samples has also been summarised. Reported treatments for samples located in the grey zone in NIPT usually included being classified into 'unclassified' or 'no call' followed by following up and/or karyotyping analysis.What do the results of this study add? This study investigated the performance of the grey zone on Ion Proton DA8600 with clinical samples; and it present an alternative treatment for samples in grey zone that reclassified them as negative or positive by the second run of sequencing.What are the implications of these findings for clinical practice and/or further research? Our own data for the performance of the grey zone in the cfDNA assay on the semiconductor sequencing platform might provide raw materials for other researchers' meta-analysis, cohort study, or other studies. Details of Z score distributions of chromosomes in grey zone, results of the second run of NIPT for samples in the grey zone, and false negative samples in the grey zone would help lab technicians better analyse the NIPT results and help doctors to improve genetic counselling.
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Affiliation(s)
- Chunhua Zhang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Quanze He
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Longwei Qiao
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Hong Li
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Ting Wang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
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Gug C, Mozos I, Ratiu A, Tudor A, Gorduza EV, Caba L, Gug M, Cojocariu C, Furau C, Furau G, Vaida MA, Stoicanescu D. Genetic Counseling and Management: The First Study to Report NIPT Findings in a Romanian Population. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:medicina58010079. [PMID: 35056387 PMCID: PMC8777823 DOI: 10.3390/medicina58010079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/18/2021] [Accepted: 12/30/2021] [Indexed: 04/25/2023]
Abstract
Background and Objectives: Non-invasive prenatal testing (NIPT) has been confirmed as the most accurate screening test for trisomies 21, 18, 13, sex chromosomes aneuploidies and several microdeletions. This study aimed to assess the accuracy of cell free DNA testing based on low-level whole-genome sequencing to screen for these chromosomal abnormalities and to evaluate the clinical performance of NIPT. Materials and Methods: 380 consecutive cases from a single genetic center, from Western Romania were included in this retrospective study. Cell-free nucleic acid extraction from maternal blood, DNA sequencing and analysis of sequenced regions were performed by BGI Hong Kong and Invitae USA to determine the risk of specific fetal chromosomal abnormalities. In high-risk cases the results were checked by direct analysis of fetal cells obtained by invasive methods: 6 chorionic villus sampling and 10 amniocenteses followed by combinations of QF-PCR, karyotyping and aCGH. Results: NIPT results indicated low risk in 95.76% of cases and high risk in 4.23%. Seven aneuploidies and one microdeletion were confirmed, the other results were found to be a false-positive. A gestational age of up to 22 weeks had no influence on fetal fraction. There were no significant differences in fetal fraction across the high and low risk groups. Conclusions: This is the first study in Romania to report the NIPT results. The confirmation rate was higher for autosomal aneuploidies compared to sex chromosome aneuploidies and microdeletions. All cases at risk for trisomy 21 were confirmed. Only one large fetal microdeletion detected by NIPT has been confirmed. False positive NIPT results, not confirmed by invasive methods, led to the decision to continue the pregnancy. The main limitation of the study is the small number of patients included. NIPT can be used as a screening method for all pregnancies, but in high-risk cases, an invasive confirmation test was performed.
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Affiliation(s)
- Cristina Gug
- Department of Microscopic Morphology, “Victor Babeş” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (C.G.); (D.S.)
| | - Ioana Mozos
- Department of Functional Sciences, Discipline of Pathophysiology, “Victor Babes” University of Medicine and Pharmacy, 300173 Timisoara, Romania
- Center for Translational Research and Systems Medicine, “Victor Babes” University of Medicine and Pharmacy, 300173 Timisoara, Romania
- Correspondence: ; Tel.: +40-745610004
| | - Adrian Ratiu
- Department of Obstetrics and Gynecology II, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
- Obstetrics-Gynecology Clinic IV, Municipal Emergency Clinical Hospital, 300231 Timisoara, Romania
| | - Anca Tudor
- Department of Functional Sciences, Discipline of Medical Informatics and Biostatistics, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Eusebiu Vlad Gorduza
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (E.V.G.); (L.C.)
| | - Lavinia Caba
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (E.V.G.); (L.C.)
| | - Miruna Gug
- Faculty of Medicine, “Victor Babeş” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (M.G.); (C.C.)
| | - Catalina Cojocariu
- Faculty of Medicine, “Victor Babeş” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (M.G.); (C.C.)
| | - Cristian Furau
- Life Sciences Department, Faculty of Medicine, “Vasile Goldis“ Western University of Arad, 310414 Arad, Romania;
| | - Gheorghe Furau
- General Medicine Department, Faculty of Medicine, “Vasile Goldis“ Western University of Arad, 310414 Arad, Romania;
| | - Monica Adriana Vaida
- Department of Anatomy and Embryology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Dorina Stoicanescu
- Department of Microscopic Morphology, “Victor Babeş” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (C.G.); (D.S.)
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Clinical utility of expanded NIPT for chromosomal abnormalities and etiology analysis of cytogenetic discrepancies cases. J Assist Reprod Genet 2022; 39:267-279. [PMID: 35000096 PMCID: PMC8866633 DOI: 10.1007/s10815-021-02351-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/29/2021] [Indexed: 01/03/2023] Open
Abstract
PURPOSE This study is to assess the performance of expanded noninvasive prenatal testing (NIPT) in detecting chromosome aneuploidies and chromosome copy number variants (CNVs), and elucidate the discordant cases between NIPT and fetal karyotype. METHODS A total of 2139 single pregnancies have been recruited and sequenced with expanded NIPT. Karyotype analysis and CNV sequencing (CNV-seq) of amniotic fluid were performed in 22 of 23 high-risk, three low-risk NIPT pregnant women with abnormal ultrasound findings in the follow-up, and three non-reportable NIPT pregnant women. The genetic investigation of discordant results between NIPT and amniocytes in three cases was proceeded. Placental samples, fetal samples from the limb, hip, umbilical cord, and maternal peripheral blood leukocytes were collected for CNV-Seq. RESULTS Expanded NIPT revealed a total of 23 positive pregnancies and yielded the overall positive predictive value (PPV) 65.2%. For T21, T18, and XXY, all the PPV was 100% respectively. For CNVs > 10 Mb and 5-10 Mb, the PPV was 42.8% and 16.7%, respectively. The genetic investigation of placental and fetal samples indicated different levels of placental and fetal mosaicism contributing to two of three verified discordant results. CONCLUSIONS The results showed that screening for CNVs with expanded NIPT is promising although the accuracy rate remains insufficient. The different occurring time of mitotic non-disjunction of different chromosome in early development of embryo results in varying levels of chromosomal mosaicism in different placental and fetal tissues. The result highlights the significance of comprehensive cytogenetic validation of placental and fetal specimens with an inconsistent NIPT results.
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Mokveld T, Al-Ars Z, Sistermans EA, Reinders M. WisecondorFF: Improved Fetal Aneuploidy Detection from Shallow WGS through Fragment Length Analysis. Diagnostics (Basel) 2021; 12:59. [PMID: 35054227 PMCID: PMC8774687 DOI: 10.3390/diagnostics12010059] [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: 11/29/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/18/2022] Open
Abstract
In prenatal diagnostics, NIPT screening utilizing read coverage-based profiles obtained from shallow WGS data is routinely used to detect fetal CNVs. From this same data, fragment size distributions of fetal and maternal DNA fragments can be derived, which are known to be different, and often used to infer fetal fractions. We argue that the fragment size has the potential to aid in the detection of CNVs. By integrating, in parallel, fragment size and read coverage in a within-sample normalization approach, it is possible to construct a reference set encompassing both data types. This reference then allows the detection of CNVs within queried samples, utilizing both data sources. We present a new methodology, WisecondorFF, which improves sensitivity, while maintaining specificity, relative to existing approaches. WisecondorFF increases robustness of detected CNVs, and can reliably detect even at lower fetal fractions (<2%).
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Affiliation(s)
- Tom Mokveld
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, 2628 XE Delft, The Netherlands;
| | - Zaid Al-Ars
- Computer Engineering, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands;
| | - Erik A. Sistermans
- Department of Human Genetics and Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands;
| | - Marcel Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, 2628 XE Delft, The Netherlands;
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14
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Xie X, Zhou H, Zhao Q, Lu Y, Meng Y. Application of expanded noninvasive prenatal test in prenatal diagnosis of fetuses with increased nuchal translucency. J Matern Fetal Neonatal Med 2021; 35:6213-6218. [PMID: 34649482 DOI: 10.1080/14767058.2021.1909564] [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: 10/20/2022]
Abstract
OBJECTIVES To investigate the efficiency of the upgraded noninvasive prenatal test (NIPT-Plus) in fetuses with increased nuchal translucency (NT). METHODS Fetuses with an increased NT at or above 2.5 mm were selected for prenatal diagnosis. Amniotic fluid was collected from all cases for karyotype analysis and copy number variation sequencing (CNV-seq), and cell-free fetal DNA (cfDNA) in maternal blood was tested using Noninvasive Prenatal Test (NIPT-Plus) before amniocentesis in some cases. The results of amniocentesis with different NT thicknesses were analyzed and compared with those of NIPT-Plus. RESULTS A total of 125 eligible patients were divided into group A (2.5 mm ≤ NT < 3.0 mm) and group B (NT ≥ 3.0 mm). In group A, the detection rate of chromosomal aneuploidy and pathogenic copy number variation (CNV) was 10.6% and 6.4%, respectively. The total chromosome abnormality rate in group B (34.7%) was significantly higher than that in group A (17%). In 72 patients who underwent NIPT-Plus and amniocentesis, chromosomal aneuploidy accounted for 80.8% of the total chromosomal abnormalities. Among 21 cases of chromosomal aneuploidy, NIPT-Plus detected 20 cases. The sensitivity and specificity of NIPT-Plus toward aneuploidy detection were 95.2% and 100%, respectively. Among the five cases of pathogenic CNV, only two were detected using NIPT-Plus. CONCLUSION NIPT-plus is recommended as the first choice for fetal diagnosis in pregnant women with 2.5 mm ≤ NT < 3.0 mm who do not accept invasive prenatal diagnosis. When NT ≥ 3.0 mm and NIPT-Plus detects chromosomal aneuploidy, a rapid prenatal diagnosis can be performed through amniocentesis. In cases where NIPT-Plus yields negative results, amniocentesis still needs to be performed to detect chromosome microdeletions/duplications in order to avoid a missed diagnosis.
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Affiliation(s)
- Xiaoxiao Xie
- Medical School of Chinese PLA, Chinese PLA General hospital, Beijing, China
| | | | | | - Yanping Lu
- Medical School of Chinese PLA, Chinese PLA General hospital, Beijing, China
| | - Yuanguang Meng
- Medical School of Chinese PLA, Chinese PLA General hospital, Beijing, China
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15
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Wang J, Zhang B, Zhou L, Zhou Q, Chen Y, Yu B. Comprehensive Evaluation of Non-invasive Prenatal Screening to Detect Fetal Copy Number Variations. Front Genet 2021; 12:665589. [PMID: 34335682 PMCID: PMC8322773 DOI: 10.3389/fgene.2021.665589] [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: 02/08/2021] [Accepted: 06/15/2021] [Indexed: 11/25/2022] Open
Abstract
Objective To evaluate the effectiveness of non-invasive prenatal screening (NIPS) in prenatal screening of fetal pathogenic copy number variants (CNVs). Materials and Methods We evaluated the prenatal screening capacity using traditional and retrospective approaches. For the traditional method, we evaluated 24,613 pregnant women who underwent NIPS; cases which fetal CNVs were suggested underwent prenatal diagnosis with chromosomal microarray analysis (CMA). For the retrospective method, we retrospectively evaluated 47 cases with fetal pathogenic CNVs by NIPS. A systematic literature search was performed to compare the evaluation efficiency. Results Among the 24,613 pregnant women who received NIPS, 124 (0.50%) were suspected to have fetal CNVs. Of these, 66 women underwent prenatal diagnosis with CMA and 13 had true-positive results. The positive predictive value (PPV) of NIPS for fetal CNVs was 19.7%. Among 1,161 women who did not receive NIPS and underwent prenatal diagnosis by CMA, 47 were confirmed to have fetal pathogenic CNVs. Retesting with NIPS indicated that 24 of these 47 cases could also be detected by NIPS, representing a detection rate (DR) of 51.1%. In total, 10 publications, namely, six retrospective studies and four prospective studies, met our criteria and were selected for a detailed full-text review. The reported DRs were 61.10–97.70% and the PPVs were 36.11–80.56%. The sizes of CNVs were closely related to the accuracy of NIPS detection. The DR was 41.9% (13/31) in fetuses with CNVs ≤ 3 Mb, but was 55.0% (11/20) in fetuses with CNVs > 3 Mb. Finally, to intuitively show the CNVs accurately detected by NIPS, we mapped all CNVs to chromosomes according to their location, size, and characteristics. NIPS detected fetal CNVs in 2q13 and 4q35. Conclusion The DR and PPV of NIPS for fetal CNVs were approximately 51.1% and 19.7%, respectively. Follow-up molecular prenatal diagnosis is recommended in cases where NIPS suggests fetal CNVs.
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Affiliation(s)
- Jing Wang
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, China
| | - Bin Zhang
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, China
| | - Lingna Zhou
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, China
| | - Qin Zhou
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, China
| | - Yingping Chen
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, China
| | - Bin Yu
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, China
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Zhang J, Tang X, Hu J, He G, Wang J, Zhu Y, Zhu B. Investigation on combined copy number variation sequencing and cytogenetic karyotyping for prenatal diagnosis. BMC Pregnancy Childbirth 2021; 21:496. [PMID: 34238233 PMCID: PMC8265053 DOI: 10.1186/s12884-021-03918-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/28/2021] [Indexed: 11/10/2022] Open
Abstract
Background We aimed to evaluate the clinical value of copy number variation-sequencing (CNV-Seq) in combination with cytogenetic karyotyping in prenatal diagnosis. Methods CNV-Seq and cytogenetic karyotyping were performed in parallel for 9452 prenatal samples for comparison of the diagnostic performance of the two methods, and to evaluate the screening performance of maternal age, maternal serum screening, fetal ultrasound scanning and noninvasive prenatal testing (NIPT) for fetal pathogenic copy number variation (CNV). Results Among the 9452 prenatal samples, traditional karyotyping detected 704 cases (7.5%) of abnormal cytogenetic karyotypes, 171 (1.8%) chromosome polymorphism, 20 (0.2%) subtle structural variations, 74 (0.7%) mutual translocation (possibly balanced), 52 (0.6%) without karyotyping results, and 8431 (89.2%) normal cytogenetic karyotypes. Among the 8705 cases with normal karyotype, polymorphism, mutual translocation, or marker chromosome, CNV-Seq detected 63 cases (0.7%) of pathogenic chromosome microdeletion/duplication. Retrospectively, noninvasive prenatal testing (NIPT) had high sensitivity and specificity for the screening of fetal pathogenic CNV, and NIPT combining with maternal age, maternal serum screening or fetal ultrasound scanning, which improved the screening performance. Conclusion The combined application of cytogenetic karyotyping and CNV-Seq significantly improved the detection rate of fetal pathogenic chromosome microdeletion/duplication. NIPT was recommended for the screening of pathogenic chromosome microdeletion/duplication, and NIPT combining with other screening methods further improved the screening performance for pathogenic fetal CNV.
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Affiliation(s)
- Jinman Zhang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China.,Department of Obstetrics and Gynecology, First People's Hospital of Yunnan Province, No. 157, Jinbi Road, Xishan District, Kunming, Yunnan, 650032, People's Republic of China
| | - Xinhua Tang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China.,Department of Obstetrics and Gynecology, First People's Hospital of Yunnan Province, No. 157, Jinbi Road, Xishan District, Kunming, Yunnan, 650032, People's Republic of China
| | - Jilin Hu
- Department of Obstetrics and Gynecology, First People's Hospital of Yunnan Province, No. 157, Jinbi Road, Xishan District, Kunming, Yunnan, 650032, People's Republic of China
| | - Guilin He
- Department of Obstetrics and Gynecology, First People's Hospital of Yunnan Province, No. 157, Jinbi Road, Xishan District, Kunming, Yunnan, 650032, People's Republic of China
| | - Jian Wang
- Shanghai Children's Medical Center, Shanghai, 200127, People's Republic of China
| | - Yingting Zhu
- Research and Development Department, TissueTech, Inc., 7235 Corporate Center Drive, Suite B, Miami, Florida, 33126, USA.
| | - Baosheng Zhu
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China. .,Department of Obstetrics and Gynecology, First People's Hospital of Yunnan Province, No. 157, Jinbi Road, Xishan District, Kunming, Yunnan, 650032, People's Republic of China.
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Ali TM, Mateu-Brull E, Balaguer N, Dantas C, Borges HR, de Oliveira MQG, Rodrigo L, Campos-Galindo I, Navarro R, Milán M. Inherited unbalanced reciprocal translocation with 3q duplication and 5p deletion in a foetus revealed by cell-free foetal DNA (cffDNA) testing: a case report. Eur J Med Res 2021; 26:64. [PMID: 34187576 PMCID: PMC8243479 DOI: 10.1186/s40001-021-00535-5] [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: 03/16/2021] [Accepted: 06/18/2021] [Indexed: 11/17/2022] Open
Abstract
Background Since 2011, screening maternal blood for cell-free foetal DNA (cffDNA) fragments has offered a robust clinical tool to classify pregnancy as low or high-risk for Down, Edwards, and Patau syndromes. With recent advances in molecular biology and improvements in data analysis algorithms, the screening’s scope of analysis continues to expand. Indeed, screening now encompassess additional conditions, including aneuploidies for sex chromosomes, microdeletions and microduplications, rare autosomal trisomies, and, more recently, segmental deletions and duplications called copy number variations (CNVs). Yet, the ability to detect CNVs creates a new challenge for cffDNA analysis in couples in which one member carries a structural rearrangement such as a translocation or inversion. Case presentation We report a segmental duplication of the long arm of chromosome 3 and a segmental deletion of the short arm of chromosome 5 detected by cffDNA analysis in a 25-year-old pregnant woman. The blood sample was sequenced on a NextSeq 550 (Illumina) using the VeriSeq NIPT Solution v1 assay. G-band karyotyping in amniotic fluid only detected an abnormality in chromosome 5. Next-generation sequencing in amniocytes confirmed both abnormalities and identified breakpoints in 3q26.32q29 and 5p13.3p15. The foetus died at 21 weeks of gestation due to multiple abnormalities, and later G-band karyotyping in the parents revealed that the father was a carrier of a balanced reciprocal translocation [46,XY,t(3;5)(q26.2;p13)]. Maternal karyotype appeared normal. Conclusion This case provides evidence that extended cffDNA can detect, in addition to aneuploidies for whole chromosomes, large segmental aneuploidies. In some cases, this may indicate the presence of chromosomal rearrangements in a parent. Such abnormalities are outside the scope of standard cffDNA analysis targeting chromosomes 13, 18, 21, X, and Y, potentially leading to undiagnosed congenital conditions.
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Affiliation(s)
- Taccyanna M Ali
- Laboratório Igenomix, Laboratório de Genética E Medicina Reprodutiva, Sao Paulo, Sao Paulo, Brazil
| | - Emilia Mateu-Brull
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Nuria Balaguer
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Camila Dantas
- Laboratório Igenomix, Laboratório de Genética E Medicina Reprodutiva, Sao Paulo, Sao Paulo, Brazil
| | | | | | - Lorena Rodrigo
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Inmaculada Campos-Galindo
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Roser Navarro
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Miguel Milán
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain.
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Olenev AS, Baranova EE, Sagaydak OV, Galaktionova AM, Kuznetsova ES, Kaplanova MT, Belenikin MS, Songolova EN. Adoption of a non-invasive prenatal test (NIPT) in prenatal screening in Moscow: first results. RUSSIAN OPEN MEDICAL JOURNAL 2021. [DOI: 10.15275/rusomj.2021.0110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The objective — To assess the effectiveness of including NIPT in the structure of prenatal diagnostics in Moscow.
Material and Methods — Totally 5,181 pregnancies undergoing screening for fetal trisomy using NIPT during the period from 01.04.2020 to 30.09.2020 in Russia. According to the results of biochemical blood test, the patients were divided into two groups: group of high risk (cut-off ≥1:100) (n=208) and group of intermediate risk (cut-off 1:101 – 1:2500) (n=4,973). Patients at high-risk cell-free DNA (cfDNA) were offered an invasive procedure, followed by genetic analysis (cytogenetic or molecular karyotyping).
Results — Among the analysed samples, 117 (2.3%) had a high risk of the following common fetal chromosome abnormalities by NIPT: trisomy 21 in 50 cases, trisomy 18 in 17 cases, trisomy 13 in 5 cases, and sex chromosome aneuploidy (SCA) in 22 cases. Additionally, rare autosomal trisomies and/or subchromosomal arrangements were revealed in 23 cases. We found associations between cfDNA concentration and high risk of aneuploidies (particularly trisomy 21) and fetal sex and between low fetal fraction (FF) and body mass index (BMI) as well as maternal weight. Additionally, a high risk of trisomy 21 was associated with the term gestation.
Conclusion — The effectiveness of technological resources that are based on cfDNA testing for detecting abnormal fetal chromosome numbers and other chromosomal anomalies is high and reduce rates of false positive results. Therefore, NIPT should be more widely used as a first-line screening method.
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Affiliation(s)
| | - Elena E. Baranova
- Russian Medical Academy of Continuous Professional Education Department of medical genetics
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Lai Y, Zhu X, He S, Dong Z, Tang Y, Xu F, Chen Y, Meng L, Tao Y, Yi S, Su J, Huang H, Luo J, Leung TY, Wei H. Performance of Cell-Free DNA Screening for Fetal Common Aneuploidies and Sex Chromosomal Abnormalities: A Prospective Study from a Less Developed Autonomous Region in Mainland China. Genes (Basel) 2021; 12:478. [PMID: 33806256 PMCID: PMC8067030 DOI: 10.3390/genes12040478] [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: 02/03/2021] [Revised: 03/01/2021] [Accepted: 03/19/2021] [Indexed: 12/24/2022] Open
Abstract
To evaluate the performance of noninvasive prenatal screening (NIPS) in the detection of common aneuploidies in a population-based study, a total of 86,262 single pregnancies referred for NIPS were prospectively recruited. Among 86,193 pregnancies with reportable results, follow-up was successfully conducted in 1160 fetuses reported with a high-risk result by NIPS and 82,511 cases (95.7%) with a low-risk result. The screen-positive rate (SPR) of common aneuploidies and sex chromosome abnormalities (SCAs) provided by NIPS were 0.7% (586/83,671) and 0.6% (505/83,671), respectively. The positive predictive values (PPVs) for Trisomy 21, Trisomy 18, Trisomy 13 and SCAs were calculated as 89.7%, 84.0%, 52.6% and 38.0%, respectively. In addition, less rare chromosomal abnormalities, including copy number variants (CNVs), were detected, compared with those reported by NIPS with higher read-depth. Among these rare abnormalities, only 23.2% (13/56) were confirmed by prenatal diagnosis. In total, four common trisomy cases were found to be false negative, resulting in a rate of 0.48/10,000 (4/83,671). In summary, this study conducted in an underdeveloped region with limited support for the new technology development and lack of cost-effective prenatal testing demonstrates the importance of implementing routine aneuploidy screening in the public sector for providing early detection and precise prognostic information.
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Affiliation(s)
- Yunli Lai
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
- Guangxi Clinical Research Center for Fetal Diseases, Nanning 530000, China
| | - Xiaofan Zhu
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; (X.Z.); (Z.D.); (T.Y.L.)
- Genetics and Prenatal Diagnosis Center, The First Affiliation Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Sheng He
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Zirui Dong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; (X.Z.); (Z.D.); (T.Y.L.)
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518000, China
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Yanqing Tang
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Fuben Xu
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Yun Chen
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Lintao Meng
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Yuli Tao
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Shang Yi
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Jiasun Su
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Hongqian Huang
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Jingsi Luo
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; (X.Z.); (Z.D.); (T.Y.L.)
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518000, China
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Hongwei Wei
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Guangxi Clinical Research Center for Fetal Diseases, Nanning 530000, China
- Department of Obstetrics and Gynaecology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
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Identification of copy number variants by NGS-based NIPT at low sequencing depth. Eur J Obstet Gynecol Reprod Biol 2020; 256:297-301. [PMID: 33310305 DOI: 10.1016/j.ejogrb.2020.11.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/20/2020] [Accepted: 11/06/2020] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To explore the clinical utility of detecting chromosome copy number variants (CNVs) in the fetus by noninvasive prenatal testing (NIPT) using the low-pass whole-genome sequencing. METHODS Eight hundred and seventy-three singleton pregnancies with chromosomal microarray analysis (CMA) available between January 2017 to December 2019 and stored enough plasma sample for NIPT testing were included in this study. The CMA results show that forty-eight pregnancies with CNVs and eight hundred and twenty-five pregnancies are normal. Each pregnancy's plasma sample was blindly tested with NIPT at a depth of 0.51-1.19x for CNVs detection. The performance of the NIPT method for CNVs detection compared with the CMA method is evaluated. RESULTS A total of fifty-two CNVs ranging from 0.1-47.3 Mb identified in forty-eight samples were identified by NIPT, of which thirty-four CNVs were consistent with CMA results. Additionally, eighteen CNVs were missed by NIPT. The overall sensitivity and specificity for the detection of CNVs were 65.38% (95% CI: 51.76%-76.89%) and 97.45% (95% CI: 96.12%-98.35%), respectively. However, for the detection of CNVs larger than 2 Mb and CNVs less than 2Mb, the sensitivities were 81.58% (95% CI: 66.27%-91.09%) and 21.43% (95% CI: 6.84%-48.32%), respectively. CONCLUSION Our study demonstrated that the NIPT might be an alternative method for screening CNVs comparable with other studies. However, CNVs less than 2Mb in length shows poor sensitivity by NIPT. Noninvasive CNVs detection based on the NIPT method still needs more clinical validation studies and technical improvement to achieve clinically acceptable accuracy.
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21
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Xiang J, Ding Y, Song X, Mao J, Liu M, Liu Y, Huang C, Zhang Q, Wang T. Clinical Utility of SNP Array Analysis in Prenatal Diagnosis: A Cohort Study of 5000 Pregnancies. Front Genet 2020; 11:571219. [PMID: 33240322 PMCID: PMC7677511 DOI: 10.3389/fgene.2020.571219] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/19/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Single nucleotide polymorphism array (SNP-array) has been introduced for prenatal diagnosis. We aimed to evaluate the clinical value of SNP-array in the diagnosis of fetal chromosomal anomalies. METHODS A retrospective study was conducted on 5000 cases tested by SNP-array, and the results of 4022 cases analyzed by both karyotyping and SNP-array were compared. RESULTS SNP-array analysis of 5000 samples revealed that the overall abnormality detection rate by SNP-array was 12.3%, and the overall detection rate of clinically significant copy number variations (CNVs) by SNP-array was 2.6%. SNP-array identified clinically significant submicroscopic CNVs in 4.5% fetuses with anomaly on ultrasonography, in 1.6% of fetuses with advanced maternal age (AMA), in 2.5% of fetuses with abnormal result on maternal serum screening, in 2.9% of fetuses with abnormal non-invasive prenatal testing (NIPT) results and in 3.0% of fetuses with other indications. Of the 4022 samples analyzed by both karyotyping and SNP-array, SNP-array could identify all the aneuploidy and triploidy detected by karyotyping but did not identify balanced structural chromosomal abnormalities and low-level mosaicism detected by karyotyping. CONCLUSION SNP-array could additionally identify clinically significant submicroscopic CNVs, and we recommend the combination of SNP-array analysis and karyotyping in prenatal diagnosis.
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Affiliation(s)
- Jingjing Xiang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Yang Ding
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Xiaoyan Song
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Jun Mao
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Minjuan Liu
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Yinghua Liu
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Chao Huang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Qin Zhang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Ting Wang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
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Flowers NJ, Burgess T, Giouzeppos O, Shi G, Love CJ, Hunt CE, Scarff KL, Archibald AD, Pertile MD. Genome-wide noninvasive prenatal screening for carriers of balanced reciprocal translocations. Genet Med 2020; 22:1944-1955. [PMID: 32807973 DOI: 10.1038/s41436-020-0930-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Balanced reciprocal translocation carriers are at increased risk of producing gametes with unbalanced forms of the translocation leading to miscarriage, fetal anomalies, and birth defects. We sought to determine if genome-wide cell-free DNA based noninvasive prenatal screening (gw-NIPS) could provide an alternative to prenatal diagnosis for carriers of these chromosomal rearrangements. METHODS This pilot series comprises a retrospective analysis of gw-NIPS and clinical outcome data from 42 singleton pregnancies where one parent carried a balanced reciprocal translocation. Gw-NIPS was performed between August 2015 and March 2018. Inclusion criteria required at least one translocation segment to be ≥15 Mb in size. RESULTS Forty samples (95%) returned an informative result; 7 pregnancies (17.5%) were high risk for an unbalanced translocation and confirmed after diagnostic testing. The remaining 33 informative samples were low risk and confirmed after diagnostic testing or normal newborn physical exam. Test sensitivity of 100% (95% confidence interval [CI]: 64.6-100%) and specificity of 100% (95% CI: 89.6-100%) were observed for this pilot series. CONCLUSION We demonstrate that gw-NIPS is a potential option for a majority of reciprocal translocation carriers. Further confirmation of this methodology could lead to adoption of this noninvasive alternative.
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Affiliation(s)
- Nicola Jane Flowers
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Trent Burgess
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Olivia Giouzeppos
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Grace Shi
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Clare Jane Love
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Clare Elizabeth Hunt
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Katrina Louise Scarff
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Alison Dalton Archibald
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Mark Domenic Pertile
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia. .,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.
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Iwarsson E, Conner P. Detection rates and residual risk for a postnatal diagnosis of an atypical chromosome aberration following combined first-trimester screening. Prenat Diagn 2020; 40:852-859. [PMID: 32274819 DOI: 10.1002/pd.5698] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 03/16/2020] [Accepted: 04/01/2020] [Indexed: 01/06/2023]
Abstract
OBJECTIVES To determine the detection rates of all types of chromosome aberrations and the residual risk for postnatal diagnosis of an atypical chromosome aberration depending on the strategy for further investigation with either noninvasive prenatal testing (NIPT) or invasive testing in pregnancies with increased risk following combined first-trimester screening (cFTS). METHODS A review of all pregnancies examined with cFTS during 2010 to 2017. RESULTS The cohort consisted of 129 493 pregnancies. There were 852 (0.7%) clinically significant chromosome aberrations, including aberrations detected later on or after birth. A total of 12% were atypical chromosome aberrations. Considering that 40% were detected due to a miscarriage/intrauterine fetal death or a malformation on ultrasound there is a 0.05% (1:2000) background risk of a postnatal diagnosis of a liveborn child with an atypical chromosome aberration if no further invasive test is performed during pregnancy. If all women with an increased risk (≥1:200) had an invasive test and NIPT was performed up to a risk of 1:1000, 95% of common trisomies/sex chromosome aberrations and 55% of atypical aberrations would be detected. CONCLUSIONS If NIPT was offered to all women with an increased risk following cFTS it would imply that three times as many children would be born with an atypical chromosome aberration.
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Affiliation(s)
- Erik Iwarsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Peter Conner
- Center for Fetal Medicine, Department of Obstetrics and Gynecology, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
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Luo Y, Lin J, Sun Y, Qian Y, Wang L, Chen M, Dong M, Jin F. Non-invasive prenatal screening for Emanuel syndrome. Mol Cytogenet 2020; 13:9. [PMID: 32158503 PMCID: PMC7057502 DOI: 10.1186/s13039-020-0476-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/07/2020] [Indexed: 12/27/2022] Open
Abstract
Objective The aim of this study was to validate the results of two Emanuel syndromes detected by non-invasive prenatal screening (NIPS) screening using invasive methods, providing clinical performance of NIPS on chromosome microduplication detection. Methods NIPS was performed to diagnose the Emanuel syndrome. Amniocentesis or cordocentesis was performed to confirm the positive screening result of Emanuel syndrome cases. Fetal sample was detected by karyotyping, fluorescence in situ hybridization (FISH), and single nucleotide polymorphism array (SNP Array). Parental karyotyping and FISH were also carried out. Results Two cases with chromosomal abnormalities of 11q23.3q25 and 22q11.1q11.21 were found by NIPS. Chromosomal karyotyping showed that the two fetuses each have a small supernumerary marker chromosome (sSMC), SNP Array further demonstrated double duplications approximately 18 Mb in 11q23.3q25 and 3 Mb in 22q11.1q11.21. FISH confirmed that the small supernumerary marker chromosome (sSMC) was ish der(22)t(11;22) (TUPLE1+, ARSA-). Ultrasound scan and MRI showed some structure malformations in two fetuses. The two mothers were found to be a balanced carrier: 46,XX, t(11;22)(q23.3;q11.2). Conclusion NIPS could effectively identify Emanuel syndrome, which may indicate risks of a parent being a balanced rearrangement carrier. The followed confirmation test for positive sample is necessary and ensures the accuracy of the diagnosis.
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Affiliation(s)
- Yuqin Luo
- 1Department of Reproductive Genetics, Women's Hospital,School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310006 Zhejiang China.,2Ministry of Education, Key Laboratory of Reproductive Genetics (Zhejiang University), Hangzhou, People's Republic of China
| | - Jie Lin
- 2Ministry of Education, Key Laboratory of Reproductive Genetics (Zhejiang University), Hangzhou, People's Republic of China
| | - Yixi Sun
- 1Department of Reproductive Genetics, Women's Hospital,School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310006 Zhejiang China.,2Ministry of Education, Key Laboratory of Reproductive Genetics (Zhejiang University), Hangzhou, People's Republic of China
| | - Yeqing Qian
- 1Department of Reproductive Genetics, Women's Hospital,School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310006 Zhejiang China.,2Ministry of Education, Key Laboratory of Reproductive Genetics (Zhejiang University), Hangzhou, People's Republic of China
| | - Liya Wang
- 1Department of Reproductive Genetics, Women's Hospital,School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310006 Zhejiang China.,2Ministry of Education, Key Laboratory of Reproductive Genetics (Zhejiang University), Hangzhou, People's Republic of China
| | - Min Chen
- 1Department of Reproductive Genetics, Women's Hospital,School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310006 Zhejiang China.,2Ministry of Education, Key Laboratory of Reproductive Genetics (Zhejiang University), Hangzhou, People's Republic of China
| | - Minyue Dong
- 1Department of Reproductive Genetics, Women's Hospital,School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310006 Zhejiang China.,2Ministry of Education, Key Laboratory of Reproductive Genetics (Zhejiang University), Hangzhou, People's Republic of China
| | - Fan Jin
- 1Department of Reproductive Genetics, Women's Hospital,School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310006 Zhejiang China.,2Ministry of Education, Key Laboratory of Reproductive Genetics (Zhejiang University), Hangzhou, People's Republic of China.,3Centre of Reproductive Medicine, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Cui W, Liu X, Zhang Y, Wang Y, Chu G, He R, Zhao Y. Evaluation of non-invasive prenatal testing to detect chromosomal aberrations in a Chinese cohort. J Cell Mol Med 2019; 23:7873-7878. [PMID: 31454164 PMCID: PMC6815821 DOI: 10.1111/jcmm.14614] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/02/2019] [Accepted: 08/06/2019] [Indexed: 11/27/2022] Open
Abstract
The aim of this study was to evaluate the clinical feasibility of non‐invasive prenatal testing (NIPT) to detect foetal copy number variations (CNVs). Next‐generation sequencing for detecting foetal copy number variations (CNVs) was performed on the collected samples from 161 pregnancies with ultrasound anomalies and negative NIPT results for aneuploidy. The performance of NIPT for detecting chromosome aberrations was calculated. The sensitivity and specificity of NIPT for detecting CNVs > 1 Mb were 83.33% and 99.34%; the PPV and negative predictive rate (NPV) were 90.91% and 98.68%. Non‐invasive prenatal testing can be performed to detect chromosomal aberrations in first trimester with high performance for CNVs, and occasional discordant cases are unavoidable.
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Affiliation(s)
- Wanting Cui
- Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaoliang Liu
- Shengjing Hospital of China Medical University, Shenyang, China
| | - Yuanyuan Zhang
- Shengjing Hospital of China Medical University, Shenyang, China
| | - Yueping Wang
- Shengjing Hospital of China Medical University, Shenyang, China
| | - Guoming Chu
- Shengjing Hospital of China Medical University, Shenyang, China
| | - Rong He
- Shengjing Hospital of China Medical University, Shenyang, China
| | - Yanyan Zhao
- Shengjing Hospital of China Medical University, Shenyang, China
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26
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Raman L, Baetens M, De Smet M, Dheedene A, Van Dorpe J, Menten B. PREFACE: In silico pipeline for accurate cell-free fetal DNA fraction prediction. Prenat Diagn 2019; 39:925-933. [PMID: 31219182 PMCID: PMC6771918 DOI: 10.1002/pd.5508] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/16/2019] [Accepted: 06/15/2019] [Indexed: 12/12/2022]
Abstract
Objective During routine noninvasive prenatal testing (NIPT), cell‐free fetal DNA fraction is ideally derived from shallow‐depth whole‐genome sequencing data, preventing the need for additional experimental assays. The fraction of aligned reads to chromosome Y enables proper quantification for male fetuses, unlike for females, where advanced predictive procedures are required. This study introduces PREdict FetAl ComponEnt (PREFACE), a novel bioinformatics pipeline to establish fetal fraction in a gender‐independent manner. Methods PREFACE combines the strengths of principal component analysis and neural networks to model copy number profiles. Results For sets of roughly 1100 male NIPT samples, a cross‐validated Pearson correlation of 0.9 between predictions and fetal fractions according to Y chromosomal read counts was noted. PREFACE enables training with both male and unlabeled female fetuses. Using our complete cohort (nfemale = 2468, nmale = 2723), the correlation metric reached 0.94. Conclusions Allowing individual institutions to generate optimized models sidelines between‐laboratory bias, as PREFACE enables user‐friendly training with a limited amount of retrospective data. In addition, our software provides the fetal fraction based on the copy number state of chromosome X. We show that these measures can predict mixed multiple pregnancies, sex chromosomal aneuploidies, and the source of observed aberrations. What's already known about this topic?
Cell‐free fetal DNA fraction is an important estimate during noninvasive prenatal testing (NIPT). Most techniques to establish fetal fraction require experimental procedures, which impede routine execution.
What does this study add?
PREFACE is a novel software to accurately predict fetal fraction based on solely shallow‐depth whole‐genome sequencing data, the fundamental base of a default NIPT assay. In contrast to previous efforts, PREFACE enables user‐friendly model training with a limited amount of retrospective data.
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Affiliation(s)
- Lennart Raman
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium.,Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Machteld Baetens
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Matthias De Smet
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium
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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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28
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Zhang C, Liang B, Qiao L, Xuan L, Li H, He Q, Wu X, Lu J, Yu B, Wang T. Effect quantification and value prediction of factors in noninvasive detection for specific fetal copy number variants by semiconductor sequencing. Mol Genet Genomic Med 2019; 7:e00718. [PMID: 31115175 PMCID: PMC6625335 DOI: 10.1002/mgg3.718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/08/2019] [Accepted: 04/15/2019] [Indexed: 12/20/2022] Open
Abstract
Background The detection limit of noninvasive prenatal testing (NIPT) by next generation sequencing for any given fetal copy number variants (CNV) can be influenced by several factors. In this study, we quantified the effects and predicted the value of parameters for CNVs detection by NIPT. Methods Genomic DNA from patient's leucocytes with 3.16 Mb microdeletion in 22q11.21 was mixed with DNA from aborted fetal tissues without CNV at various concentrations by an enzyme digestion method. Abnormal DNA at 0% served as negative control. Sequencing of mixture samples (at 0%, 4%, 12%, and 20%) by Ion Proton Sequencer was performed at flow 500, with WISECONDOR as the pipeline in CNV‐calling and bin of 500, 750 and 1,000 kb for counting unique reads. The parameters were evaluated with Box–Behnken design. The region with Z score ≦−3 was marked as a potential microdeletion. Results The equation of Z score depending on fetal fraction, unique read number and bin size was obtained by Box–Behnken design. The negative effect was quantified as the coefficient in the equation. The smallest values of these parameters were defined as 4 M unique read number, and 10.08% fetal DNA concentration at bin of 750 kb for detecting subchromosomal microdeletion of 3.16 Mb. Conclusion The quantification of effect and value of parameters as well as the method used in this study can benefit the establishment of quality standards for CNVs detection and interpretation of CNVs detection results.
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Affiliation(s)
- Chunhua Zhang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Bo Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Longwei Qiao
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Liming Xuan
- Basecare Medical Device Co., Ltd, Suzhou, China
| | - Hong Li
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Quanze He
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Xiaojuan Wu
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Jiafeng Lu
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Bin Yu
- Changzhou Women and Children Health Hospital affiliated to Nanjing Medical University, Changzhou, China
| | - Ting Wang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
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Yu D, Zhang K, Han M, Pan W, Chen Y, Wang Y, Jiao H, Duan L, Zhu Q, Song X, Hong Y, Chen C, Wang J, Hui F, Huang L, Chen C, Du Y. Noninvasive prenatal testing for fetal subchromosomal copy number variations and chromosomal aneuploidy by low-pass whole-genome sequencing. Mol Genet Genomic Med 2019; 7:e674. [PMID: 31004415 PMCID: PMC6565572 DOI: 10.1002/mgg3.674] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/27/2019] [Accepted: 03/06/2019] [Indexed: 12/20/2022] Open
Abstract
Background Expanding noninvasive prenatal testing (NIPT) to include the detection of fetal subchromosomal copy number variations (CNVs) significantly decreased the sensitivity and specificity. Developing analytic pipeline to achieve high performance in the noninvasive detection of CNVs will largely contribute to the application of CNVs screening in clinical practice. Methods We developed the Noninvasively Prenatal Subchromosomal Copy number variation Detection (NIPSCCD) method based on low‐pass whole‐genome sequencing, and evaluated its efficacy in detecting fetal CNVs and chromosomal aneuploidies with 20,003 pregnant women. Results Totally, NIPSCCD identified 36 CNVs, including 29 CNVs consistent and 7 CNVs inconsistent with amniocytes tests. Additionally, seven fetal CNVs identified by amniocytes testing were undetected by NIPSCCD. The sensitivities for detecting CNVs > 10 Mb, 5 Mb–10 Mb, and CNVs < 5 Mb were 91.67%, 100.00%, and 68.42%, respectively. Moreover, NIPSCCD identified 103/ true positive trisomy 21/18/13 cases and 21 false positives, producing an overall 100.00% sensitivity and 99.89% specificity. Conclusion NIPSCCD showed a good performance in detecting fetal subchromosomal CNVs, especially for CNVs >10 Mb, and can be incorporated into the routine NIPT chromosomal aneuploidies screening with high sensitivity and specificity.
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Affiliation(s)
- Dongyi Yu
- Genetic Testing Center, Qingdao Women & Children Hospital, Qingdao University, Qingdao, China
| | - Kai Zhang
- Genetic Testing Center, Qingdao Women & Children Hospital, Qingdao University, Qingdao, China
| | - Meiyan Han
- Genetic Testing Center, Qingdao Women & Children Hospital, Qingdao University, Qingdao, China
| | - Wei Pan
- The Center of Prenatal Diagnosis, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Ying Chen
- Central Lab, Wuxi Maternity and Child Health Care Hospital, Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Yunfeng Wang
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Hongyan Jiao
- The Branch Center of Prenatal Diagnosis, Hebei Maternity and Child Healthcare Hospital, Shijiazhuang, China
| | - Ling Duan
- Department of Obstetrics, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Qiying Zhu
- Department of Obstetrics, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Xiaojie Song
- Department of Obstetrics and Gynecology, Wuhan Women and Child Care Service Hospital, Wuhan, China
| | - Yan Hong
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Chen Chen
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Juan Wang
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Feng Hui
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | | | | | - Yang Du
- Annoroad Gene Technology Co., Ltd, Beijing, China
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Zhu Y, Shan Q, Zheng J, Cai Q, Yang H, Zhang J, Du X, Jin F. Comparison of Efficiencies of Non-invasive Prenatal Testing, Karyotyping, and Chromosomal Micro-Array for Diagnosing Fetal Chromosomal Anomalies in the Second and Third Trimesters. Front Genet 2019; 10:69. [PMID: 30915098 PMCID: PMC6421281 DOI: 10.3389/fgene.2019.00069] [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: 07/18/2018] [Accepted: 01/28/2019] [Indexed: 01/06/2023] Open
Abstract
In this study, we aimed to compare the efficiency of non-invasive prenatal testing (NIPT), karyotyping, and chromosomal micro-array (CMA) for the diagnosis of fetal chromosomal anomalies in the second and third trimesters. Pregnant women, who underwent amniocenteses for prenatal genetic diagnoses during their middle and late trimesters, were recruited at the Prenatal Diagnosis Center of Taizhou City. Maternal blood was separated for NIPT, and amniotic fluid cells were cultured for karyotyping and CMA. The diagnostic efficiency of NIPT for detecting fetal imbalanced anomalies was compared with karyotyping and CMA. A total of 69 fetal chromosomal imbalances were confirmed by CMA, 37 were diagnosed by NIPT and 35 were found by karyotyping. The sensitivities of NIPT and karyotyping for diagnosing aneuploidy were 96.3% and 100% respectively. Only one mosaic sexual chromosome monosomy was misdiagnosed by NIPT, whereas the sensitivity of NIPT and karyotyping was 70% and 30%, respectively, for detecting pathogenic deletions and duplications sized from 5-20 Mb. Taken together, our results suggest that the efficiency of NIPT was similar to the formula karyotyping for detecting chromosome imbalance in the second and third trimesters.
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Affiliation(s)
- Yiyang Zhu
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Department of Prenatal Diagnosis, Enze Women's Hospital, Taizhou Hospital of Zhejiang Province, Zhejiang University, Taizhou, China.,Taizhou Centers of Prenatal Screening, Taizhou Women and Children's Hospital, Wenzhou Medical University, Taizhou, China
| | - Qunda Shan
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Department of Prenatal Diagnosis, Lishui Maternal and Child Health Care Hospital, Lishui, China
| | - Jiayong Zheng
- Department of Gynecology and Obstetrics, Wenzhou People's Hospital, Wenzhou Maternal and Child Health Care Hospital, Wenzhou City Key Laboratory of Gynecology and Obstetrics, Wenzhou, China
| | - Qunxi Cai
- Department of Prenatal Diagnosis, Enze Women's Hospital, Taizhou Hospital of Zhejiang Province, Zhejiang University, Taizhou, China
| | - Huanli Yang
- Department of Prenatal Diagnosis, Enze Women's Hospital, Taizhou Hospital of Zhejiang Province, Zhejiang University, Taizhou, China
| | - Jianhong Zhang
- Taizhou Centers of Prenatal Screening, Taizhou Women and Children's Hospital, Wenzhou Medical University, Taizhou, China
| | - Xiaodong Du
- Department of Prenatal Diagnosis, Lishui Maternal and Child Health Care Hospital, Lishui, China
| | - Fan Jin
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Hangzhou, China
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Luo Y, Jia B, Yan K, Liu S, Song X, Chen M, Jin F, Du Y, Wang J, Hong Y, Cao S, Li D, Dong M. Pilot study of a novel multi-functional noninvasive prenatal test on fetus aneuploidy, copy number variation, and single-gene disorder screening. Mol Genet Genomic Med 2019; 7:e00597. [PMID: 30767419 PMCID: PMC6465655 DOI: 10.1002/mgg3.597] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 12/26/2018] [Accepted: 01/04/2019] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND The noninvasive prenatal testing (NIPT) has been successfully used in the clinical screening of fetal trisomy 13, 18, and 21 in the last few years and researches on detecting sub-chromosomal copy number variations (CNVs) and monogenic diseases are also in progress. To date, multiple tests are needed in order to complete a full set of fetus disorder screening, which is costly and time consuming. Therefore, an integrated 3-in-1 NIPT approach will be in great demand by routine clinical practice in the near future. METHODS We designed a target capture sequencing panel with an associate bioinformatics pipeline to create a novel multi-functional NIPT method and we evaluated its performance by testing 22 clinical samples containing aneuploidy, CNV, and single-gene disorder. Chromosomal aneuploidy and CNV were detected based on the Z-value approach, whereas single-gene disorder was identified by using the "pseudo-tetraploid" model to estimate the best-suited genotype for each locus. RESULTS The performance of this newly constructed 3-in-1 system was promising. We achieved a 100% detection rate for chromosomal aneuploidies (7/7), a 100% diagnosis rate for fetus CNVs larger than 20 Mb (3/3), and an 86.4% accuracy for single-gene disorder screening (19/22). CONCLUSION For the first time, we showed that it is possible to use just a single NIPT test to detect three distinct types of fetus disorder and laid a foundation for developing a cheaper, faster, and multi-functional NIPT method in the future.
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Affiliation(s)
- Yuqin Luo
- The Department of Obstetrics and Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Bei Jia
- The Center for Prenatal and Hereditary Disease Diagnosis, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Kai Yan
- The Department of Obstetrics and Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Siping Liu
- The Center for Prenatal and Hereditary Disease Diagnosis, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaojie Song
- Department of Gynecology and Obstetrics, Wuhan Medical and Health Center for Women and Children, Wuhan, Hubei, China
| | - Mingfa Chen
- Department of Prenatal Diagnosis, Nanping Maternity and Child Health Hospital, Nanping, Fujian, China
| | - Fan Jin
- The Department of Obstetrics and Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yang Du
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Juan Wang
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Yan Hong
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Sha Cao
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Dawei Li
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Minyue Dong
- The Department of Obstetrics and Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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Mak A, Lee H, Poon CF, Kwok SL, Ma T, Chan KYK, Kan A, Tang M, Leung KY. Factors associated with common and atypical chromosome abnormalities after positive combined first-trimester screening in Chinese women: a retrospective cohort study. BMC Pregnancy Childbirth 2019; 19:55. [PMID: 30717698 PMCID: PMC6360741 DOI: 10.1186/s12884-019-2205-y] [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: 03/06/2018] [Accepted: 01/28/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND When cell-free DNA (cfDNA) testing is used as a secondary screening tool following combined first-trimester screening (cFTS), cFTS is used to estimate the prior risk for chromosome abnormalities. This study aimed to assess the factors that are associated with common and atypical abnormalities following cFTS, including cFTS risk, advanced maternal age, increased nuchal translucency (NT) ≥3.5 mm, and abnormal levels of serum markers. METHODS We reviewed a historical cohort of 1855 Chinese women carrying singleton pregnancies with a positive cFTS [at a threshold of 1:250 for trisomy (T) 21 or 1:180 for T18] in one public hospital over a five-year period. All chromosome abnormalities were confirmed by invasive prenatal diagnosis (IPD) with karyotyping, with or without array comparative genomic hybridization. Using multivariable binary logistic regression analysis, we determined the parameters that were associated with common and atypical abnormalities. RESULTS Overall, the prevalence of common and atypical abnormalities was 6.2 and 1.2%, respectively, and the prevalence increased with the risk of T21 by cFTS. In pregnancies with a risk of T21 > 1 in 100, a high risk of both T21 and T18, an increased NT, or a pregnancy-associated plasma A (PAPP-A) level < 0.2 multiple of medians (MoM), the prevalence of common abnormalities was 12.2, 64.7, 25.5 and 33.8%, respectively, while that of atypical abnormalities was 1.6, 3.9, 4.2, and 7.4%, respectively. In the multivariable binary logistic regression analysis, out of these four factors, only two (increased NT and PAPP_A < 0.2 MoM) were significant predictors of common and atypical abnormalities, respectively. Of all positive cFTS pregnancies, 50.4% did not have any of these four factors, and the prevalence of common and atypical abnormalities was 1.1 and 0.6%, respectively. There were three atypical abnormalities, all of which were mosaicism, and they were detected among women with IPD alone. The ages of these women were ≥ 35 years. All three pregnancies were continued after proper counseling. After giving birth, only one child had mild abnormalities, while the other two were phenotypically normal. CONCLUSIONS Our study identified factors associated with common and atypical abnormalities after cFTS. These factors can be used to estimate the prior risk for these abnormalities to help with post-cFTS counseling in terms of choosing between cfDNA testing and IPD.
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Affiliation(s)
- Annisa Mak
- Department of Obstetrics and Gynaecology, Queen Elizabeth Hospital, 30 Gascoigne Road, Hong Kong, SAR, China
| | - Helena Lee
- Department of Obstetrics and Gynaecology, Queen Elizabeth Hospital, 30 Gascoigne Road, Hong Kong, SAR, China
| | - C F Poon
- Department of Obstetrics and Gynaecology, Queen Elizabeth Hospital, 30 Gascoigne Road, Hong Kong, SAR, China
| | - S L Kwok
- Department of Obstetrics and Gynaecology, Queen Elizabeth Hospital, 30 Gascoigne Road, Hong Kong, SAR, China
| | - Teresa Ma
- Department of Obstetrics and Gynaecology, Queen Elizabeth Hospital, 30 Gascoigne Road, Hong Kong, SAR, China
| | - K Y K Chan
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, The University of Hong Kong, 102 Pokfulam Road, Hong Kong, SAR, China
| | - Anita Kan
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, The University of Hong Kong, 102 Pokfulam Road, Hong Kong, SAR, China
| | - Mary Tang
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, The University of Hong Kong, 102 Pokfulam Road, Hong Kong, SAR, China
| | - K Y Leung
- Department of Obstetrics and Gynaecology, Queen Elizabeth Hospital, 30 Gascoigne Road, Hong Kong, SAR, China.
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Wan J, Li R, Zhang Y, Jing X, Yu Q, Li F, Li Y, Zhang L, Yi C, Li J, Li D, Liao C. Pregnancy outcome of autosomal aneuploidies other than common trisomies detected by noninvasive prenatal testing in routine clinical practice. Prenat Diagn 2018; 38:849-857. [PMID: 30078205 DOI: 10.1002/pd.5340] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 12/17/2022]
Abstract
OBJECTIVE The objective of the study is to report the incidence and pregnancy outcome of autosomal aneuploidies other than common trisomies 21, 18, and 13 detected by noninvasive prenatal testing (NIPT) at a single center. METHODS Pregnant women undergoing NIPT from February 2015 to January 2018 in our center were offered expanded screening to include rare autosomal aneuploidies. Aneuploidies included extra copy chromosomes (most likely trisomies) and decreased copy chromosomes (most likely monosomies). The pregnancy outcomes of women consenting to the expanded NIPT screen were recorded. RESULTS Expanded NIPT was performed in 15 362 pregnancies. A total of 59 autosomal aneuploidies other than the 3 common trisomies were detected, with a positive screening rate of 0.38% (59/15 362). The screen positive rate was higher in women aged above 35 years than in those younger (0.44% vs 0.32%, P < .05). Of the screen positive results, 30.5% (18/59) were because of extra copies for chromosomes trisomy 7, 10.2% (6/59) for chromosome 22, and 8.5% (5/59) for chromosomes 8 and 16 respectively, while other choromosomes were less frequently involved. Decreased copy chromosomes were less common: 6.8% (4/59) for chromosomes 14 and 13. Mixed aneuploidies with increased copies for some chromosomes and decreased copies for others were also noted. Invasive prenatal diagnosis was performed in 61% (36/59) of the cases. Invasive test results and clinical follow-ups demonstrated that most (94.9%, 56/59) of the rare aneuploidies were false positives, probably resulting from confined placental mosaicism. Only 1 case (1.7%, 1/59) with NIPT report of extra copies of chromosome 7 and without ultrasound evidence of fetal abnormality was confirmed to be fetal mosaicism by microarray test. Uniparental disomy of whole chromosome 2 was identified by microarray analysis in 1 case with extra copy chromosome 2 detected by NIPT. Loss of heterozygocity of chromosome 7q11.23-q21.11 was detected in another case with extra copy chromosome 7. Fortunately, pregnancy outcomes of both cases were normal. Two fetal deaths attributed to severe fetal growth restriction were associated with extra copies of chromosome 16 at expanded NIPT. CONCLUSIONS Autosomal aneuploidies other than trisomies 21, 18, and 13 are not uncommon in routine clinical NIPT practice. Extra copies of chromosomes in rare cases can be associated with uniparental disomy. Most rare aneuploidies at NIPT have good pregnancy outcomes. Thus, invasive testing should be used with caution for these aneuploidies in routine clinical practice.
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Affiliation(s)
- Junhui Wan
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, P.R. China
| | - Ru Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, P.R. China
| | - Yongling Zhang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, P.R. China
| | - Xiangyi Jing
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, P.R. China
| | - Qiuxia Yu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, P.R. China
| | - Fatao Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, P.R. China
| | - Yan Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, P.R. China
| | - Lina Zhang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, P.R. China
| | - Cuixing Yi
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, P.R. China
| | - Jian Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, P.R. China
| | - Dongzhi Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, P.R. China
| | - Can Liao
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, P.R. China
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Genome-wide detection of additional fetal chromosomal abnormalities by cell-free DNA testing of 15,626 consecutive pregnant women. SCIENCE CHINA-LIFE SCIENCES 2018; 62:215-224. [PMID: 30076564 DOI: 10.1007/s11427-017-9344-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/21/2018] [Indexed: 12/18/2022]
Abstract
Cell-free DNA (cfDNA) testing for common fetal trisomies (T21, T18, T13) is highly effective. However, the usefulness of cfDNA testing in detecting other chromosomal abnormalities is unclear. We evaluated the performance of cfDNA testing for genome-wide abnormalities, and analyzed the incremental yield by reporting extra abnormalities. We performed genome-wide cfDNA testing in 15,626 consecutive pregnancies prospectively enrolled in this study. cfDNA testing results were reported and counseling was given depending on the presence of extra chromosomal abnormalities. cfDNA testing identified 190 cases (1.2%) of chromosomal abnormalities including 100 common trisomies and 90 additional abnormalities. By expanding the cfDNA reporting range to genome-wide abnormalities, the false positive rate increased to 0.39% (P<0.001) and positive predictive value (PPV) was reduced to 65.58% (P=0.42). However, the detection yield increased from 0.44% to 0.65% (P=0.014), and cfDNA testing detected 38.61% (39/101) additional abnormalities with no ultrasound and biochemical screening findings. cfDNA testing outperformed biochemical screening by showing 60 times higher true positive rate and fewer false negative results. Genome-wide cfDNA testing significantly increased the diagnostic yield by detecting extra abnormalities, especially those without diagnostic indications. Genome-wide cfDNA testing has fewer false positive and false negative results compared with biochemical screening.
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