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Tang X, Du Y, Chen M, Zhang Y, Wang Z, Zhang F, Tan J, Yin T, Wang L. Relationships among maternal monosomy X mosaicism, maternal trisomy, and discordant sex chromosome aneuploidies. Clin Chim Acta 2024; 554:117770. [PMID: 38199578 DOI: 10.1016/j.cca.2024.117770] [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: 10/04/2023] [Revised: 01/05/2024] [Accepted: 01/06/2024] [Indexed: 01/12/2024]
Abstract
OBJECTIVE To explore the impact of maternal factors on the false-positive fetal sex chromosome aneuploidies (SCAs) results obtained through noninvasive prenatal screening (NIPS). METHODS We retrospectively analyzed pregnant women with high-risk SCAs as revealed using NIPS between January 2017 and December 2022. Clinical data such as results of invasive prenatal diagnoses, copy number variation sequencing (CNV-seq) and pregnancy outcomes were analysed. RESULTS Overall, 177 (0.6 %) women with SCA-positive results were collected from 27,941 patients who had undergone NIPS. Among them, 110 (62.2 %) pregnant women chose prenatal diagnosis and 39 (35.5 %) cases were confirmed. For the women with monosomy X false-positive results from the NIPS, 53.1 % (17/32) were found to be maternal mosaicism monosomy X. In cases with 47, XXX false-positive results, 60 % (6/10) of them were maternal 47,XXX (5 cases) or maternal mosaicism 47,XXX (1 case). One (1/6, 16.7 %) case of maternal mosaicism monosomy X was detected in the false positive results of 47, XXY/47, XYY revealed. The incidence rate of maternal sex chromosome abnormalities was positively correlated with the Z-score of ChrX. When the Z-score of ChrX ≥ 15, more than 50 % of pregnant women were found to be maternal sex chromosome abnormalities, and when Z-score ≥ 30, the incidence rate was as high as 100 %. CONCLUSIONS Maternal monosomy X mosaicism and trisomy X respectively played an important role in the discordance of 45, X and 47, XXX revealed by NIPS. CNV-seq was recommended for the pregnant women at risk of maternal sex chromosome abnormalities, which could help clinicians to provide more accurate and efficient advice during genetic counseling and to guide appropriate prenatal diagnosis strategy for the next pregnancy.
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Affiliation(s)
- Xinxin Tang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Yunqiu Du
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Min Chen
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Yue Zhang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Zhiwei Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Fang Zhang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Juan Tan
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Ting Yin
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Leilei Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China.
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Li ZQ, Kang WL, Tang SJ, Mao Y, Fang T, Jiang JJ, Li XH. Effect of maternal age on foetal chromosomal defects: an investigation based on non-invasive prenatal testing. J OBSTET GYNAECOL 2023; 43:2287125. [PMID: 38069630 DOI: 10.1080/01443615.2023.2287125] [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: 06/15/2023] [Accepted: 11/18/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND This study aimed to evaluate the value of non-invasive prenatal testing (NIPT) in the prenatal screening of foetal aneuploidy-associated diseases at different gestational ages. METHODS Briefly, cell-free foetal DNAs were extracted from plasma first, followed by DNA sequencing and bioinformatics analyses for chromosome aneuploidy (T21, T18, and T13), sex chromosome aneuploidy (SCA), and microdeletion/microduplication. Subsequently, the positive results were subject to karyotype analyses. RESULTS The pregnant women included in this study were divided into six groups, and the results, such as chromosome diagnoses, and clinical phenotypes, were collected for data analyses. According to the results of the data analysis, the positivity rates of foetal chromosomal abnormalities in pregnant women under 20, 20-24, 25-29, 30-34, 35-39, and >40 years old were 0%, 0.17%, 0.25%, 0.27%, 0.60%, and 1.66%, respectively. The positive predictive value (PPV) in the 20-24 years group was 41.67%, that in the 25-29 years group was 62.5%, that in the 30-34 years group was 66.67%, that in the 35-39 years group was 90.74%, and that in the >40 years group was 90.32%. CONCLUSION Overall, NIPT detection in elderly pregnant women has excellent clinical application value in reducing the incidence of either birth defects or abortion caused by invasive chromosome examination.
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Affiliation(s)
- Zhi-Qiang Li
- The Laboratory of Clinical Genomics, Hefei KingMed Diagnostics Ltd, Hefei, China
| | - Wei-Ling Kang
- The Laboratory of Clinical Genomics, Hefei KingMed Diagnostics Ltd, Hefei, China
| | - Si-Jie Tang
- The Aoyang Cancer Institute, Affiliated Aoyang Hospital of Jiangsu University, Suzhou, China
| | - Yuan Mao
- The Laboratory of Clinical Genomics, Hefei KingMed Diagnostics Ltd, Hefei, China
| | - Ting Fang
- The Laboratory of Clinical Genomics, Hefei KingMed Diagnostics Ltd, Hefei, China
| | - Jia-Jia Jiang
- The Aoyang Cancer Institute, Affiliated Aoyang Hospital of Jiangsu University, Suzhou, China
| | - Xiao-Hua Li
- The Laboratory of Clinical Genomics, Hefei KingMed Diagnostics Ltd, Hefei, China
- The Aoyang Cancer Institute, Affiliated Aoyang Hospital of Jiangsu University, Suzhou, China
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Cai L, Zeng Q, Gao C, Wu W, Shen J, Wu BL, Wang DW, Cui Y, Liu J. Majority of transferred mosaic embryos developed healthy live births revealed by a preclinical study using embryonic morphology assessment and noninvasive PGT-A on cell-free DNA in blastocoel fluid. J Assist Reprod Genet 2022; 39:2483-2504. [PMID: 36422765 PMCID: PMC9723046 DOI: 10.1007/s10815-022-02651-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/25/2022] [Indexed: 11/27/2022] Open
Abstract
PURPOSE This preclinical study aimed to evaluate whether using transferred mosaic embryos (primarily selected by embryonic morphology assessment (EMA) and compared by the noninvasive preimplantation genetic testing for aneuploidy (niPGT-A) on cell-free DNA in blastocoel fluid (BF)) increases the rates of clinical pregnancies (CPs) and healthy live births (HLBs) and to investigate whether niPGT-A could provide valuable genetic information for the EMA-selected transferred mosaic embryos. METHODS This study collected 215 blastocyst culture samples and 182 BF samples. Cell-free DNA from the BF was amplified and examined by next-generation sequencing-based niPGT-A. All 182 patients underwent EMA. However, only 147 underwent in vitro fertilization and embryo transfer, and only 113 clinical outcomes were followed up. Comprehensive chromosome screening for the chorionic villus sampling of spontaneous miscarriages and noninvasive prenatal testing for ongoing pregnancies were also performed. RESULTS The implantation rate was 77.55% in 147 transferred high-quality embryos selected by EMA. Among 113 CPs, 16 led to spontaneous miscarriage (14.16%), and 97 resulted in HLBs (85.84%). According to the niPGT-A results for 113 patients with clinical outcomes, 80.4% had CP (euploid, 20.54%; single aneuploid, 1.79%; mosaic chromosome aneuploid and/or segmental aneuploid, 58.04%). Of all the mosaic aneuploids, 90.76% were false positive, transforming to euploid. CONCLUSIONS Transferred EMA-selected embryos showed higher implantation rates. The niPGT-A of BF provided valuable genetic status ("-ploid") information, which helped reduce aneuploid-induced implantation failure and miscarriage, thereby increasing the CP and HLB rates. Additionally, majority of the transferred embryos with complex/chaotic mosaic aneuploid would likely develop HLBs.
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Affiliation(s)
- Lingbo Cai
- State Key Laboratory of Reproductive Medicine, The Center for Clinical Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Qiao Zeng
- State Key Laboratory of Reproductive Medicine, The Center for Clinical Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Chao Gao
- State Key Laboratory of Reproductive Medicine, The Center for Clinical Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Wei Wu
- State Key Laboratory of Reproductive Medicine, The Center for Clinical Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Jiandong Shen
- State Key Laboratory of Reproductive Medicine, The Center for Clinical Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Bai-Lin Wu
- Institute of Biomedical Science, Fudan University, Children's Hospital and Shanghai Medical College, Fudan University, Shanghai, 2100032, China
- Departments of Pathology and Laboratory Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Dao Wu Wang
- State Key Laboratory of Reproductive Medicine, Genetic Laboratory, The Center for Clinical Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Yugui Cui
- State Key Laboratory of Reproductive Medicine, The Center for Clinical Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Jiayin Liu
- State Key Laboratory of Reproductive Medicine, The Center for Clinical Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
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Lyu Z, Huang C. Systematic analysis of the causes of NIPS sex chromosome aneuploidy false-positive results. Mol Genet Genomic Med 2022; 10:e1963. [PMID: 35535634 PMCID: PMC9266605 DOI: 10.1002/mgg3.1963] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 04/01/2022] [Accepted: 04/18/2022] [Indexed: 11/11/2022] Open
Abstract
OBJECTIVE To investigate the underlying causes of false positives in NIPT of fetal sex chromosomal aneuploidies using fetal cell-free DNA from maternal plasma. METHODS In the present study, we focus on a cohort of 23,984 pregnancy cases with NIPT. Karyotyping and FISH analysis were employed to verify the NIPT detected false-positive results of fetal sex chromosomal aneuploidies, and a comparative CNV sequencing on positive and negative NIPT cases was uniquely performed to elucidate the underlying causes. RESULTS A total of 166 cases (0.69%) were identified as fetal sex chromosomal abnormalities, while 84 cases were found to be false-positive results possibly associated with maternal X chromosomal aneuploidies (n = 8), maternal X chromosomal structural abnormalities (n = 1), maternal CNVs (n = 4) as well as known placental mosaicism (n = 1). Furthermore, our study showed that the maternal chromosome CNV between 1-1.6 Mb was associated with false-positive NIPT results in sex chromosomal abnormalities. CONCLUSION Our research demonstrated the spectrum of factors causing false positives in NIPT of fetal sex chromosomal abnormalities based on a large cohort. The effective maternal CNV size cut-off identified in our study could integrate into bioinformatics algorithms for reducing the false-positive rate, however, further investigation is necessary to confirm this.
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Affiliation(s)
- Zhaoru Lyu
- Queen Mary College, Nanchang University, Nanchang, China
| | - Chunhong Huang
- School of Basic Medical Sciences, Nanchang University, Nanchang, China
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Li X, Wang L, Yao Z, Ruan F, Hu Z, Song W. Clinical evaluation of non-invasive prenatal screening in 32,394 pregnancies from Changzhi Maternal and Child Health Care Hospital of Shanxi China. J Med Biochem 2021; 41:341-346. [PMID: 36042897 PMCID: PMC9375529 DOI: 10.5937/jomb0-33513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/01/2021] [Indexed: 11/02/2022] Open
Abstract
Non-invasive prenatal screening (NIPS)was performed in 32,394 pregnancies, out of which results were available in 32,361 (99.9%) of them.Among the 32,361confirmed samples, 164 cases had positive results and 32197 cases had negative results. Of these positive cases, 116 cases were trisomy 21, 34 cases were trisomy 18 and 14 cases were trisomy 13. No false negative results were found in this cohort. The overall sensitivity and specificity were 100% and 99.91%, respectively. There was no significant difference in test performance between the 7,316 high-risk and 25,045 low-risk pregnancies,(sensitivity, 100% vs 100% (P >0.05); specificity, 99.96% vs 99.95% (P > 0.05)). Factors contributing to false-positive results included fetal CNVs, fetal mosaicism and typically producing Z scores between 3 and 4. Moreover, we analyze NIPT whole-genome sequencing to investigate the Single Nucleotide Polymorphisms (SNPs) associations with drug response or risk of disease. As compare to the 1000g East Asian genome data, the results reveal a significant difference in 7,285,418 SNPs variants of Shanxi pregnant women including 19,293 clinvar recorded variants and 7,266,125 non- clinvar recorded. Our findings showed that NIPS was an effective assay that may be applied as routine screening for fetal trisomies in the prenatal setting. In addition, this study also provides an accurate assessment of significant differencein 7,285,418 SNPs variants in Shanxi pregnant women that were previously unavailable to clinicians in Shanxi population.
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Affiliation(s)
- XiaoZe Li
- Changzhi Maternal and Child Health Care Hospital Affiliated Hospital of Changzhi Medical College, Department of Medical Genetic, Changzhi City, Shanxi Province, China
| | - LiHong Wang
- Changzhi Maternal and Child Health Care Hospital Affiliated Hospital of Changzhi Medical College, Department of Medical Genetic, Changzhi City, Shanxi Province, China
| | - ZeRong Yao
- Changzhi Maternal and Child Health Care Hospital Affiliated Hospital of Changzhi Medical College, Department of Medical Genetic, Changzhi City, Shanxi Province, China
| | - FangYing Ruan
- Changzhi Maternal and Child Health Care Hospital Affiliated Hospital of Changzhi Medical College, Department of Medical Genetic, Changzhi City, Shanxi Province, China
| | - ZhiPeng Hu
- Changzhi Maternal and Child Health Care Hospital Affiliated Hospital of Changzhi Medical College, Department of Medical Genetic, Changzhi City, Shanxi Province, China
| | - WenXia Song
- Changzhi Maternal and Child Health Care Hospital Affiliated Hospital of Changzhi Medical College, Department of Medical Genetic, Changzhi City, Shanxi Province, China
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6
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Zhou L, Zhang B, Liu J, Shi Y, Wang J, Yu B. The Optimal Cutoff Value of Z-scores Enhances the Judgment Accuracy of Noninvasive Prenatal Screening. Front Genet 2021; 12:690063. [PMID: 34367249 PMCID: PMC8336938 DOI: 10.3389/fgene.2021.690063] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/14/2021] [Indexed: 11/15/2022] Open
Abstract
Objective To evaluate the accuracy of Z-scores of noninvasive prenatal screening (NIPS) in predicting 21, 18 trisomy, and X chromosome aneuploidy. Methods A total of 39,310 prenatal women were recruited for NIPS from September 2015 to September 2020. Interventional prenatal diagnosis was applied to verify the diagnosis of NIPS-positive results. Logistic regression analysis was employed to relate the Z-scores to the positive predictive value (PPV) of NIPS-positive results. Using receiver operating characteristic (ROC) curves, we calculated the optimal cutoff value of Z-scores to predict fetal chromosome aneuploidy. According to the cutoff value, NIPS-positive results were divided into the medium Z-value (MZ) and high Z-value (HZ) groups, and PPV was calculated to access the accuracy of Z-scores. Results A total of 288 effective values of Z-scores were used as the final data set. The logistics regression analysis revealed that Z-scores were significantly associated with true-positive results for 21 trisomy (T21) and 18 trisomy (T18) (P < 0.05), whereas the same was not observed for X chromosome aneuploids (P > 0.05). The optimal cutoff value of the Z-score for T21, T18, XO, XXX, and XXY indicated by ROC curve analysis were 5.79, 6.05, −9.56, 5.89, and 4.47, and the area under the curve (AUC) were 0.89, 0.80, 0.48, 0.42, and 0.45, respectively. PPV in the HZ group was higher than that in the MZ group, and the application of the cutoff value reduced the false discovery rate (FDR), which was only 2.9% in the HZ group compared with 61.1% in the MZ group for T21 and T18. The difference in total PPV between the MZ and HZ groups for X chromosome aneuploids was statistically significant. Moreover, the PPV for XXX and XXY seemed to increase with Z-scores but not for XO. Conclusion The Z-score is helpful for the accurate judgment of NIPS results and for clinical prenatal counseling. Especially for T21 and T18, Z-scores have an excellent clinical association, which is superior to that seen with X chromosome aneuploids. In addition, using Z-scores to judge NIPS results offers a certain reference value for XXX and XXY but not for XO.
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Affiliation(s)
- Lingna Zhou
- 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
| | - Jianbing Liu
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, China
| | - Ye Shi
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, China
| | - Jing Wang
- 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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Lu X, Wang C, Sun Y, Tang J, Tong K, Zhu J. Noninvasive prenatal testing for assessing foetal sex chromosome aneuploidy: a retrospective study of 45,773 cases. Mol Cytogenet 2021; 14:1. [PMID: 33407708 PMCID: PMC7786464 DOI: 10.1186/s13039-020-00521-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/09/2020] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE To assess the positive predictive value (PPV) of noninvasive prenatal testing (NIPT) as a screening test for sex chromosome aneuploidy (SCA) with different maternal characteristics and prenatal decisions in positive cases. MATERIALS AND METHODS We retrospectively analysed 45,773 singleton pregnancies with different characteristics that were subjected to NIPT in the Maternity and Child Health Hospital of Anhui Province. The results were validated by karyotyping. Clinical data, diagnostic results, and data on pregnancy outcomes were collected. RESULTS In total, 314 cases were SCA positive by NIPT; among those, 143 underwent invasive prenatal diagnostic testing, and 58 were true-positive. Overall, the PPVs for 45,X, 47,XXX, 47,XXY and 47,XYY were 12.5%, 51.72%, 66.67% and 83.33%, respectively. Interestingly, when only pregnant women of advanced maternal age (AMA) were screened, the PPVs for 45,X, 47,XXX, 47,XXY and 47,XYY were 23.81%, 53.33%, 78.95%, and 66.67%, respectively. The frequency of SCA was significantly higher in the AMA group than in the non-AMA group. The frequencies of 47,XXX and 47,XXY were significantly correlated with maternal age. CONCLUSION NIPT performed better in predicting sex chromosome trisomies than monosomy X, and patients with 45,X positive foetuses were more eager to terminate pregnancy than those with 47,XXX and 47,XYY. AMA may be a risk factor of having a foetus with SCA. Our findings may assist in genetic counselling of AMA pregnant women. Our pre- and posttest counselling are essential for familiarizing pregnant women with the benefits and limitations of NIPT, which may ease their anxiety and enable them to make informed choices for further diagnosis and pregnancy decisions.
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Affiliation(s)
- Xinran Lu
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China.,Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Chaohong Wang
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Yuxiu Sun
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Junxiang Tang
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Keting Tong
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Jiansheng Zhu
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China. .,Maternity and Child Health Hospital of Anhui Province, Hefei, China.
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Zhang B, Zhou Q, Chen Y, Shi Y, Zheng F, Liu J, Yu B. High false‐positive non‐invasive prenatal screening results for sex chromosome abnormalities: Are maternal factors the culprit? Prenat Diagn 2020; 40:463-469. [PMID: 31318441 DOI: 10.1002/pd.5529] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 07/03/2019] [Accepted: 07/15/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Bin Zhang
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| | - Qin Zhou
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| | - Yingping Chen
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| | - Ye Shi
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| | - Fangxiu Zheng
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| | - Jianbing Liu
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| | - Bin Yu
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
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Chen M, Jiang F, Guo Y, Yan H, Wang J, Zhang L, Zeng X, Li S, Li Y, Li N, Zhang C, Zhu W, Du B, Wang Y, Lan Z, Luo X, Luo F, Chen D. Validation of fetal DNA fraction estimation and its application in noninvasive prenatal testing for aneuploidy detection in multiple pregnancies. Prenat Diagn 2019; 39:1273-1282. [PMID: 31671222 DOI: 10.1002/pd.5597] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 07/12/2019] [Accepted: 09/15/2019] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To analyze the fetal fraction, fetal sex, and chromosomal aneuploidy in multiple pregnancies using noninvasive prenatal testing (NIPT). METHOD A total of 362 pregnant women including 203 singleton pregnancies, 69 twins, and 90 higher-order multiple pregnancies were recruited. Fetal fractions estimated by size ratio-based and Y chromosome-based approaches in singleton pregnancies with male fetus were used as source data to establish the model. The model was then applied to multiple pregnancies for fetal fraction estimation. By comparing the fetal fractions estimated by size ratio to those estimated by Y chromosome or autosomal chromosomes, fetal sex and chromosomal aneuploidy can be analyzed. RESULTS The size ratio-based approach has been well established in estimating fetal fractions for twin and higher-order multiple pregnancies. Fetal fraction had a positive correlation with gestational age in twin and triplet pregnancies. Fetal sex was determined with accuracies of 98.6% (95% CI, 92.19%-99.96%) in twins and 97.6% (95% CI, 91.76%-99.71%) in triplet pregnancies. Four trisomy 21, one trisomy 18, and one trisomy 13 cases were detected by NIPT. Two trisomy 21 singleton pregnancies and one trisomy 21 twin pregnancy were confirmed by karyotyping. CONCLUSION Fetal sex and chromosomal aneuploidy in multiple pregnancies can be determined using NIPT.
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Affiliation(s)
- Min Chen
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, China.,The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, China.,Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, China.,Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, China
| | - Fuman Jiang
- School of Automation Science and Engineering, South China University of Technology, Guangzhou, China.,Guangzhou Jingke Medical Laboratory, Guangzhou, China.,Shenzhen Jingke Genetic Science and Technology Co., Ltd., Shenzhen, China
| | - Yulai Guo
- Guangzhou Jingke Medical Laboratory, Guangzhou, China
| | - Huanchen Yan
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, China.,The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, China.,Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, China.,Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, China
| | - Jiayan Wang
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, China.,The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, China.,Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, China.,Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, China
| | - Longmei Zhang
- Guangzhou Jingke Medical Laboratory, Guangzhou, China
| | - XiaoJing Zeng
- Guangzhou Jingke Medical Laboratory, Guangzhou, China
| | - Sheng Li
- Guangzhou Jingke Medical Laboratory, Guangzhou, China
| | - Yufan Li
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, China.,The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, China.,Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, China.,Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, China
| | - Nan Li
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, China.,The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, China.,Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, China.,Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, China
| | | | - Wentao Zhu
- Guangzhou Jingke Medical Laboratory, Guangzhou, China
| | - Bole Du
- Guangzhou Jingke Medical Laboratory, Guangzhou, China
| | - Yang Wang
- Guangzhou Jingke Medical Laboratory, Guangzhou, China
| | - Zhiheng Lan
- Guangzhou Jingke Medical Laboratory, Guangzhou, China
| | - Xingcheng Luo
- Guangzhou Jingke Medical Laboratory, Guangzhou, China
| | - Fei Luo
- School of Automation Science and Engineering, South China University of Technology, Guangzhou, China
| | - Dunjin Chen
- Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, China.,The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, China.,Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, China.,Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, China
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Zhu J, Qi H, Cao S, Cai L, Wen X, Tang G, Wan Q, Chen C, Wang J, Zeng W, Luo Y. Detection of a rare de novo 18p terminal deletion with inverted duplication in a Chinese pregnant woman. Mol Genet Genomic Med 2019; 7:e868. [PMID: 31317671 PMCID: PMC6732341 DOI: 10.1002/mgg3.868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/16/2019] [Accepted: 07/07/2019] [Indexed: 01/07/2023] Open
Abstract
Background The 18p terminal deletion with inverted duplication is an extremely rare chromosome structure abnormality and the common clinical manifestations include intellectual disability and speech delay, etc. Up to now, only three confirmed cases were reported in Europe, and here, for the first time in the Asian population, we report a case of de novo 18p inv‐dup‐del in a Chinese pregnant woman. This structural variation was accidentally discovered by the noninvasive prenatal testing (NIPT) during her prenatal examination. Methods Next generation sequencing (NGS) based copy number variations (CNVs) screening and karyotype analysis were performed to verify the type and heredity of the rearrangement, and the fluorescent in situ hybridization (FISH) analysis was also used to confirm the terminal deletion and inverted duplication. Results The patient has a de novo 18p11.31‐18p11.1 inverted duplication with a 6.2 Mb 18p terminal deletion. This rare chromosome imbalance, most likely caused by the U‐type exchange mechanism, resulted in the aberrant phenotype of mental disability, speech delay, seizure, and strabismus. However, the rearrangement was not inherited by her unborn child. Conclusion This report added a new type of variation to the spectrum of 18p terminal deletion with inverted duplication, and demonstrated that the maternal chromosome rearrangement discovered in NIPT should not just be consider as an interference factor but also a potential indicator of previously undiscovered pathogenic chromosome structure variations in pregnant women.
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Affiliation(s)
- Jianjiang Zhu
- Prenatal Diagnosis Center, Beijing Haidian Maternal and Child Health Hospital, Beijing, P. R. China
| | - Hong Qi
- Prenatal Diagnosis Center, Beijing Haidian Maternal and Child Health Hospital, Beijing, P. R. China
| | - Sha Cao
- Annoroad Gene Technology Co. Ltd, Beijing, P. R. China
| | - Lirong Cai
- Prenatal Diagnosis Center, Beijing Haidian Maternal and Child Health Hospital, Beijing, P. R. China
| | - Xiaohui Wen
- Prenatal Diagnosis Center, Beijing Haidian Maternal and Child Health Hospital, Beijing, P. R. China
| | - Guodong Tang
- Prenatal Diagnosis Center, Beijing Haidian Maternal and Child Health Hospital, Beijing, P. R. China
| | - Qian Wan
- Annoroad Gene Technology Co. Ltd, Beijing, P. R. China
| | - Chen Chen
- Annoroad Gene Technology Co. Ltd, Beijing, P. R. China
| | - Juan Wang
- Annoroad Gene Technology Co. Ltd, Beijing, P. R. China
| | - Wen Zeng
- Prenatal Diagnosis Center, Beijing Haidian Maternal and Child Health Hospital, Beijing, P. R. China
| | - Yao Luo
- Prenatal Diagnosis Center, Beijing Haidian Maternal and Child Health Hospital, Beijing, P. R. China
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11
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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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12
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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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13
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Wilkins-Haug L, Zhang C, Cerveira E, Ryan M, Mil-Homens A, Zhu Q, Reddi H, Lee C, Bianchi DW. Biological explanations for discordant noninvasive prenatal test results: Preliminary data and lessons learned. Prenat Diagn 2019; 38:445-458. [PMID: 29633279 DOI: 10.1002/pd.5260] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/25/2018] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Maternal plasma cell-free DNA (cfDNA) analysis is a powerful screening tool for Down syndrome. In a pilot series, we examined biologic causes of discordance between the cfDNA test results and the fetal karyotype. We also explored the feasibility of obtaining trio biospecimens by using parental engagement. METHODS A convenience sample of women with discordant cfDNA results were recruited by their care providers. We provided shipping materials and instructions for biospecimen collection. Maternal, newborn, and placental samples were examined with droplet digital PCR. RESULTS Thirteen of 15 women successfully had biospecimens obtained remotely. High-quality DNA was extracted in 12 of 13 women. Presumed biologic etiologies for discordance were identified in 7 of 12 women: 3 cases from additional clinical review (male renal transplant, vanishing twin, and colon cancer) and 4 cases from additional laboratory investigation using droplet digital PCR (3 with confined placental mosaicism and 1 with true fetal mosaicism). CONCLUSIONS Understanding the biology behind cfDNA-fetal karyotype discordancy is useful for follow-up clinical care. Our study suggests that most cases could be resolved by using a trio biospecimen protocol and parental involvement. To improve accuracy, additional sequencing of biospecimens will be required.
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Affiliation(s)
- Louise Wilkins-Haug
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Eliza Cerveira
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mallory Ryan
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Adam Mil-Homens
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Qihui Zhu
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Honey Reddi
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Charles Lee
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Diana W Bianchi
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA.,Prenatal Genomics and Therapy Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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14
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Dheedene A, Sante T, De Smet M, Vanbellinghen JF, Grisart B, Vergult S, Janssens S, Menten B. Implementation of non-invasive prenatal testing by semiconductor sequencing in a genetic laboratory. Prenat Diagn 2016; 36:699-707. [PMID: 27176606 PMCID: PMC5108441 DOI: 10.1002/pd.4841] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/15/2016] [Accepted: 05/10/2016] [Indexed: 12/16/2022]
Abstract
OBJECTIVES To implement non-invasive prenatal testing (NIPT) for fetal aneuploidies with semiconductor sequencing in an academic cytogenomic laboratory and to evaluate the first 15-month experience on clinical samples. METHODS We validated a NIPT protocol for cell-free fetal DNA sequencing from maternal plasma for the detection of trisomy 13, 18 and 21 on a semiconductor sequencing instrument. Fetal DNA fraction calculation for all samples and several quality parameters were implemented in the workflow. One thousand eighty-one clinical NIPT samples were analysed, following the described protocol. RESULTS Non-invasive prenatal testing was successfully implemented and validated on 201 normal and 74 aneuploid samples. From 1081 clinical samples, 17 samples showed an abnormal result: 14 trisomy 21 samples, one trisomy 18 and one trisomy 16 were detected. Also a maternal copy number variation on chromosome 13 was observed, which could potentially lead to a false positive trisomy 13 result. One sex discordant result was reported, possibly attributable to a vanishing twin. Moreover, our combined fetal fraction calculation enabled a more reliable risk estimate for trisomy 13, 18 and 21. CONCLUSIONS Non-invasive prenatal testing for trisomy 21, 18 and 13 has a very high specificity and sensitivity. Because of several biological phenomena, diagnostic invasive confirmation of abnormal results remains required. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Annelies Dheedene
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Tom Sante
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Matthias De Smet
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Jean-François Vanbellinghen
- Plateforme de Biologie Moléculaire, Département des Laboratoires, Cliniques Universitaires Saint-Luc, Bruxelles, Belgium
| | - Bernard Grisart
- Centre de Génétique Humaine, Institut de Pathologie et Génétique, Charleroi, Belgium
| | - Sarah Vergult
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Sandra Janssens
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
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