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Kwan AHW, Gil MM, Xue S, Kwok YKY, Lau D, Fung J, Chan A, Choy KW, Leung TY, Poon LC. Cell-free DNA test for fetal chromosomal abnormalities in multiple pregnancies. Acta Obstet Gynecol Scand 2024. [PMID: 38924543 DOI: 10.1111/aogs.14901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 05/07/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
INTRODUCTION This study aimed to report the screening performance of cell-free DNA (cfDNA) testing for chromosomal abnormalities in twins, triplets, and vanishing twin pregnancies. MATERIAL AND METHODS Data were obtained from pregnant women with a multiple pregnancy or a vanishing twin pregnancy at ≥10 weeks' gestation who requested self-financed cfDNA testing between May 2015 and December 2021. Those that had positive screening results had diagnostic confirmatory procedures after counseling and consent. The performance of screening of the cfDNA test was determined by calculating confirmation rate and combined false-positive rate (cFPR). RESULTS Data from 292 women were included after exclusion of those lost to follow-up, with no-result on cfDNA testing, or had reductions. Of the 292 pregnancies, 10 (3.4%) were triplets, including no cases of trisomy 21 and trisomy 18; 249 (85.3%) were twins, including 3 cases of trisomy 21 and no cases of trisomy 18 and 13; and 33 (11.3%) were vanishing twins, including 3 cases of trisomy 21 and 1 case of trisomy 18. The median (IQR) maternal age was 34 years (31-37). For triplet pregnancies, the initial no-result rate was 10.3% (95% confidence interval [CI] 3.6-26.4), all with results after redraw. For twin pregnancies, the initial no-result rate was 12.9% (95% CI 9.6-17.0), and the no-result rate after redraw was 1.6% (95% CI 0.7-3.6). For vanishing twins, there were no cases with no-result. All triplets had low-risk cfDNA results. The confirmation rate for trisomy 21 was 100% with a FPR at 0% due to the small number of positive cases for twins. For vanishing twins, one high-risk case for trisomy 21 and the only high-risk case for trisomy 18 were confirmed with a cFPR of 8.3% (n = 2/24; 95% CI 2.3-25.9). CONCLUSIONS cfDNA testing in twin pregnancies has sufficient screening performance for trisomy 21 but the number of affected cases for other conditions is limited to draw any meaningful conclusion. The use of cfDNA testing in triplet pregnancies and vanishing twins remains an area for further research.
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Affiliation(s)
- Angel H W Kwan
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong SAR
| | - Maria Mar Gil
- Obstetrics and Gynecology Department, Hospital Universitario de Torrejón, Madrid, Spain
- Francisco de Vitoria University, Madrid, Spain
| | - Shuwen Xue
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong SAR
| | - Yvonne K Y Kwok
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong SAR
| | | | - Joanna Fung
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong SAR
| | - Andrea Chan
- Department of Obstetrics and Gynecology, United Christian Hospital, New Kowloon, Hong Kong SAR
| | - Kwong Wai Choy
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong SAR
| | - Tak Yeung Leung
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong SAR
| | - Liona C Poon
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong SAR
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Boddupally K, Rani Thuraka E. Artificial intelligence for prenatal chromosome analysis. Clin Chim Acta 2024; 552:117669. [PMID: 38007058 DOI: 10.1016/j.cca.2023.117669] [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: 10/06/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/27/2023]
Abstract
This review article delves into the rapidly advancing domain of prenatal diagnostics, with a primary focus on the detection and management of chromosomal abnormalities such as trisomy 13 ("Patau syndrome)", "trisomy 18 (Edwards syndrome)", and "trisomy 21 (Down syndrome)". The objective of the study is to examine the utilization and effectiveness of novel computational methodologies, such as "machine learning (ML)", "deep learning (DL)", and data analysis, in enhancing the detection rates and accuracy of these prenatal conditions. The contribution of the article lies in its comprehensive examination of advancements in "Non-Invasive Prenatal Testing (NIPT)", prenatal screening, genomics, and medical imaging. It highlights the potential of these techniques for prenatal diagnosis and the contributions of ML and DL to these advancements. It highlights the application of ensemble models and transfer learning to improving model performance, especially with limited datasets. This also delves into optimal feature selection and fusion of high-dimensional features, underscoring the need for future research in these areas. The review finds that ML and DL have substantially improved the detection and management of prenatal conditions, despite limitations such as small sample sizes and issues related to model generalizability. It recognizes the promising results achieved through the use of ensemble models and transfer learning in prenatal diagnostics. The review also notes the increased importance of feature selection and high-dimensional feature fusion in the development and training of predictive models. The findings underline the crucial role of AI and machine learning techniques in early detection and improved therapeutic strategies in prenatal diagnostics, highlighting a pressing need for further research in this area.
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Affiliation(s)
- Kavitha Boddupally
- JNTUH University, India; CVR College of Engineering, ECE, Hyderabad, India.
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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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Allsopp RC, Page K, Ambasager B, Wadsley MK, Acheampong E, Ntereke TP, Guo Q, Lall GM, Gleason KLT, Wren E, Nteliopoulos G, Rushton AJ, Coombes RC, Shaw JA. A Rapid, Shallow Whole Genome Sequencing Workflow Applicable to Limiting Amounts of Cell-Free DNA. Clin Chem 2023; 69:510-518. [PMID: 36747279 DOI: 10.1093/clinchem/hvac220] [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: 07/05/2022] [Accepted: 12/02/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND Somatic copy number alterations (sCNAs) acquired during the evolution of breast cancer provide valuable prognostic and therapeutic information. Here we present a workflow for screening sCNAs using picogram amounts of cell-free DNA (cfDNA) and single circulating tumor cells (CTCs). METHODS We repurposed the Ion ReproSeq PGS™ preimplantation genetic testing kit to perform shallow whole genome sequencing on 178 cfDNA samples (300 pg) and individual CTCs from 10 MBC patients with metastatic breast cancer (MBC) recovered by CellSearch®/DEPArray™. Results were analyzed using a tailored ichorCNA workflow. RESULTS sCNAs were detected in cfDNA of 41/105 (39%) patients with MBC and 3/23 (13%) primary breast cancers on follow-up (PBC FU), all of whom subsequently relapsed. In 8 of 10 MBCs, individual CTCs had a higher copy number count than matched cfDNA. The median tumor fraction detected by ichorCNA was 0.34 (range 0.17-0.58) for MBC and 0.36 (range 0.31-0.37) for PBC FU. Patients with detectable tumor fraction (≥ 0.1) and TFx and OncomineTM variants had significantly lower overall survival rates (P values P = 0.002 and P < 0.0001 for the log-rank test, respectively). CONCLUSIONS The ReproSeq PGS assay is rapid, at approximately $120 per sample, providing both a sCNA profile and estimation of the tumor DNA fraction from limiting cfDNA template (300pg) and individual CTCs. The approach could be used to examine the copy number landscape over time to guide treatment decisions, support future trial designs, and be applied to low volume blood spot samples enabling remote monitoring.
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Affiliation(s)
- Rebecca C Allsopp
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
| | - Karen Page
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
| | - Bana Ambasager
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, UK
| | - Marc K Wadsley
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
| | - Emmanuel Acheampong
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
| | - Tumisang P Ntereke
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
| | - Qi Guo
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
| | - Gurdeep Matharu Lall
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
| | - Kelly L T Gleason
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, UK
| | - Evie Wren
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, UK
| | - Georgios Nteliopoulos
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, UK
| | - Amelia J Rushton
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, UK
| | - R Charles Coombes
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, UK
| | - Jacqueline A Shaw
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
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Shear MA, Swanson K, Garg R, Jelin AC, Boscardin J, Norton ME, Sparks TN. A systematic review and meta-analysis of cell-free DNA testing for detection of fetal sex chromosome aneuploidy. Prenat Diagn 2023; 43:133-143. [PMID: 36588186 PMCID: PMC10268789 DOI: 10.1002/pd.6298] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/05/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023]
Abstract
OBJECTIVES The aim was to determine the accuracy of cell-free DNA testing (cfDNA) for detecting sex chromosome aneuploidies (SCA) in singleton pregnancies. METHODS A systematic review and meta-analysis was performed to assess cfDNA accuracy for prenatal detection of 45,X, 47,XXY, 47,XXX and 47,XYY. Inclusion was restricted to studies published between January 2010 and December 2021 reporting both cfDNA and confirmatory diagnostic test results. RESULTS For 45,X, the sensitivity was 98.8% (95%CI 94.6%-100%), specificity 99.4% (95%CI 98.7%-99.9%) and positive predictive value (PPV) 14.5% (95%CI 7.0%-43.8%). For 47,XXY, the sensitivity was 100% (95%CI 99.6%-100%), specificity 100% (95%CI 99.9%-100%) and PPV 97.7% (95%CI 78.6%-100%). For 47,XXX, the sensitivity was 100% (95%CI 96.9%-100%), specificity 99.9% (95%CI 99.7%-100%) and PPV 61.6% (95%CI 37.6%-95.4%). For 47,XYY, the sensitivity was 100% (95%CI 91.3%-100%), specificity 100% (95% CI 100%-100%) and PPV 100% (95%CI 76.5%-100%). All four SCAs had estimated negative predictive values (NPV) exceeding 99.99%, though false negatives were reported. CONCLUSIONS This analysis suggests that cfDNA is a reliable screening test for SCA, though both false negatives and false positives were reported. These estimates of test performance are derived from pregnancies at high pretest risk for aneuploidy, limiting the generalisability to average risk pregnancies.
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Affiliation(s)
- Matthew A. Shear
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California, San Francisco, California, USA
- Department of Pediatrics, Division of Medical Genetics, University of California, San Francisco, California, USA
| | - Kate Swanson
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California, San Francisco, California, USA
- Department of Pediatrics, Division of Medical Genetics, University of California, San Francisco, California, USA
| | - Ria Garg
- Department of Pediatrics, Division of Medical Genetics, University of California, San Francisco, California, USA
| | - Angie C. Jelin
- Department of Gynecology and Obstetrics, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - John Boscardin
- Department of Medicine, University of California, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Mary E. Norton
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California, San Francisco, California, USA
- Department of Pediatrics, Division of Medical Genetics, University of California, San Francisco, California, USA
- Institute of Human Genetics, University of California, San Francisco, California, USA
- Center for Maternal Fetal Precision Medicine, University of California, San Francisco, California, USA
| | - Teresa N. Sparks
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California, San Francisco, California, USA
- Institute of Human Genetics, University of California, San Francisco, California, USA
- Center for Maternal Fetal Precision Medicine, University of California, San Francisco, California, USA
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Yang SY, Kang KM, Kim SY, Lim SY, Jang HY, Hong K, Cha DH, Shim SH, Joung JG. Combined Model-Based Prediction for Non-Invasive Prenatal Screening. Int J Mol Sci 2022; 23:ijms232314990. [PMID: 36499318 PMCID: PMC9737181 DOI: 10.3390/ijms232314990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
The risk of chromosomal abnormalities in the child increases with increasing maternal age. Although non-invasive prenatal testing (NIPT) is a safe and effective prenatal screening method, the accuracy of the test results needs to be improved owing to various testing conditions. We attempted to achieve a more accurate and robust prediction of chromosomal abnormalities by combining multiple methods. Here, three different methods, namely standard Z-score, normalized chromosome value, and within-sample reference bin, were used for 1698 reference and 109 test samples of whole-genome sequencing. The logistic regression model combining the three methods achieved a higher accuracy than any single method. In conclusion, the proposed method offers a promising approach for increasing the reliability of NIPT.
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Affiliation(s)
- So-Yun Yang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
| | - Kyung Min Kang
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06135, Republic of Korea
| | - Sook-Young Kim
- CHA Future Medicine Research Institute, CHA Bundang Medical Center, Seongnam 13488, Republic of Korea
| | - Seo Young Lim
- Department of Biomedical Engineering, Hankuk University of Foreign Studies, Yongin 17035, Republic of Korea
| | - Hee Yeon Jang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06135, Republic of Korea
| | - Kirim Hong
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul 06135, Republic of Korea
| | - Dong Hyun Cha
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06135, Republic of Korea
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul 06135, Republic of Korea
| | - Sung Han Shim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06135, Republic of Korea
- Correspondence: (S.H.S.); (J.-G.J.); Tel.: +82-31-881-7182 (J.-G.J.); +82-31-881-7148 (S.H.S.)
| | - Je-Gun Joung
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
- CHA Future Medicine Research Institute, CHA Bundang Medical Center, Seongnam 13488, Republic of Korea
- Institute for Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Republic of Korea
- Correspondence: (S.H.S.); (J.-G.J.); Tel.: +82-31-881-7182 (J.-G.J.); +82-31-881-7148 (S.H.S.)
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Lee J, Lee SM, Ahn JM, Lee TR, Kim W, Cho EH, Ki CS. Development and performance evaluation of an artificial intelligence algorithm using cell-free DNA fragment distance for non-invasive prenatal testing (aiD-NIPT). Front Genet 2022; 13:999587. [DOI: 10.3389/fgene.2022.999587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/09/2022] [Indexed: 11/30/2022] Open
Abstract
With advances in next-generation sequencing technology, non-invasive prenatal testing (NIPT) has been widely implemented to detect fetal aneuploidies, including trisomy 21, 18, and 13 (T21, T18, and T13). Most NIPT methods use cell-free DNA (cfDNA) fragment count (FC) in maternal blood. In this study, we developed a novel NIPT method using cfDNA fragment distance (FD) and convolutional neural network-based artificial intelligence algorithm (aiD-NIPT). Four types of aiD-NIPT algorithm (mean, median, interquartile range, and its ensemble) were developed using 2,215 samples. In an analysis of 17,678 clinical samples, all algorithms showed >99.40% accuracy for T21/T18/T13, and the ensemble algorithm showed the best performance (sensitivity: 99.07%, positive predictive value (PPV): 88.43%); the FC-based conventional Z-score and normalized chromosomal value showed 98.15% sensitivity, with 40.77% and 36.81% PPV, respectively. In conclusion, FD-based aiD-NIPT was successfully developed, and it showed better performance than FC-based NIPT methods.
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Demko Z, Prigmore B, Benn P. A Critical Evaluation of Validation and Clinical Experience Studies in Non-Invasive Prenatal Testing for Trisomies 21, 18, and 13 and Monosomy X. J Clin Med 2022; 11:jcm11164760. [PMID: 36012999 PMCID: PMC9410356 DOI: 10.3390/jcm11164760] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/28/2022] [Accepted: 08/11/2022] [Indexed: 11/25/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) for trisomies 21, 18, 13 and monosomy X is widely utilized with massively parallel shotgun sequencing (MPSS), digital analysis of selected regions (DANSR), and single nucleotide polymorphism (SNP) analyses being the most widely reported methods. We searched the literature to find all NIPT clinical validation and clinical experience studies between January 2011 and January 2022. Meta-analyses were performed using bivariate random-effects and univariate regression models for estimating summary performance measures across studies. Bivariate meta-regression was performed to explore the influence of testing method and study design. Subgroup and sensitivity analyses evaluated factors that may have led to heterogeneity. Based on 55 validation studies, the detection rate (DR) was significantly higher for retrospective studies, while the false positive rate (FPR) was significantly lower for prospective studies. Comparing the performance of NIPT methods for trisomies 21, 18, and 13 combined, the SNP method had a higher DR and lower FPR than other methods, significantly so for MPSS, though not for DANSR. The performance of the different methods in the 84 clinical experience studies was consistent with validation studies. Clinical positive predictive values of all NIPT methods improved over the last decade. We conclude that all NIPT methods are highly effective for fetal aneuploidy screening, with performance differences across methodologies.
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Affiliation(s)
| | | | - Peter Benn
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
- Correspondence:
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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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Schneider L, Usherwood T, Tripathi A. A microfluidic platform for high-purity cell free DNA extraction from plasma for non-invasive prenatal testing. Prenat Diagn 2022; 42:240-253. [PMID: 35032044 DOI: 10.1002/pd.6092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/22/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Increase the yield and purity of cell-free DNA (cfDNA) extracted from plasma for non-invasive prenatal testing (NIPT) as inefficiencies in this extraction and purification can dramatically affect the sensitivity and specificity of the test. METHODS This work integrates cfDNA extraction from plasma with a microfluidic chip platform by combining magnetic bead-based extraction and electroosmotic flow on the microfluidic chip. Various wash buffers and voltage conditions were simulated using COMSOL Multiphysics Modeling and tested experimentally. RESULTS When performing the first wash step of this assay on the microfluidic chip with 300 V applied across the channel there was a six-fold increase in the A260 /A230 ratio showing a significant improvement (p value 0.0005) in the purity of the extracted sample all while maintaining a yield of 68.19%. These values are critical as a high yield results in more sample to analyze and an increase in A260 /A230 ratio corresponds to a decrease in salt contaminants such as guanidinium thiocyanate which can interfere with downstream processes during DNA library preparation and potentially hinder the NIPT screening results. CONCLUSIONS This technique has the potential to improve NIPT outcomes and other clinically relevant workflows that use cfDNA as an analyte such as cancer detection.
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Affiliation(s)
- Lindsay Schneider
- Center for Biomedical Engineering, Brown University, Providence, Rhode Island, USA
| | - Thomas Usherwood
- Center for Biomedical Engineering, Brown University, Providence, Rhode Island, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, Brown University, Providence, Rhode Island, USA
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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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12
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Paluoja P, Teder H, Ardeshirdavani A, Bayindir B, Vermeesch J, Salumets A, Krjutškov K, Palta P. Systematic evaluation of NIPT aneuploidy detection software tools with clinically validated NIPT samples. PLoS Comput Biol 2021; 17:e1009684. [PMID: 34928946 PMCID: PMC8722721 DOI: 10.1371/journal.pcbi.1009684] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/03/2022] [Accepted: 11/27/2021] [Indexed: 11/18/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) is a powerful screening method for fetal aneuploidy detection, relying on laboratory and computational analysis of cell-free DNA. Although several published computational NIPT analysis tools are available, no prior comprehensive, head-to-head accuracy comparison of the various tools has been published. Here, we compared the outcome accuracies obtained for clinically validated samples with five commonly used computational NIPT aneuploidy analysis tools (WisecondorX, NIPTeR, NIPTmer, RAPIDR, and GIPseq) across various sequencing depths (coverage) and fetal DNA fractions. The sample set included cases of fetal trisomy 21 (Down syndrome), trisomy 18 (Edwards syndrome), and trisomy 13 (Patau syndrome). We determined that all of the compared tools were considerably affected by lower sequencing depths, such that increasing proportions of undetected trisomy cases (false negatives) were observed as the sequencing depth decreased. We summarised our benchmarking results and highlighted the advantages and disadvantages of each computational NIPT software. To conclude, trisomy detection for lower coverage NIPT samples (e.g. 2.5M reads per sample) is technically possible but can, with some NIPT tools, produce troubling rates of inaccurate trisomy detection, especially in low-FF samples. Non-invasive prenatal testing analysis relies on computational algorithms that are used for inferring chromosomal aneuploidies, such as chromosome 21 triploidy in the case of Down syndrome. However, the performance of these algorithms has not been compared on the same clinically validated data. Here we conducted a head-to-head comparison of WGS-based NIPT aneuploidy detection tools. Our findings indicate that at and below 2.5M reads per sample, the least accurate algorithm would miss detection of almost a third of trisomy cases. Furthermore, we describe and quantify a previously undocumented aneuploidy risk uncertainty that is mainly relevant in cases of very low sequencing coverage (at and below 1.25M reads per sample) and could, in the worst-case scenario, lead to a false negative rate of 245 undetected trisomies per 1,000 trisomy cases. Our findings underscore the importance of the informed selection of NIPT software tools in combination with sequencing coverage, which directly impacts NIPT sequencing cost and accuracy.
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Affiliation(s)
- Priit Paluoja
- Doctoral Programme in Population Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Competence Centre for Health Technologies, Tartu, Estonia
| | - Hindrek Teder
- Competence Centre for Health Technologies, Tartu, Estonia
- Institute of Biomedicine and Translational Medicine, Department of Biomedicine, University of Tartu, Tartu, Estonia
| | | | - Baran Bayindir
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Andres Salumets
- Competence Centre for Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Kaarel Krjutškov
- Competence Centre for Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Priit Palta
- Competence Centre for Health Technologies, Tartu, Estonia
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- * E-mail:
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13
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Assessment and Clinical Utility of a Non-Next-Generation Sequencing-Based Non-Invasive Prenatal Testing Technology. Curr Issues Mol Biol 2021; 43:958-964. [PMID: 34449543 PMCID: PMC8929113 DOI: 10.3390/cimb43020068] [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: 06/29/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/17/2022] Open
Abstract
Background: Rolling-circle replication (RCR) is a novel technology that has not been applied to cell-free DNA (cfDNA) testing until recently. Given the cost and simplicity advantages of this technology compared to other platforms currently used in cfDNA analysis, an assessment of RCR in clinical laboratories was performed. Here, we present the first validation study from clinical laboratories utilizing RCR technology. Methods: 831 samples from spontaneously pregnant women carrying a singleton fetus, and 25 synthetic samples, were analyzed for the fetal risk of trisomy 21 (T21), trisomy 18 (T18) and trisomy 13 (T13), by three laboratories on three continents. All the screen-positive pregnancies were provided post-test genetic counseling and confirmatory diagnostic invasive testing (e.g., amniocentesis). The screen-negative pregnancies were routinely evaluated at birth for fetal aneuploidies, using newborn examinations, and any suspected aneuploidies would have been offered diagnostic testing or confirmed with karyotyping. Results: The study found rolling-circle replication to be a highly viable technology for the clinical assessment of fetal aneuploidies, with 100% sensitivity for T21 (95% CI: 82.35-100.00%); 100.00% sensitivity for T18 (71.51-100.00%); and 100.00% sensitivity for T13 analyses (66.37-100.00%). The specificities were >99% for each trisomy (99.7% (99.01-99.97%) for T21; 99.5% (98.62-99.85%) for T18; 99.7% (99.03-99.97%) for T13), along with a first-pass no-call rate of 0.93%. Conclusions: The study showed that using a rolling-circle replication-based cfDNA system for the evaluation of the common aneuploidies would provide greater accuracy and clinical utility compared to conventional biochemical screening, and it would provide comparable results to other reported cfDNA methodologies.
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14
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Qu L, Wu Q, Yang X, Wang W, Xu B, Shan G, Liang L, Wang S, Zhang J. Adaptive parameter of standard deviation enhances the power of noninvasive prenatal screens. J Matern Fetal Neonatal Med 2021; 35:6356-6362. [PMID: 33910452 DOI: 10.1080/14767058.2021.1912001] [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: 10/21/2022]
Abstract
PURPOSE Traditional Z-test methods during noninvasive prenatal screens (NIPS) use the fixed parameter of standard deviation (SD), which ignores the influence of actual sequencing read counts of a sample on the results. The aim of this study is to eliminate the influence of the sequencing depth of individual samples on the results and enhance the power of NIPS. METHODS In this study, we propose an improved NIPS method, which calculates the SD in the Z-score process adaptively according to the actual read count of the test sample. Our approach obtained the SD linear fitting function along with the read count with a large number of reference samples, in which SD and read count fit well. The effectiveness of our enhanced NIPS method was evaluated on three common trisomy syndromes and five recurrent CNV syndromes with 3219 and 6592 samples based on whole genome sequencing of maternal peripheral blood. RESULTS A total of 3,219 pregnant samples have been used for validating the proposed method on detecting fetal trisomy syndromes (T13, T18, and T21), in which eight false negative (FN) samples have been corrected as true positive (TP) and eight false positive (FP) samples have been fixed as true negative (TN) with our proposed adaptive-SD method. Another 6592 samples were used to compare the two methods on detecting five recurrent fetal copy number variation (CNV) syndromes, in which the FP samples have decreased from 99 to 39. CONCLUSIONS Our adaptive-SD NIPS method shows more power on detecting both trisomy syndromes and five recurrent CNVs in the pregnant samples with diverse read counts. Besides, our proposed method contributes to lower FP and FN samples than the traditional Z-test method in NIPS. Our results show that our enhanced NIPS methods are effective in detecting both abnormal fetal trisomy syndromes and recurrent CNV syndromes in pregnant women.
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Affiliation(s)
- Li Qu
- Beijing USCI Medical Laboratory, Beijing, China
| | - Qixi Wu
- Beijing USCI Medical Laboratory, Beijing, China
| | - Xiaoke Yang
- Department of Gynecology and Obstetrics, Beijing Hospital, National Center for Geriatrics, Beijing, China
| | - Weiwei Wang
- Beijing USCI Medical Laboratory, Beijing, China
| | - Bing Xu
- Beijing USCI Medical Laboratory, Beijing, China
| | | | - Lin Liang
- Department of Gynecology and Obstetrics, Beijing Hospital, National Center for Geriatrics, Beijing, China
| | - Shaowei Wang
- Department of Gynecology and Obstetrics, Beijing Hospital, National Center for Geriatrics, Beijing, China
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15
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Soukkhaphone B, Lindsay C, Langlois S, Little J, Rousseau F, Reinharz D. Non-invasive prenatal testing for the prenatal screening of sex chromosome aneuploidies: A systematic review and meta-analysis of diagnostic test accuracy studies. Mol Genet Genomic Med 2021; 9:e1654. [PMID: 33755350 PMCID: PMC8172189 DOI: 10.1002/mgg3.1654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 10/31/2020] [Accepted: 02/19/2021] [Indexed: 12/19/2022] Open
Abstract
Background There is little evidence on the performance of non‐invasive prenatal testing (NIPT) for the detection of fetal sex chromosomal imbalances. In this review, we aimed to appraise and synthesize the literature on the performance of NIPT for the prenatal detection of fetal sex chromosome aneuploidies. Methods We performed our literature search in PubMed, Embase, Cochrane Library, Web of Science, and CADTH. Study selection and data extraction were performed by two reviewers independently. There were no restrictions on the study population. Meta‐analyses were performed with “R” software. Pooled sensitivities and specificities with their 95% CI were estimated using a random‐effects model. Heterogeneity between studies was assessed by a Q test. Results Based on 11 studies in high prior risk pregnancies, including 116 affected fetuses in aggregate, Massively Parallel Shotgun Sequencing (MPSS) had a sensitivity of 93.9% (95% CI 84.1%, 97.8%) and a specificity of 99.6% (95% CI 98.7%, 99.9%) for the detection of 45,X. Based on four studies in high‐risk pregnancies, with 83 affected fetuses in aggregate, Targeted Massively Parallel Sequencing (TMPS) had a sensitivity of 83.2% (95% CI 49.6%, 96.2%) and specificity was 99.8% (95% CI 98.3%, 100%) for the detection of 45,X. In mixed‐risk pregnancies, the sensitivity of TMPS for the detection of 45,X was 90.9% (2 studies; 95% CI 70%, 97.7%) and specificity 99.9% (2 studies; 95% CI 99.4%, 100%); MPSS data were not available in such pregnancies. Based on smaller numbers of studies, and small numbers of affected fetuses in either high‐risk or mixed‐risk pregnancies (using either MPSS or TMPS), the sensitivities and specificities were equal to or greater than 76.2% for 47,XXX, 47,XXY and 47, XYY. The test failures for SCAs were 0.2% (95% CI 0%, 13.6%) for MPSS and 5.6% (95% CI 3.7%, 8.4%) for TMPS. Conclusion High‐quality studies are still desirable in order to estimate the performance of NIPT for the detection of sex chromosome imbalances.
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Affiliation(s)
| | - Carmen Lindsay
- CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada
| | | | | | - Francois Rousseau
- Laval University, Quebec City, QC, Canada.,Hôpital Saint-François d'Assise, Quebec, QC, Canada
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16
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Alyafee Y, Al Tuwaijri A, Alam Q, Umair M, Haddad S, Alharbi M, Ballow M, Al Drees M, AlAbdulrahman A, Al Khaldi A, Alfadhel M. Next Generation Sequencing Based Non-invasive Prenatal Testing (NIPT): First Report From Saudi Arabia. Front Genet 2021; 12:630787. [PMID: 33613643 PMCID: PMC7889598 DOI: 10.3389/fgene.2021.630787] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/06/2021] [Indexed: 01/09/2023] Open
Abstract
Background: Non-invasive prenatal testing (NIPT) for aneuploidy in pregnant women screening has been recently established in Saudi Arabia. We aim from this study to report our experience in the implementation of this new technology in clinical practice and to assess factors influencing cell-free fetal (cffDNA) fraction and successful NIPT reporting. Methods: In total, 200 pregnant women were subjected to the NIPT test using standard methods. Next-generation sequencing (NGS) was used to analyze cffDNA in maternal plasma. Results: Out of the 200 NIPT cases, the average age of pregnant women was 35 ± 6 years (range: 21–48 years). The average cffDNA fraction of reported cases was 13.72% (range: 3–31%). Out of these 200 cases, 187 (93.5%) were at low risk, while 13 (6.5%) cases revealed high risk for aneuploidy. Among these chromosomal abnormalities, 7 (3.5%) cases of Down’s syndrome, 5 (2.5%) Edwards’ Syndrome, and only 1 case of (0.5%) Patau’s syndrome was observed. Out of the 13 high-risk cases, 2 (15.3%) were found in women below the age of 30. Conclusion: This is the first study reporting the successful implementation of an in-house NIPT screening service in Saudi Arabia. Our data showed high accuracy and sensitivity to detect high-risk cases indicating the usefulness of such a technique as an alternative to invasive testing and (hopefully) will change the common screening practice for pregnant women in Saudi Arabia.
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Affiliation(s)
- Yusra Alyafee
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Abeer Al Tuwaijri
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Qamre Alam
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Shahad Haddad
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Mashael Alharbi
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Maryam Ballow
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Mohammed Al Drees
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Abdulkareem AlAbdulrahman
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Aziza Al Khaldi
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia.,Genetics and Precision Medicine Department (GPM), King Abdullah Specialized Children's Hospital, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, MNG-HA, Riyadh, Saudi Arabia
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17
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Industry, experts and the role of the 'invisible college' in the dissemination of non-invasive prenatal testing in the US. Soc Sci Med 2020; 270:113635. [PMID: 33385622 DOI: 10.1016/j.socscimed.2020.113635] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/23/2020] [Accepted: 12/17/2020] [Indexed: 11/20/2022]
Abstract
Enthusiasm for so-called 'personalized' or 'precision' medicine has encouraged the growth of the molecular diagnostics industry and the proliferation of high-priced proprietary tests that can predict, diagnose or inform the treatment of diverse clinical conditions. Through a case study of non-invasive prenatal testing (NIPT), we explore how the mechanisms governing the development and dissemination of this novel prenatal screening test are most aptly understood as a 'regulatory regime.' We describe how private actors tied to the manufacturers of this test form a network of "experts" that contribute to the coordination of this regime by virtue of their efforts to navigate the governance of test adoption and also form spaces in which the standards governing test adoption are developed. We draw attention to private actors in this regime to demonstrate that they are a constitutive element of the public policy system governing biomedical innovation and adoption. Through this case study of NIPT we deepen our previous analysis of the role of consultants in navigating and shaping a regulatory regime (Holloway and Miller, 2020) and offer new insight about how scientists work with consultants to shape a regulatory regime that serves industry interests. Our work indicates that the private actors tied to the manufacturers of NIPT (experts employed by industry to court scientists and lobby payers, scientists collaborating with industry, key opinion leaders involved with clinical practice guidelines, lobbyists and consultants), constitute an 'invisible college' that navigates the governance of test adoption. The formations and negotiations over standards for NIPT identified in this paper comprise a new institutional norm: a polycentric regulatory regime permeated by commercial interests. The institutionalization of this regime has implications for accountability, transparency and test quality amidst a proliferation of new proprietary molecular tests.'
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Analysis of cell-free DNA in a consecutive series of 13,607 routine cases for the detection of fetal chromosomal aneuploidies in a single center in Germany. Arch Gynecol Obstet 2020; 303:1407-1414. [PMID: 33151425 PMCID: PMC8087552 DOI: 10.1007/s00404-020-05856-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023]
Abstract
Purpose Noninvasive prenatal testing (NIPT) is a highly sensitive and specific method for detection of fetal chromosomal aneuploidies from maternal plasma. The objective of this study was to determine the performance of a new paired-end sequencing-based NIPT assay in 13,607 pregnancies from a single center in Germany. Methods Samples from 13,607 pregnant women who previously underwent NIPT were analyzed using VeriSeq NIPT Solution v2 assay for presence of common fetal trisomies and monosomy X. Follow-up to determine clinical truth was carried out. Results Of the 13,607 cases, 13,509 received a NIPT call resulting in a low study failure rate of 0.72%. There were 188 (1.4%) high-risk calls: 117 trisomy 21, 34 trisomy 18, 23 trisomy 13, one trisomy 21 + 13, and 13 monosomy X. High sensitivities and specificities of ≥ 98.89% were reported for all four aneuploidy conditions. Of the high-risk cases, clinical follow-up data were available for 77.1% (145/188). Clinical follow-up of high-risk calls revealed an overall positive predictive value of 84.8% (potential range 65.4–88.3%). NIPT results were provided for samples across a range of fetal fractions, down to 2% fetal fraction. Conclusion The VeriSeq NIPT Solution v2 assay detected fetal chromosomal aneuploidies across a range of fetal fractions with high sensitivities and specificities observed based on known clinical outcomes, a high overall PPV, and a low failure rate. Electronic supplementary material The online version of this article (10.1007/s00404-020-05856-0) contains supplementary material, which is available to authorized users.
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19
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Gordevičius J, Narmontė M, Gibas P, Kvederavičiūtė K, Tomkutė V, Paluoja P, Krjutškov K, Salumets A, Kriukienė E. Identification of fetal unmodified and 5-hydroxymethylated CG sites in maternal cell-free DNA for non-invasive prenatal testing. Clin Epigenetics 2020; 12:153. [PMID: 33081811 PMCID: PMC7574562 DOI: 10.1186/s13148-020-00938-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/14/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Massively parallel sequencing of maternal cell-free DNA (cfDNA) is widely used to test fetal genetic abnormalities in non-invasive prenatal testing (NIPT). However, sequencing-based approaches are still of high cost. Building upon previous knowledge that placenta, the main source of fetal circulating DNA, is hypomethylated in comparison to maternal tissue counterparts of cfDNA, we propose that targeting either unmodified or 5-hydroxymethylated CG sites specifically enriches fetal genetic material and reduces numbers of required analytical sequencing reads thereby decreasing cost of a test. METHODS We employed uTOPseq and hmTOP-seq approaches which combine covalent derivatization of unmodified or hydroxymethylated CG sites, respectively, with next generation sequencing, or quantitative real-time PCR. RESULTS We detected increased 5-hydroxymethylcytosine (5hmC) levels in fetal chorionic villi (CV) tissue samples as compared with peripheral blood. Using our previously developed uTOP-seq and hmTOP-seq approaches we obtained whole-genome uCG and 5hmCG maps of 10 CV tissue and 38 cfDNA samples in total. Our results indicated that, in contrast to conventional whole genome sequencing, such epigenomic analysis highly specifically enriches fetal DNA fragments from maternal cfDNA. While both our approaches yielded 100% accuracy in detecting Down syndrome in fetuses, hmTOP-seq maintained such accuracy at ultra-low sequencing depths using only one million reads. We identified 2164 and 1589 placenta-specific differentially modified and 5-hydroxymethylated regions, respectively, in chromosome 21, as well as 3490 and 2002 Down syndrome-specific differentially modified and 5-hydroxymethylated regions, respectively, that can be used as biomarkers for identification of Down syndrome or other epigenetic diseases of a fetus. CONCLUSIONS uTOP-seq and hmTOP-seq approaches provide a cost-efficient and sensitive epigenetic analysis of fetal abnormalities in maternal cfDNA. The results demonstrated that T21 fetuses contain a perturbed epigenome and also indicated that fetal cfDNA might originate from fetal tissues other than placental chorionic villi. Robust covalent derivatization followed by targeted analysis of fetal DNA by sequencing or qPCR presents an attractive strategy that could help achieve superior sensitivity and specificity in prenatal diagnostics.
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Affiliation(s)
- Juozas Gordevičius
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, 10257, Vilnius, Lithuania
| | - Milda Narmontė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, 10257, Vilnius, Lithuania
| | - Povilas Gibas
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, 10257, Vilnius, Lithuania
| | - Kotryna Kvederavičiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, 10257, Vilnius, Lithuania
| | - Vita Tomkutė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, 10257, Vilnius, Lithuania
| | - Priit Paluoja
- Competence Centre On Health Technologies, Teaduspargi 13, 50411, Tartu, Estonia.,Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Kaarel Krjutškov
- Competence Centre On Health Technologies, Teaduspargi 13, 50411, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, L. Puusepa 8, 50406, Tartu, Estonia
| | - Andres Salumets
- Competence Centre On Health Technologies, Teaduspargi 13, 50411, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, L. Puusepa 8, 50406, Tartu, Estonia.,Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, HUS, PO Box 140, 00029, Helsinki, Finland.,Estonian Genome Center, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Edita Kriukienė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, 10257, Vilnius, Lithuania. .,Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, 10257, Vilnius, Lithuania.
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20
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Hancock S, Ben‐Shachar R, Adusei C, Oyolu CB, Evans EA, Kang HP, Haverty C, Muzzey D. Clinical experience across the fetal-fraction spectrum of a non-invasive prenatal screening approach with low test-failure rate. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2020; 56:422-430. [PMID: 31671482 PMCID: PMC7496885 DOI: 10.1002/uog.21904] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/08/2019] [Accepted: 10/17/2019] [Indexed: 06/10/2023]
Abstract
OBJECTIVE To describe our clinical experience across the entire range of fetal-fraction (FF) measurements of a non-invasive prenatal screen (NIPS) that uses whole- genome sequencing (WGS). METHODS We analyzed retrospectively results from 58 105 singleton pregnancies that underwent NIPS on a customized WGS platform during an 8-month period and assessed clinical test performance for trisomy 21, trisomy 18 and trisomy 13. Pregnancy outcomes were sought for all screen-positive patients and for 18% of screen-negative patients. As differences in outcome-collection response rates could artificially impact test-performance calculations, we computed inferred sensitivity, specificity, positive predictive values (PPV) and negative predictive values adjusted for ascertainment bias. RESULTS The screening test yielded a result for 99.9% (n = 58 048) of patients, meaning that approximately 1 in 1000 patients received a test failure (i.e. test failure rate = 0.1%). Of pregnancies with a test result, 572 (1%) screened positive for one of the common aneuploidies (362 for trisomy 21, 142 for trisomy 18 and 68 for trisomy 13). Informative outcomes were received for 237 (41.4%) patients with a screen-positive result and 3258 (5.7%) of those with a screen-negative result. In the full cohort, inferred sensitivities for trisomy 21, trisomy 18 and trisomy 13 were 99.7%, 96.8% and 94.3%, respectively, and PPVs were 93.1%, 85.2% and 48.4%, respectively. If a FF threshold of 4% had been employed to guard against false negatives, calculated sensitivities for the three aneuploidies would not have changed significantly, yet, importantly, the overall test-failure rate would have increased to 6.6% (n = 3829), impacting 1 in 15 women. CONCLUSIONS Our clinical experience demonstrates that a customized WGS-based NIPS without a FF threshold achieves high accuracy while maintaining a low test-failure rate of 0.1%. As such, alternative strategies to ensure high accuracy of detection of common aneuploidies in samples with low FF (such as redraw after test failure, redrawing at a later gestational age, risk scoring based on FF) are not necessary for this screening approach. © 2019 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of the International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- S. Hancock
- Myriad Women's HealthSouth San FranciscoCAUSA
| | - R. Ben‐Shachar
- Myriad Women's HealthSouth San FranciscoCAUSA
- Myriad GeneticsSalt Lake CityUTUSA
| | - C. Adusei
- Myriad Women's HealthSouth San FranciscoCAUSA
| | - C. B. Oyolu
- Myriad Women's HealthSouth San FranciscoCAUSA
| | - E. A. Evans
- Myriad Women's HealthSouth San FranciscoCAUSA
| | - H. P. Kang
- Myriad Women's HealthSouth San FranciscoCAUSA
| | - C. Haverty
- Myriad Women's HealthSouth San FranciscoCAUSA
| | - D. Muzzey
- Myriad Women's HealthSouth San FranciscoCAUSA
- Myriad GeneticsSalt Lake CityUTUSA
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Strategy for Use of Genome-Wide Non-Invasive Prenatal Testing for Rare Autosomal Aneuploidies and Unbalanced Structural Chromosomal Anomalies. J Clin Med 2020; 9:jcm9082466. [PMID: 32752152 PMCID: PMC7464024 DOI: 10.3390/jcm9082466] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/25/2020] [Accepted: 07/28/2020] [Indexed: 11/23/2022] Open
Abstract
Atypical fetal chromosomal anomalies are more frequent than previously recognized and can affect fetal development. We propose a screening strategy for a genome-wide non-invasive prenatal test (NIPT) to detect these atypical chromosomal anomalies (ACAs). Two sample cohorts were tested. Assay performances were determined using Cohort A, which consisted of 192 biobanked plasma samples—42 with ACAs, and 150 without. The rate of additional invasive diagnostic procedures was determined using Cohort B, which consisted of 3097 pregnant women referred for routine NIPT. Of the 192 samples in Cohort A, there were four initial test failures and six discordant calls; overall sensitivity was 88.1% (37/42; CI 75.00–94.81) and specificity was 99.3% (145/146; CI 96.22–99.88). In Cohort B, there were 90 first-pass failures (2.9%). The rate of positive results indicating an anomaly was 1.2% (36/3007) and 0.57% (17/3007) when limited to significant unbalanced chromosomal anomalies and trisomies 8, 9, 12, 14, 15, 16, and 22. These results show that genome-wide NIPT can screen for ACAs with an acceptable sensitivity and a small increase in invasive testing, particularly for women with increased risk following maternal serum screening and by limiting screening to structural anomalies and the most clinically meaningful trisomies.
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22
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Abstract
Introduction Non-invasive prenatal testing (NIPT) using cell-free foetal DNA has been widely accepted in recent years for detecting common foetal chromosome aneuploidies, such as trisomies 13, 18 and 21, and sex chromosome aneuploidies. In this study, the practical clinical performance of our foetal DNA testing was evaluated for analysing all chromosome aberrations among 7113 pregnancies in Italy. Methods This study was a retrospective analysis of collected NIPT data from the Ion S5 next-generation sequencing platform obtained from Altamedica Medical Centre in Rome, Italy. Results In this study, NIPT showed 100% sensitivity and 99.9% specificity for trisomies 13, 18 and 21. Out of the 7113 samples analysed, 74 cases (1%) were positive by NIPT testing; foetal karyotyping and follow-up results validated 2 trisomy 13 cases, 5 trisomy 18 cases, 58 trisomy 21 cases and 10 sex chromosome aneuploidy cases. There were no false-negative results. Conclusion In our hands, NIPT had high sensitivity and specificity for common chromosomal aneuploidies such as trisomies 13, 18 and 21.
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Budis J, Gazdarica J, Radvanszky J, Szucs G, Kucharik M, Strieskova L, Gazdaricova I, Harsanyova M, Duris F, Minarik G, Sekelska M, Nagy B, Turna J, Szemes T. Combining count- and length-based z-scores leads to improved predictions in non-invasive prenatal testing. Bioinformatics 2020; 35:1284-1291. [PMID: 30219853 DOI: 10.1093/bioinformatics/bty806] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/16/2018] [Accepted: 09/13/2018] [Indexed: 02/06/2023] Open
Abstract
MOTIVATION Non-invasive prenatal testing or NIPT is currently among the top researched topic in obstetric care. While the performance of the current state-of-the-art NIPT solutions achieve high sensitivity and specificity, they still struggle with a considerable number of samples that cannot be concluded with certainty. Such uninformative results are often subject to repeated blood sampling and re-analysis, usually after two weeks, and this period may cause a stress to the future mothers as well as increase the overall cost of the test. RESULTS We propose a supplementary method to traditional z-scores to reduce the number of such uninformative calls. The method is based on a novel analysis of the length profile of circulating cell free DNA which compares the change in such profiles when random-based and length-based elimination of some fragments is performed. The proposed method is not as accurate as the standard z-score; however, our results suggest that combination of these two independent methods correctly resolves a substantial portion of healthy samples with an uninformative result. Additionally, we discuss how the proposed method can be used to identify maternal aberrations, thus reducing the risk of false positive and false negative calls. AVAILABILITY AND IMPLEMENTATION The open-source code of the proposed methods, together with test data, is freely available for non-commercial users at github web page https://github.com/jbudis/lambda. SUPPLEMENTARY INFORMATION Supplementary materials are available at Bioinformatics online.
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Affiliation(s)
- Jaroslav Budis
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia.,Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia
| | - Juraj Gazdarica
- Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Jan Radvanszky
- Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Gabor Szucs
- Department of Applied Mathematics and Statistics, Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia
| | | | - Lucia Strieskova
- Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Iveta Gazdaricova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Maria Harsanyova
- Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Frantisek Duris
- Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia
| | | | | | - Balint Nagy
- Department of Human Genetics, University of Debrecen, Debrecen, Hungary
| | - Jan Turna
- Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia.,Comenius University Science Park, Bratislava, Slovakia
| | - Tomas Szemes
- Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia.,Comenius University Science Park, Bratislava, Slovakia
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24
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Implementation of cell-free DNA-based non-invasive prenatal testing in a National Health Service Regional Genetics Laboratory. Genet Res (Camb) 2019; 101:e11. [PMID: 31813398 PMCID: PMC7044975 DOI: 10.1017/s0016672319000119] [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] [Indexed: 12/16/2022] Open
Abstract
Background Non-invasive prenatal testing (NIPT) for the detection of foetal aneuploidy through analysis of cell-free DNA (cfDNA) in maternal blood is offered routinely by many healthcare providers across the developed world. This testing has recently been recommended for evaluative implementation in the UK National Health Service (NHS) foetal anomaly screening pathway as a contingent screen following an increased risk of trisomy 21, 18 or 13. In preparation for delivering a national service, we have implemented cfDNA-based NIPT in our Regional Genetics Laboratory. Here, we describe our validation and verification processes and initial experiences of the technology prior to rollout of a national screening service. Methods Data are presented from more than 1000 patients (215 retrospective and 840 prospective) from ‘high- and low-risk pregnancies’ with outcome data following birth or confirmatory invasive prenatal sampling. NIPT was by the Illumina Verifi® test. Results Our data confirm a high-fidelity service with a failure rate of ~0.24% and a high sensitivity and specificity for the detection of foetal trisomy 13, 18 and 21. Secondly, the data show that a significant proportion of patients continue their pregnancies without prenatal invasive testing or intervention after receiving a high-risk cfDNA-based result. A total of 46.5% of patients referred to date were referred for reasons other than high screen risk. Ten percent (76/840 clinical service referrals) of patients were referred with ultrasonographic finding of a foetal structural anomaly, and data analysis indicates high- and low-risk scan indications for NIPT. Conclusions NIPT can be successfully implemented into NHS regional genetics laboratories to provide high-quality services. NHS provision of NIPT in patients with high-risk screen results will allow for a reduction of invasive testing and partially improve equality of access to cfDNA-based NIPT in the pregnant population. Patients at low risk for a classic trisomy or with other clinical indications are likely to continue to access cfDNA-based NIPT as a private test.
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25
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杨 兴, 郭 晓, 钟 进, 陈 志, 吴 水. [Noninvasive prenatal genetic testing in 6804 pregnant women aged less than 35 years with positive results in serum screening]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2019; 39:1350-1356. [PMID: 31852638 PMCID: PMC6926076 DOI: 10.12122/j.issn.1673-4254.2019.11.13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate the feasibility of noninvasive prenatal genetic testing for detecting chromosome aneuploid in pregnant women aged less than 35 years with positive results in serum screening. METHODS We analyzed the plasma cellfree fetal DNA in a total of 6804 pregnant women aged less than 35 years with singleton pregnancy from Foshan maternal and child health care hospital, whose weeks of gestation ranged from 12 to 24 weeks with ages on the expected date of confinement of 21-34 years. According to the results of serum screening, the women were divided to high-risk group and critical-risk group. Amniocentesis or cordocentesis was carried out if the results of noninvasive prenatal genetic testing were positive, and karyotyping or/and high-throughput sequencing was performed as the golden standard. All the women were followed up by telephone calls to assess the accuracy of the prenatal testing. RESULTS Noninvasive prenatal testing was successfully completed in all the 6081 cases. In the high-risk group, 70 women with positive results were tested by noninvasive prenatal testing, among whom 53 were confirmed by karyotyping or high-throughput sequencing. In this group, the sensitivity, specificity and positive predictive value of trisomy 21 syndrome detection was 95.65%, 99.91% and 88.0%, respectively, with a false positive rate of 0.09% and a false negative rate of 4.35%; the sensitivity, specificity and positive predictive value for trisomy 18 syndrome was 100%, 100% and 100%, respectively, with false positive and false negative rates of 0; the false positive rate and false negative rate for trisomy 13 syndrome was 0.09% and 0, respectively; the sensitivity, specificity and positive predictive value for sex chromosome aneuploid as 100%, 99.80% and 30.0%, respectively, with a false positive rate of 0.2% and a false negative rate of 0; the sensitivity, specificity and positive predictive value for other chromosome aneuploid was 100%, 99.88% and 16.60%, respectively, with a false positive rate of 0.18% and a false negative rate of 0. In the critical risk group, 54 women with positive results received noninvasive prenatal genetic testing, among whom 36 were confirmed by karyotyping or high-throughput sequencing. The sensitivity, specificity and positive predictive value for trisomy 21 syndrome were all 100% and the false positive rate and false negative rate were both 0; the false positive rate was 0.11% and the false negative rate was 0 for trisomy 18 syndrome; the false positive rate and false negative rate for trisomy 13 syndrome was 0.04% and 0, respectively; the sensitivity, specificity and positive predictive value for sex chromosome aneuploid was 100%, 99.79% and 50.0%, respectively, with a false positive rate of 0.21% and a false negative rate of 0; the false positive rate for other chromosome aneuploid was 0.18% and the false negative rate was 0. No significant differences were found between the two groups in the sensitivity, specificity, positive predictive value and false positive rate for detection of trisomy 21 syndrome and sex chromosome aneuploid (P>0.05). CONCLUSIONS Noninvasive prenatal genetic testing is necessary for high-risk pregnant women with critical-risk in serum screening who refuse invasive prenatal diagnosis, and it is highly sensitive and specific fir detecting chromosome aneuploid with low false positive and false negative rates.
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Affiliation(s)
- 兴坤 杨
- />佛山市妇幼保健院产前诊断中心,广东 佛山 528000Prenatal Diagnosis Center, Foshan Maternal and Child Health Care Hosoital, Foshan 528000, China
| | - 晓玲 郭
- />佛山市妇幼保健院产前诊断中心,广东 佛山 528000Prenatal Diagnosis Center, Foshan Maternal and Child Health Care Hosoital, Foshan 528000, China
| | - 进 钟
- />佛山市妇幼保健院产前诊断中心,广东 佛山 528000Prenatal Diagnosis Center, Foshan Maternal and Child Health Care Hosoital, Foshan 528000, China
| | - 志华 陈
- />佛山市妇幼保健院产前诊断中心,广东 佛山 528000Prenatal Diagnosis Center, Foshan Maternal and Child Health Care Hosoital, Foshan 528000, China
| | - 水娟 吴
- />佛山市妇幼保健院产前诊断中心,广东 佛山 528000Prenatal Diagnosis Center, Foshan Maternal and Child Health Care Hosoital, Foshan 528000, China
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26
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Jiang F, Yang X, He X, Yang M. Circulating DNA, a Potentially Sensitive and Specific Diagnostic Tool for Future Medicine. Dose Response 2019; 17:1559325819891010. [PMID: 31827416 PMCID: PMC6886285 DOI: 10.1177/1559325819891010] [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: 09/20/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 11/28/2022] Open
Abstract
Liquid biopsy has the great potential of detecting early diseases before deterioration and is valued for screening abnormalities at early stage. In oncology, circulating DNA derived from shed cancer cells reflects the tissue of origin, so it could be used to locate tissue sites during early screening. However, the heterogenous parameters of different types limit the clinical application, making it inaccessible to encompass all the cancer types. Instead, for reproducible scenario as pregnancy, fetal cell-free DNA has been well utilized for screening aneuploidies. Noninvasive and convenient as is, it would be of great value in the next decades far more than early diagnosis. This review recapitulates the discovery and development of tumor and fetal cell-free DNA. The common factors are also present that could be taken into consideration when collecting, transporting, and preserving samples. Meanwhile, several protocols used for purifying cell-free DNA, either classic ones or through commercial kits, are compared carefully. In addition, the development of technologies for analyzing cell-free DNA have been summarized and discussed in detail, especially some up-to-date approaches. At the end, the potential prospect of circulating DNA is bravely depicted. In summary, although there would be a lot of efforts before it’s prevalent, cell-free DNA remains a promising tool in point-of-care diagnostic medicine.
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Affiliation(s)
- Fan Jiang
- Department of Rehabilitation Medicine, The First People's Hospital of Wenling, Wenzhou Medical University, Wenling, Zhejiang, China
| | - Xiaoxiao Yang
- Department of Rehabilitation Medicine, The First People's Hospital of Wenling, Wenzhou Medical University, Wenling, Zhejiang, China
| | - Xiping He
- Department of Rehabilitation Medicine, The First People's Hospital of Wenling, Wenzhou Medical University, Wenling, Zhejiang, China
| | - Mingming Yang
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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27
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Koumbaris G, Achilleos A, Nicolaou M, Loizides C, Tsangaras K, Kypri E, Mina P, Sismani C, Velissariou V, Christopoulou G, Constantoulakis P, Manolakos E, Papoulidis I, Stambouli D, Ioannides M, Patsalis P. Targeted capture enrichment followed by NGS: development and validation of a single comprehensive NIPT for chromosomal aneuploidies, microdeletion syndromes and monogenic diseases. Mol Cytogenet 2019; 12:48. [PMID: 31832098 PMCID: PMC6873497 DOI: 10.1186/s13039-019-0459-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/29/2019] [Indexed: 12/22/2022] Open
Abstract
Background Non-invasive prenatal testing (NIPT) has been widely adopted for the detection of fetal aneuploidies and microdeletion syndromes, nevertheless, limited clinical utilization has been reported for the non-invasive prenatal screening of monogenic diseases. In this study, we present the development and validation of a single comprehensive NIPT for prenatal screening of chromosomal aneuploidies, microdeletions and 50 autosomal recessive disorders associated with severe or moderate clinical phenotype. Results We employed a targeted capture enrichment technology powered by custom TArget Capture Sequences (TACS) and multi-engine bioinformatics analysis pipeline to develop and validate a novel NIPT test. This test was validated using 2033 cell-fee DNA (cfDNA) samples from maternal plasma of pregnant women referred for NIPT and paternal genomic DNA. Additionally, 200 amniotic fluid and CVS samples were used for validation purposes. All NIPT samples were correctly classified exhibiting 100% sensitivity (CI 89.7–100%) and 100% specificity (CI 99.8–100%) for chromosomal aneuploidies and microdeletions. Furthermore, 613 targeted causative mutations, of which 87 were unique, corresponding to 21 monogenic diseases, were identified. For the validation of the assay for prenatal diagnosis purposes, all aneuploidies, microdeletions and point mutations were correctly detected in all 200 amniotic fluid and CVS samples. Conclusions We present a NIPT for aneuploidies, microdeletions, and monogenic disorders. To our knowledge this is the first time that such a comprehensive NIPT is available for clinical implementation.
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Affiliation(s)
- George Koumbaris
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Nicosia, 2409 Cyprus
| | | | - Michalis Nicolaou
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Nicosia, 2409 Cyprus
| | | | | | - Elena Kypri
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Nicosia, 2409 Cyprus
| | - Petros Mina
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Nicosia, 2409 Cyprus
| | - Carolina Sismani
- 2The Cyprus Institute of Neurology and Genetics, International Airport Avenue, 6, Ayios Dometios, Nicosia, 2370 Cyprus.,Cyprus School of Molecular Medicine, International Airport Avenue, 6, Ayios Dometios, Nicosia, 2370 Cyprus
| | - Voula Velissariou
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Nicosia, 2409 Cyprus.,Cytogenetics and Molecular Genetics Department, Bioiatriki Healthcare Group, Athens, Greece
| | | | | | | | | | | | - Marios Ioannides
- NIPD Genetics Public Company Ltd, Neas Engomis 31, Nicosia, 2409 Cyprus
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Gazdarica J, Budis J, Duris F, Turna J, Szemes T. Adaptable Model Parameters in Non-Invasive Prenatal Testing Lead to More Stable Predictions. Int J Mol Sci 2019; 20:ijms20143414. [PMID: 31336782 PMCID: PMC6678500 DOI: 10.3390/ijms20143414] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 12/14/2022] Open
Abstract
Recent advances in massively parallel shotgun sequencing opened up new options for affordable non-invasive prenatal testing (NIPT) for fetus aneuploidy from DNA material extracted from maternal plasma. Tests typically compare chromosomal distributions of a tested sample with a control set of healthy samples with unaffected fetuses. Deviations above certain threshold levels are concluded as positive findings. The main problem with this approach is that the variance of the control set is dependent on the number of sequenced fragments. The higher the amount, the more precise the estimation of actual chromosomal proportions is. Testing a sample with a highly different number of sequenced reads as used in training may thus lead to over- or under-estimation of their variance, and so lead to false predictions. We propose the calculation of a variance for each tested sample adaptively, based on the actual number of its sequenced fragments. We demonstrate how it leads to more stable predictions, mainly in real-world diagnostics with the highly divergent inter-sample coverage.
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Affiliation(s)
- Juraj Gazdarica
- Geneton Ltd., Bratislava 841 04, Slovakia.
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava 841 04, Slovakia.
- Slovak Centre of Scientific and Technical Information, Bratislava 811 04, Slovakia.
| | - Jaroslav Budis
- Geneton Ltd., Bratislava 841 04, Slovakia
- Slovak Centre of Scientific and Technical Information, Bratislava 811 04, Slovakia
- Comenius University Science Park, Comenius University, Bratislava 841 04, Slovakia
| | | | - Jan Turna
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava 841 04, Slovakia
- Slovak Centre of Scientific and Technical Information, Bratislava 811 04, Slovakia
- Comenius University Science Park, Comenius University, Bratislava 841 04, Slovakia
| | - Tomas Szemes
- Geneton Ltd., Bratislava 841 04, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava 841 04, Slovakia
- Slovak Centre of Scientific and Technical Information, Bratislava 811 04, Slovakia
- Comenius University Science Park, Comenius University, Bratislava 841 04, Slovakia
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Lee DE, Kim H, Park J, Yun T, Park DY, Kim M, Ryu HM. Clinical Validation of Non-Invasive Prenatal Testing for Fetal Common Aneuploidies in 1,055 Korean Pregnant Women: a Single Center Experience. J Korean Med Sci 2019; 34:e172. [PMID: 31222985 PMCID: PMC6589404 DOI: 10.3346/jkms.2019.34.e172] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 05/28/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Non-invasive prenatal testing (NIPT) using cell-free fetal DNA from maternal plasma for fetal aneuploidy identification is expanding worldwide. The objective of this study was to evaluate the clinical utility of NIPT for the detection of trisomies 21, 18, and 13 of high-risk fetus in a large Korean population. METHODS This study was performed retrospectively, using stored maternal plasma from 1,055 pregnant women with singleton pregnancies who underwent invasive prenatal diagnosis because of a high-risk indication for chromosomal abnormalities. The NIPT results were confirmed by karyotype analysis. RESULTS Among 1,055 cases, 108 cases of fetal aneuploidy, including trisomy 21 (n = 57), trisomy 18 (n = 42), and trisomy 13 (n = 9), were identified by NIPT. In this study, NIPT showed 100% sensitivity and 99.9% specificity for trisomy 21, and 92.9% sensitivity and 100% specificity for trisomy 18, and 100% sensitivity and 99.9% specificity for trisomy 13. The overall positive predictive value (PPV) was 98.1%. PPVs for trisomies 21, 18, and 13 ranged from 90.0% to 100%. CONCLUSION This study demonstrates that our NIPT technology is reliable and accurate when applied to maternal DNA samples collected from pregnant women. Further large prospective studies are needed to adequately assess the performance of NIPT.
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Affiliation(s)
- Da Eun Lee
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul, Korea
| | - Hyunjin Kim
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul, Korea
| | | | - Taegyun Yun
- Data Analytics CoE, SK Telecom, Seoul, Korea
| | | | - Minhyoung Kim
- Department of Obstetrics and Gynecology, Cheil General Hospital and Women's Healthcare Center, Dankook University College of Medicine, Seoul, Korea
| | - Hyun Mee Ryu
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam, Korea.
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Wald NJ, Bestwick JP, Lau KW, Huttly WJ, Ke W, Cheng R, Old RW. A simple method to allow for guanine-cytosine amplification error in prenatal DNA screening for trisomy 18. Clin Chim Acta 2019; 496:13-17. [PMID: 31211945 DOI: 10.1016/j.cca.2019.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/05/2019] [Accepted: 06/13/2019] [Indexed: 11/17/2022]
Abstract
BACKGROUND A source of error in prenatal screening for trisomies is PCR amplification error associated with guanine-cytosine (GC) content of DNA fragments in maternal plasma. We describe a simple method of allowing for this. METHODS Data from a Reflex DNA screening programme (67 trisomy 18 and 83 unaffected pregnancies) were used to compare the ratio of chromosome 18 DNA fragment counts to chromosome 8 DNA fragment counts (because chromosome 8 has a similar GC content to chromosome 18) with the percentage of chromosome 18 DNA counts using counts from all autosomes in the denominator, with and without an all autosome correction for the GC content of the DNA fragments. RESULTS A chromosome 18 to 8 ratio of DNA fragment counts was more discriminatory than the percentage of all autosome counts arising from chromosome 18 without, or with an all autosome correction for GC content bias. It achieves a high screening performance, eg. for a 0.25% false-positive rate, a 97% detection rate instead of 49% without a correction for GC content, and 91% with an all autosome correction for GC content. CONCLUSION Consideration can be given to using the ratio of chromosome 18 DNA fragment counts to chromosome 8 DNA fragment counts in cell-free DNA prenatal screening for trisomy 18, avoiding the need for more complex methods of making a correction for the GC content currently used.
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Affiliation(s)
- Nicholas J Wald
- Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
| | - Jonathan P Bestwick
- Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - King Wai Lau
- Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Wayne J Huttly
- Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Weilin Ke
- Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Ray Cheng
- Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Robert W Old
- Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
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Abstract
Prenatal testing in recent years has been moving toward non-invasive methods to determine the fetal risk for genetic disorders without incurring the risk of miscarriage. Rapid progress of modern high-throughput molecular technologies along with the discovery of cell-free fetal DNA in maternal plasma led to novel screening methods for fetal chromosomal aneuploidies. Such tests are referred to as non-invasive prenatal tests (NIPTs), non-invasive prenatal screening, or prenatal cell-free DNA screening. Owing to many advantages, the adoption of NIPT in routine clinical practice was very rapid and global. As an example, NIPT has recently become a standard screening procedure for all pregnant women in the Netherlands. On the other hand, invasive sampling procedures remain important, especially for their diagnostic value in the confirmation of NIPT-positive findings and the detection of Mendelian disorders. In this review, we focus on current trends in the field of NIPT and discuss their benefits, drawbacks, and consequences in regard to routine diagnostics.
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Affiliation(s)
- Ondrej Pös
- Faculty of Natural Sciences, Comenius University, Bratislava, 84215, Slovakia
| | - Jaroslav Budiš
- University Science Park, Comenius University, Bratislava, 84104, Slovakia
| | - Tomáš Szemes
- Faculty of Natural Sciences, Comenius University, Bratislava, 84215, Slovakia.,University Science Park, Comenius University, Bratislava, 84104, Slovakia
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32
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A gradual change of chromosome mosaicism from placenta to fetus leading to T18 false negative result by NIPS. Clin Chim Acta 2019; 495:263-268. [PMID: 30998911 DOI: 10.1016/j.cca.2019.04.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/06/2019] [Accepted: 04/10/2019] [Indexed: 11/23/2022]
Abstract
BACKGROUND Noninvasive prenatal screening (NIPS) has higher sensitivity and specificity compared to traditional prenatal screening. Nevertheless, the discordant results between the NIPS and prenatal diagnosis were occasionally reported. In current study, we investigated the genetic basis of a T18 fetus with a discordant trisomy 5 (T5) positive and trisomy 18 (T18) negative NIPS result. METHODS NIPS was used to detect fetal DNA in maternal circulating plasma based on semiconductor sequencing platform. The aneuploidies of the fetus and different part of placental tissues were investigated by copy number variation sequencing (CNV-seq) and chromosome microarray analysis (CMA). RESULTS The positive result of T5 was detected for the pregnant woman in NIPS, while T18 was found in the fetal karyotyping analysis after amniocentesis. Furthermore, placental mosaicism of T5 and T18 was found by CNV-seq and CMA, which revealed the mosaic ratio of T5 was gradually increased from umbilical cord to the placenta center, while that of T18 was gradually decreased. CONCLUSION For the reason of cell-free fetal DNA (cff DNA) in the maternal circulation originates from trophoblast cells of placenta, the level of placental mosaicism could cause false negative NIPS result in multiple aneuploidies. The present study proved that a discordant T5 positive and T18 negative NIPS result was caused by placental mosaicism. This study highlights placental mosaicism as a significant risk factor for discordant NIPS results. The result will be helpful for genetic counseling and clinical management of such pregnant woman.
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33
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Bevilacqua E, Resta S, Carlin A, Kang X, Cos Sanchez T, de Marchin J, Jani JC. Profile of women choosing the Harmony® Prenatal Test. Expert Rev Mol Diagn 2019; 18:591-599. [PMID: 29911931 DOI: 10.1080/14737159.2018.1489242] [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: 10/14/2022]
Abstract
INTRODUCTION The Harmony® Prenatal Test, a noninvasive cell-free DNA (cfDNA) method for major trisomies has been available since January 2013 at our unit, and tests were sent to the Ariosa Clinical Laboratory Improvement Amendments (CLIA) laboratory in California. From July 2017 onward, prenatal cfDNA has been reimbursed in Belgium for all pregnancies; however, since then samples are sent to a local laboratory. Little data are available on patient's profile and choices toward cfDNA and on the performance of local technology transfer centers. Areas covered: The profiles and choices of women regarding this test were evaluated. Further, the performance of cfDNA at the local laboratory was compared to the one in California. Our results showed that women from the Netherlands, as compared to Belgium, were more likely to undergo cfDNA testing for maternal request and would be less likely to undergo karyotyping if cfDNA were unavailable, therefore are better candidates for cfDNA testing, when this is used as first-line screening. Expert commentary: Our findings highlight the importance of conducting these types of studies, before decisions about clinical implementation are made by national governments and ministries of health.
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Affiliation(s)
- Elisa Bevilacqua
- a Department of Obstetrics and Gynecology , University Hospital Brugmann, Université Libre de Bruxelles , Brussels , Belgium
| | - Serena Resta
- a Department of Obstetrics and Gynecology , University Hospital Brugmann, Université Libre de Bruxelles , Brussels , Belgium
| | - Andrew Carlin
- a Department of Obstetrics and Gynecology , University Hospital Brugmann, Université Libre de Bruxelles , Brussels , Belgium
| | - Xin Kang
- a Department of Obstetrics and Gynecology , University Hospital Brugmann, Université Libre de Bruxelles , Brussels , Belgium
| | - Teresa Cos Sanchez
- a Department of Obstetrics and Gynecology , University Hospital Brugmann, Université Libre de Bruxelles , Brussels , Belgium
| | | | - Jacques C Jani
- a Department of Obstetrics and Gynecology , University Hospital Brugmann, Université Libre de Bruxelles , Brussels , Belgium
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34
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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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35
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Yu W, Lv Y, Yin S, Liu H, Li X, Liang B, Kong L, Liu C. Screening of fetal chromosomal aneuploidy diseases using noninvasive prenatal testing in twin pregnancies. Expert Rev Mol Diagn 2019; 19:189-196. [PMID: 30582381 DOI: 10.1080/14737159.2019.1562906] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
OBJECTIVES This study was aimed to report the clinical characteristics of fetal chromosomal aneuploidy diseases using noninvasive prenatal testing (NIPT) in twin pregnancies and analyze the results in terms of chorionicity, conception, and fetal fraction. METHODS A total of 1160 women with twin pregnancies were recruited from 1 October 2015, to 1 August 2017. Next-generation sequencing technology was used to detect fetal aneuploidies, such as trisomy 21, trisomy 18, trisomy 13 and trisomy X. RESULTS Aneuploidy was detected using NIPT in 26 fetuses, among which 18 fetal aneuploidies occurred in only one fetus of the twins. The rate of aneuploidy was 1.3% for dichorionic diamniotic twins and 0.5% for monochorionic diamniotic twins, respectively. The rate of aneuploidy was 1.2% for spontaneous pregnancy group and 1.1% for assisted reproductive technologies group. CONCLUSION In this study, detection of trisomy 21, trisomy 18, trisomy 13, and X abnormality in twin pregnancies was confirmed to be accurate. The aneuploidies mostly occurred in only one fetus of the twins, and trisomy 21 was the most common type. The prenatal diagnostic standard for NIPT in singleton pregnancies could perform well in twin pregnancies, which means NIPT can be popularized as routine prenatal screening in twin pregnancies.
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Affiliation(s)
- Wenqian Yu
- a Department of Obestetrics and Gybecology , Shengjing Hospital of China Medical University, Liaoning Centre for Prenatal Diagnosis , Shenyang , China.,b Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province , Benxi , China
| | - Yuan Lv
- a Department of Obestetrics and Gybecology , Shengjing Hospital of China Medical University, Liaoning Centre for Prenatal Diagnosis , Shenyang , China.,b Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province , Benxi , China
| | - Shaowei Yin
- a Department of Obestetrics and Gybecology , Shengjing Hospital of China Medical University, Liaoning Centre for Prenatal Diagnosis , Shenyang , China.,b Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province , Benxi , China
| | - Hao Liu
- a Department of Obestetrics and Gybecology , Shengjing Hospital of China Medical University, Liaoning Centre for Prenatal Diagnosis , Shenyang , China.,b Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province , Benxi , China
| | - Xue Li
- a Department of Obestetrics and Gybecology , Shengjing Hospital of China Medical University, Liaoning Centre for Prenatal Diagnosis , Shenyang , China.,b Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province , Benxi , China
| | - Bo Liang
- c Department of research and development, Basecare Medical Device Co., Ltd. , Suzhou , China
| | - Lingyin Kong
- c Department of research and development, Basecare Medical Device Co., Ltd. , Suzhou , China
| | - Caixia Liu
- a Department of Obestetrics and Gybecology , Shengjing Hospital of China Medical University, Liaoning Centre for Prenatal Diagnosis , Shenyang , China.,b Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province , Benxi , China
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36
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Johansson LF, de Weerd HA, de Boer EN, van Dijk F, Te Meerman GJ, Sijmons RH, Sikkema-Raddatz B, Swertz MA. NIPTeR: an R package for fast and accurate trisomy prediction in non-invasive prenatal testing. BMC Bioinformatics 2018; 19:531. [PMID: 30558531 PMCID: PMC6296037 DOI: 10.1186/s12859-018-2557-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/04/2018] [Indexed: 12/30/2022] Open
Abstract
Background Various algorithms have been developed to predict fetal trisomies using cell-free DNA in non-invasive prenatal testing (NIPT). As basis for prediction, a control group of non-trisomy samples is needed. Prediction accuracy is dependent on the characteristics of this group and can be improved by reducing variability between samples and by ensuring the control group is representative for the sample analyzed. Results NIPTeR is an open-source R Package that enables fast NIPT analysis and simple but flexible workflow creation, including variation reduction, trisomy prediction algorithms and quality control. This broad range of functions allows users to account for variability in NIPT data, calculate control group statistics and predict the presence of trisomies. Conclusion NIPTeR supports laboratories processing next-generation sequencing data for NIPT in assessing data quality and determining whether a fetal trisomy is present. NIPTeR is available under the GNU LGPL v3 license and can be freely downloaded from https://github.com/molgenis/NIPTeR or CRAN. Electronic supplementary material The online version of this article (10.1186/s12859-018-2557-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lennart F Johansson
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands. .,Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Hendrik A de Weerd
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,School of Bioscience, Systems biology research center, University of Skövde, Skövde, Sweden
| | - Eddy N de Boer
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Freerk van Dijk
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard J Te Meerman
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rolf H Sijmons
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Birgit Sikkema-Raddatz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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37
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Enrichment of the fetal fraction in non-invasive prenatal screening reduces maternal background interference. Sci Rep 2018; 8:17675. [PMID: 30518878 PMCID: PMC6281613 DOI: 10.1038/s41598-018-35738-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 11/09/2018] [Indexed: 12/13/2022] Open
Abstract
Measurement of cell-free fetal DNA (cffDNA) is an indispensable process for non-invasive prenatal screening (NIPS). According to recent studies, cffDNA in maternal plasma can be enriched for various lengths of fragments, and a sufficient amount of cffDNA can effectively eliminate background interference on the part of maternal DNA. Therefore, we developed a simple and effective separation method, improved NIPS (iNIPS), that enriches the fetal fraction and improves the accuracy of NIPS for fetal aneuploid detection. We adopted a novel strategy to achieve enrichment of 125–135 bp cell-free DNA (cfDNA) by e-gel electrophoresis. To evaluate clinical performance, we compared NIPS and iNIPS results from 2153 retrospective clinical samples. Of the 22 samples with NIPS results of “no call”, 17 samples were reclassified as “unaffected” (9 cases of chr13, 5 cases of chr18, and 3 cases of chr21); 2 samples remained classified as “no call” (1 case of chr18 and 1 case of chr21); and 3 samples were identified as T21 by iNIPS. The average increase in abundance of cfDNA fragments of 125–135 bp was 2.5 times, and the average decrease in maternal background interference was 1.3 times. On this basis, the detection of fetal aneuploidy was highly improved with the fetal fraction as low as 2%; iNIPS achieved 100% sensitivity and 99.90% specificity in retrospective samples.
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38
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Non-invasive prenatal aneuploidy testing: Critical diagnostic performance parameters predict sample z-score values. Clin Biochem 2018; 59:69-77. [PMID: 29958880 DOI: 10.1016/j.clinbiochem.2018.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/21/2018] [Accepted: 06/22/2018] [Indexed: 01/01/2023]
Abstract
OBJECTIVES Non-invasive prenatal aneuploidy testing (NIPT) by next-generation sequencing of circulating cell-free DNA in maternal plasma relies on chromosomal ratio (chrratio) measurements to detect aneuploid values that depart from euploid ratios. Diagnostic performances are known to depend on the fraction of fetal DNA (FF) present in maternal plasma, although how this translates into specific quantitative changes in specificity/positive predictive values and which other variables might also be important is not well understood. DESIGN & METHODS To explore this issue, theoretical relationships between FF and various measures of diagnostic performances were assessed for a range of parameter values. Empirical data from three NIPT assays were then used to validate theoretical calculations. RESULTS For a given positivity threshold, dramatic changes in specificity and positive predictive values (PPV) as a function of both FF and the coefficient of variation (CV) of the chrratio measurement were observed. Theoretically predicted and observed chrratio z-scores agreed closely, confirming the determinant impact of small changes in both FF and chrratio CV. CONCLUSIONS Evaluation of NIPT assay performances therefore requires knowledge of the FF distribution in the population in which the test is intended to be used and, in particular, of the precise value of the assay chrratio CV for each chromosome or genomic region of interest. Laboratories offering NIPT testing should carefully measure these parameters to ensure test reliability and clinical usefulness in interpreting individual patients' results.
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39
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Palomaki GE, Kloza EM. Prenatal cell-free DNA screening test failures: a systematic review of failure rates, risks of Down syndrome, and impact of repeat testing. Genet Med 2018; 20:1312-1323. [PMID: 30514979 DOI: 10.1038/gim.2018.22] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/19/2018] [Indexed: 01/12/2023] Open
Abstract
PURPOSE We systematically reviewed the published literature on test failure rates for the sequencing of cell-free DNA (cfDNA) in maternal plasma to identify Down syndrome. METHODS We searched peer-reviewed English publications with diagnostic results on all pregnancies that provided test failure rates. Data on the odds of failure in Down syndrome and euploid pregnancies and the impact of repeat testing were extracted. Random-effects modeling was then used to identify moderators that could explain variability. RESULTS Thirty articles satisfied the inclusion criteria for overall failure rates. Study location (Western and Asian with initial testing, and Western with repeat testing) were significant moderators with failure rates of 3.3, 0.6, and 1.2%, respectively (P = 0.001). The odds ratio for Down syndrome in successful versus failed tests was 0.98 (95% confidence interval: 0.62-1.55, I2 = 0%). Repeat testing from 14 large clinical cohort studies found that 83% (range: 52-100%) of failures were repeated, with 79% (range: 46-97%) being successful. CONCLUSION Lower failure rates in Asian studies may be related to not routinely measuring the fetal fraction and to fewer obese women. Repeat cfDNA testing is effective in providing reliable results after initial failures. Protocols for primary cfDNA screening should focus on Down syndrome, with less common and more structurally abnormal trisomy 18 and 13 pregnancies treated as adjuncts.
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Affiliation(s)
- Glenn E Palomaki
- Department of Pathology and Laboratory Medicine, Women and Infants Hospital, Providence, Rhode Island, USA. .,Department of Pathology and Laboratory Medicine, Alpert Medical School at Brown University, Providence, Rhode Island, USA.
| | - Edward M Kloza
- Department of Pathology and Laboratory Medicine, Women and Infants Hospital, Providence, Rhode Island, USA
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40
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Reiss RE, Discenza M, Foster J, Dobson L, Wilkins-Haug L. Sex chromosome aneuploidy detection by noninvasive prenatal testing: helpful or hazardous? Prenat Diagn 2018; 37:515-520. [PMID: 28326560 DOI: 10.1002/pd.5039] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 02/21/2017] [Accepted: 03/17/2017] [Indexed: 12/22/2022]
Abstract
OBJECTIVES To assess the incidence of sex chromosome aneuploidy (SCA) predicted by noninvasive prenatal testing (NIPT), assess test performance, and compare it with nuchal translucency (NT) screening among patients seen in our prenatal diagnosis center. METHODS We identified suspected cases of SCA by reviewing results from all NIPT samples sent from our center to commercial laboratories offering analysis by cell-free DNA between 1 December 2012 and 31 July 2015. Records of pregnancies positive for SCA were reviewed for ultrasound findings, NIPT indications, and karyotype results on maternal, fetal, and postnatal samples. Other SCA cases presenting during this period regardless of NIPT status were identified from genetic counseling and cytogenetics laboratory logbooks. RESULTS Noninvasive prenatal testing predicted SCA in 18/2851 patients (0.63%). All had diagnostic testing of fetal or newborn samples. No patients terminated pregnancies on the basis of NIPT. NIPT suggested triple X in five cases, two with elevated NT: all were confirmed on karyotype. Two Klinefelter syndrome cases were also accurately predicted by NIPT. NIPT indicated monosomy X in 11 cases. Only one was a true positive. Ten were false positives, with 46, XX found on fetal or newborn karyotype. Maternal karyotype was mosaic (45, X[4], 46, XX[26]) in one case. Over the same time period, four additional cases of 45, X were confirmed on fetal samples, all with cystic hygromas. One of these had had a false negative NIPT result. The remaining patients pursued only direct testing via CVS or amniocentesis. CONCLUSIONS Sex chromosome aneuploidy was frequently suspected on NIPT. False positive rate for monosomy X was surprisingly high (91%). Prediction of other SCA was more accurate. Diagnostic fetal chromosome analysis should be offered after abnormal NIPT or in the presence of cystic hygromas despite normal NIPT. NIPT limitations should be explained in pretest counseling. © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Rosemary E Reiss
- Center for Fetal Medicine and Prenatal Genetics, Brigham and Women's Hospital, Boston, MA, USA.,Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Marie Discenza
- Center for Fetal Medicine and Prenatal Genetics, Brigham and Women's Hospital, Boston, MA, USA.,Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Judith Foster
- Center for Fetal Medicine and Prenatal Genetics, Brigham and Women's Hospital, Boston, MA, USA.,Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Lori Dobson
- Center for Fetal Medicine and Prenatal Genetics, Brigham and Women's Hospital, Boston, MA, USA.,Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Louise Wilkins-Haug
- Center for Fetal Medicine and Prenatal Genetics, Brigham and Women's Hospital, Boston, MA, USA.,Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
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41
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Stewart CM, Kothari PD, Mouliere F, Mair R, Somnay S, Benayed R, Zehir A, Weigelt B, Dawson SJ, Arcila ME, Berger MF, Tsui DW. The value of cell-free DNA for molecular pathology. J Pathol 2018; 244:616-627. [PMID: 29380875 DOI: 10.1002/path.5048] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/23/2018] [Accepted: 01/25/2018] [Indexed: 02/06/2023]
Abstract
Over the past decade, advances in molecular biology and genomics techniques have revolutionized the diagnosis and treatment of cancer. The technological advances in tissue profiling have also been applied to the study of cell-free nucleic acids, an area of increasing interest for molecular pathology. Cell-free nucleic acids are released from tumour cells into the surrounding body fluids and can be assayed non-invasively. The repertoire of genomic alterations in circulating tumour DNA (ctDNA) is reflective of both primary tumours and distant metastatic sites, and ctDNA can be sampled multiple times, thereby overcoming the limitations of the analysis of single biopsies. Furthermore, ctDNA can be sampled regularly to monitor response to treatment, to define the evolution of the tumour genome, and to assess the acquisition of resistance and minimal residual disease. Recently, clinical ctDNA assays have been approved for guidance of therapy, which is an exciting first step in translating cell-free nucleic acid research tests into clinical use for oncology. In this review, we discuss the advantages of cell-free nucleic acids as analytes in different body fluids, including blood plasma, urine, and cerebrospinal fluid, and their clinical applications in solid tumours and haematological malignancies. We will also discuss practical considerations for clinical deployment, such as preanalytical factors and regulatory requirements. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Caitlin M Stewart
- Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Prachi D Kothari
- Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pediatric Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Florent Mouliere
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.,Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Richard Mair
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.,Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Cambridge, UK.,Division of Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, UK
| | - Saira Somnay
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia.,Centre for Cancer Research, University of Melbourne, Victoria, Australia
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Wy Tsui
- Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Duris F, Gazdarica J, Gazdaricova I, Strieskova L, Budis J, Turna J, Szemes T. Mean and variance of ratios of proportions from categories of a multinomial distribution. JOURNAL OF STATISTICAL DISTRIBUTIONS AND APPLICATIONS 2018. [DOI: 10.1186/s40488-018-0083-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Cheng YKY, Leung WC, Leung TY, Choy KW, Chiu RWK, Lo TK, Kwok KY, Sahota DS. Women's preference for non-invasive prenatal DNA testing versus chromosomal microarray after screening for Down syndrome: a prospective study. BJOG 2018; 125:451-459. [DOI: 10.1111/1471-0528.15022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2017] [Indexed: 02/02/2023]
Affiliation(s)
- YKY Cheng
- Department of Obstetrics and Gynaecology; The Chinese University of Hong Kong; Hong Kong China
| | - WC Leung
- Department of Obstetrics and Gynaecology; Kwong Wah Hospital; Hong Kong China
| | - TY Leung
- Department of Obstetrics and Gynaecology; The Chinese University of Hong Kong; Hong Kong China
| | - KW Choy
- Department of Obstetrics and Gynaecology; The Chinese University of Hong Kong; Hong Kong China
| | - RWK Chiu
- Department of Chemical Pathology; The Chinese University of Hong Kong; Hong Kong China
| | - T-K Lo
- Department of Obstetrics and Gynaecology; Princess Margaret Hospital; Hong Kong China
| | - KY Kwok
- Department of Obstetrics and Gynaecology; The Chinese University of Hong Kong; Hong Kong China
| | - DS Sahota
- Department of Obstetrics and Gynaecology; The Chinese University of Hong Kong; Hong Kong China
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Wolfberg AJ. Conflict of interest related to clinical practice is underreported: The case of noninvasive prenatal testing. Prenat Diagn 2018; 38:219-221. [PMID: 29318630 DOI: 10.1002/pd.5209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/23/2017] [Accepted: 12/30/2017] [Indexed: 11/08/2022]
Abstract
Authors of policy statements from the American College of Obstetricians and Gynecologists and from the Society for Maternal-Fetal Medicine do not acknowledge the potential for their clinical income to influence their opinions, or the positions of the societies they represent. These policy statements were published in Obstetrics and Gynecology and the American Journal of Obstetrics and Gynecology, again, without acknowledgment of the potential for conflict of interest. The case of noninvasive prenatal testing, which has threatened the role of maternal-fetal medicine in the practice of prenatal screening and diagnosis, and has significantly reduced the demand for invasive prenatal diagnosis, illustrates the importance of identifying this potential conflict.
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Affiliation(s)
- Adam J Wolfberg
- Newton-Wellesley Hospital, Ovia Health, Boston, MA, 02110, USA
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Chen F, Liu P, Gu Y, Zhu Z, Nanisetti A, Lan Z, Huang Z, Liu JS, Kang X, Deng Y, Luo L, Jiang D, Qiu Y, Pan J, Xia J, Xiong K, Liu C, Xie L, Shi Q, Li J, Zhang X, Wang W, Drmanac S, Bolund L, Jiang H, Drmanac R, Xu X. Isolation and whole genome sequencing of fetal cells from maternal blood towards the ultimate non-invasive prenatal testing. Prenat Diagn 2017; 37:1311-1321. [DOI: 10.1002/pd.5186] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/30/2017] [Accepted: 11/07/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Fang Chen
- BGI-Shenzhen; Shenzhen 518083 PR China
- MGI, BGI-Shenzhen; Shenzhen 518083 China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen; DK-2100 Copenhagen Denmark
| | - Ping Liu
- BGI-Shenzhen; Shenzhen 518083 PR China
- MGI, BGI-Shenzhen; Shenzhen 518083 China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Ying Gu
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Zhu Zhu
- BGI-Shenzhen; Shenzhen 518083 PR China
- MGI, BGI-Shenzhen; Shenzhen 518083 China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Amulya Nanisetti
- BGI-Shenzhen; Shenzhen 518083 PR China
- Complete Genomics, Inc.; 2904 Orchard Parkway San Jose CA 95134 USA
| | - Zhangzhang Lan
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Zhiwei Huang
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Jia Sophie Liu
- BGI-Shenzhen; Shenzhen 518083 PR China
- Complete Genomics, Inc.; 2904 Orchard Parkway San Jose CA 95134 USA
| | - Xiongbin Kang
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Yuqing Deng
- PEKING University Shenzhen Hospital; Shenzhen China
| | - Liqiong Luo
- Shenzhen Longhua New District People's Hospital, Affiliated Hospital Southern Medical University; Guangzhou China
| | - Dan Jiang
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Yong Qiu
- BGI-Shenzhen; Shenzhen 518083 PR China
- MGI, BGI-Shenzhen; Shenzhen 518083 China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Jianchang Pan
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Jun Xia
- BGI-Shenzhen; Shenzhen 518083 PR China
- MGI, BGI-Shenzhen; Shenzhen 518083 China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Ken Xiong
- BGI-Shenzhen; Shenzhen 518083 PR China
- Complete Genomics, Inc.; 2904 Orchard Parkway San Jose CA 95134 USA
| | - Chao Liu
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Lin Xie
- BGI-Shenzhen; Shenzhen 518083 PR China
- MGI, BGI-Shenzhen; Shenzhen 518083 China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Qianyu Shi
- BGI-Shenzhen; Shenzhen 518083 PR China
- MGI, BGI-Shenzhen; Shenzhen 518083 China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Jing Li
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Xiuqing Zhang
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Wei Wang
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Snezana Drmanac
- BGI-Shenzhen; Shenzhen 518083 PR China
- Complete Genomics, Inc.; 2904 Orchard Parkway San Jose CA 95134 USA
| | - Lars Bolund
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen; DK-2100 Copenhagen Denmark
- Department of Biomedicine, Aarhus University; Aarhus Denmark
| | - Hui Jiang
- BGI-Shenzhen; Shenzhen 518083 PR China
- MGI, BGI-Shenzhen; Shenzhen 518083 China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Radoje Drmanac
- BGI-Shenzhen; Shenzhen 518083 PR China
- Complete Genomics, Inc.; 2904 Orchard Parkway San Jose CA 95134 USA
| | - Xun Xu
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
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Badeau M, Lindsay C, Blais J, Nshimyumukiza L, Takwoingi Y, Langlois S, Légaré F, Giguère Y, Turgeon AF, Witteman W, Rousseau F. Genomics-based non-invasive prenatal testing for detection of fetal chromosomal aneuploidy in pregnant women. Cochrane Database Syst Rev 2017; 11:CD011767. [PMID: 29125628 PMCID: PMC6486016 DOI: 10.1002/14651858.cd011767.pub2] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Common fetal aneuploidies include Down syndrome (trisomy 21 or T21), Edward syndrome (trisomy 18 or T18), Patau syndrome (trisomy 13 or T13), Turner syndrome (45,X), Klinefelter syndrome (47,XXY), Triple X syndrome (47,XXX) and 47,XYY syndrome (47,XYY). Prenatal screening for fetal aneuploidies is standard care in many countries, but current biochemical and ultrasound tests have high false negative and false positive rates. The discovery of fetal circulating cell-free DNA (ccfDNA) in maternal blood offers the potential for genomics-based non-invasive prenatal testing (gNIPT) as a more accurate screening method. Two approaches used for gNIPT are massively parallel shotgun sequencing (MPSS) and targeted massively parallel sequencing (TMPS). OBJECTIVES To evaluate and compare the diagnostic accuracy of MPSS and TMPS for gNIPT as a first-tier test in unselected populations of pregnant women undergoing aneuploidy screening or as a second-tier test in pregnant women considered to be high risk after first-tier screening for common fetal aneuploidies. The gNIPT results were confirmed by a reference standard such as fetal karyotype or neonatal clinical examination. SEARCH METHODS We searched 13 databases (including MEDLINE, Embase and Web of Science) from 1 January 2007 to 12 July 2016 without any language, search filter or publication type restrictions. We also screened reference lists of relevant full-text articles, websites of private prenatal diagnosis companies and conference abstracts. SELECTION CRITERIA Studies could include pregnant women of any age, ethnicity and gestational age with singleton or multifetal pregnancy. The women must have had a screening test for fetal aneuploidy by MPSS or TMPS and a reference standard such as fetal karyotype or medical records from birth. DATA COLLECTION AND ANALYSIS Two review authors independently carried out study selection, data extraction and quality assessment (using the QUADAS-2 tool). Where possible, hierarchical models or simpler alternatives were used for meta-analysis. MAIN RESULTS Sixty-five studies of 86,139 pregnant women (3141 aneuploids and 82,998 euploids) were included. No study was judged to be at low risk of bias across the four domains of the QUADAS-2 tool but applicability concerns were generally low. Of the 65 studies, 42 enrolled pregnant women at high risk, five recruited an unselected population and 18 recruited cohorts with a mix of prior risk of fetal aneuploidy. Among the 65 studies, 44 evaluated MPSS and 21 evaluated TMPS; of these, five studies also compared gNIPT with a traditional screening test (biochemical, ultrasound or both). Forty-six out of 65 studies (71%) reported gNIPT assay failure rate, which ranged between 0% and 25% for MPSS, and between 0.8% and 7.5% for TMPS.In the population of unselected pregnant women, MPSS was evaluated by only one study; the study assessed T21, T18 and T13. TMPS was assessed for T21 in four studies involving unselected cohorts; three of the studies also assessed T18 and 13. In pooled analyses (88 T21 cases, 22 T18 cases, eight T13 cases and 20,649 unaffected pregnancies (non T21, T18 and T13)), the clinical sensitivity (95% confidence interval (CI)) of TMPS was 99.2% (78.2% to 100%), 90.9% (70.0% to 97.7%) and 65.1% (9.16% to 97.2%) for T21, T18 and T13, respectively. The corresponding clinical specificity was above 99.9% for T21, T18 and T13.In high-risk populations, MPSS was assessed for T21, T18, T13 and 45,X in 30, 28, 20 and 12 studies, respectively. In pooled analyses (1048 T21 cases, 332 T18 cases, 128 T13 cases and 15,797 unaffected pregnancies), the clinical sensitivity (95% confidence interval (CI)) of MPSS was 99.7% (98.0% to 100%), 97.8% (92.5% to 99.4%), 95.8% (86.1% to 98.9%) and 91.7% (78.3% to 97.1%) for T21, T18, T13 and 45,X, respectively. The corresponding clinical specificities (95% CI) were 99.9% (99.8% to 100%), 99.9% (99.8% to 100%), 99.8% (99.8% to 99.9%) and 99.6% (98.9% to 99.8%). In this risk group, TMPS was assessed for T21, T18, T13 and 45,X in six, five, two and four studies. In pooled analyses (246 T21 cases, 112 T18 cases, 20 T13 cases and 4282 unaffected pregnancies), the clinical sensitivity (95% CI) of TMPS was 99.2% (96.8% to 99.8%), 98.2% (93.1% to 99.6%), 100% (83.9% to 100%) and 92.4% (84.1% to 96.5%) for T21, T18, T13 and 45,X respectively. The clinical specificities were above 100% for T21, T18 and T13 and 99.8% (98.3% to 100%) for 45,X. Indirect comparisons of MPSS and TMPS for T21, T18 and 45,X showed no statistical difference in clinical sensitivity, clinical specificity or both. Due to limited data, comparative meta-analysis of MPSS and TMPS was not possible for T13.We were unable to perform meta-analyses of gNIPT for 47,XXX, 47,XXY and 47,XYY because there were very few or no studies in one or more risk groups. AUTHORS' CONCLUSIONS These results show that MPSS and TMPS perform similarly in terms of clinical sensitivity and specificity for the detection of fetal T31, T18, T13 and sex chromosome aneuploidy (SCA). However, no study compared the two approaches head-to-head in the same cohort of patients. The accuracy of gNIPT as a prenatal screening test has been mainly evaluated as a second-tier screening test to identify pregnancies at very low risk of fetal aneuploidies (T21, T18 and T13), thus avoiding invasive procedures. Genomics-based non-invasive prenatal testing methods appear to be sensitive and highly specific for detection of fetal trisomies 21, 18 and 13 in high-risk populations. There is paucity of data on the accuracy of gNIPT as a first-tier aneuploidy screening test in a population of unselected pregnant women. With respect to the replacement of invasive tests, the performance of gNIPT observed in this review is not sufficient to replace current invasive diagnostic tests.We conclude that given the current data on the performance of gNIPT, invasive fetal karyotyping is still the required diagnostic approach to confirm the presence of a chromosomal abnormality prior to making irreversible decisions relative to the pregnancy outcome. However, most of the gNIPT studies were prone to bias, especially in terms of the selection of participants.
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Affiliation(s)
- Mylène Badeau
- CHU de Québec ‐ Université LavalPopulation Health and Optimal Health Practices Research Axis45 Rue LeclercQuébec CityQCCanadaG1L 3L5
| | - Carmen Lindsay
- CHU de Québec ‐ Université LavalPopulation Health and Optimal Health Practices Research Axis45 Rue LeclercQuébec CityQCCanadaG1L 3L5
| | - Jonatan Blais
- CHAU‐Hôtel‐Dieu de LévisDepartment of Medical Biology143 Rue WolfeLévisQCCanadaG6V 3Z1
- Faculty of Medicine, Université LavalDepartment of Molecular Biology, Medical Biochemistry and PathologyQuebec CityQuebecCanada
| | - Leon Nshimyumukiza
- University of AlbertaSchool of Public Health8303 112 StreetEdmontonAlbertaCanadaT6G 2T4
| | - Yemisi Takwoingi
- University of BirminghamInstitute of Applied Health ResearchEdgbastonBirminghamUKB15 2TT
| | - Sylvie Langlois
- University of British ColumbiaDepartment of Medical Genetics, Faculty of MedicineC234, 4500 Oak StreetVancouverBCCanadaV6H 3N1
| | - France Légaré
- CHU de Québec ‐ Université LavalPopulation Health and Optimal Health Practices Research Axis45 Rue LeclercQuébec CityQCCanadaG1L 3L5
| | - Yves Giguère
- CHU de Québec ‐ Université LavalReproductive, Mother and Child Health Research Axis10, rue de l'Espinay, A2‐226Québec CityQCCanadaG1L 3L5
- Faculty of Medicine, Université LavalDepartment of Molecular Biology, Medical Biochemistry and Pathology10, rue de l'EspinayQuébec CityQcCanadaG1L 3L5
| | - Alexis F Turgeon
- CHU de Québec ‐ Université Laval, Université LavalDepartment of Anesthesiology and Critical Care Medicine, Division of Critical Care Medicine, and Population Health and Optimal Health Practices Research Unit, CHU de Québec ‐ Université Laval Research Center1401, 18eme rueQuebec CityQCCanadaG1J 1Z4
- CHU de Québec Research Center, Université LavalPopulation Health and Optimal Health Practices Research Axis1401, 18eme rueQuébec CityQuébecCanadaG1J 1Z4
| | - William Witteman
- CHU de Québec ‐ Université LavalPopulation Health and Optimal Health Practices Research Axis45 Rue LeclercQuébec CityQCCanadaG1L 3L5
| | - François Rousseau
- Faculty of Medicine, Université LavalDepartment of Molecular Biology, Medical Biochemistry and Pathology10, rue de l'EspinayQuébec CityQcCanadaG1L 3L5
- CHU de Québec Research Center, Université LavalPopulation Health and Optimal Health Practices Research Axis1401, 18eme rueQuébec CityQuébecCanadaG1J 1Z4
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Chen M, Fu XY, Luo YQ, Qian YQ, Pan L, Wang LY, Dong MY. Detection of fetal duplication 16p11.2q12.1 by next-generation sequencing of maternal plasma and invasive diagnosis. J Matern Fetal Neonatal Med 2017; 32:38-45. [PMID: 28882078 DOI: 10.1080/14767058.2017.1369947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
OBJECTIVE The objective of study is to report the feasibility of non-invasive prenatal screening (NIPS) combined with invasive detection by chromosomal analysis in identifying fetal duplication, providing clinical performance of NIPS on copy number variations (CNVs) detection. MATERIAL AND METHODS NIPS was offered to a 35-year-old pregnant woman. Amniocentesis was performed to confirm the positive screening result. Fetal sample was detected by karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA). Parental karyotyping was also conducted. RESULTS NIPS result was positive for chromosome 16, indicating an extra copy of chromosome 16. FISH and chromosomal karyotyping revealed that the fetus had a marker chromosome derived from chromosome 16. CMA further demonstrated an approximately 19-Mb duplication in chromosome 16. The final fetal karyotype was 47,XY,+mar. ish der (16)(D16Z3+).arr 16p11.2q12.1 (30 624 186-49 696 337 × 3). Ultrasound scan and MRI showed some structure malformations. CONCLUSIONS A protocol for CNVs detection by combining a series of genetic methods was presented in this study and a novel marker duplication 16p11.2q12.1 was reported. With the ability to identify subchromosomal deletions and duplications in fetus, NIPS could reduce the possibility of invasive diagnosis. The followed confirmation test for positive sample is necessary and ensures the accuracy of the diagnosis.
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Affiliation(s)
- Min Chen
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| | - Xiao-Ying Fu
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| | - Yu-Qin Luo
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| | - Ye-Qing Qian
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| | - Ling Pan
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| | - Li-Ya Wang
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| | - Min-Yue Dong
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
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Jin J, Yang J, Chen Y, Huang J. Systematic review and meta-analysis of non-invasive prenatal DNA testing for trisomy 21: implications for implementation in China. Prenat Diagn 2017; 37:864-873. [PMID: 28686807 DOI: 10.1002/pd.5111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 05/20/2017] [Accepted: 07/03/2017] [Indexed: 12/27/2022]
Abstract
OBJECTIVES To systematically review clinical validation studies of massive parallel sequencing (MPS) technology in prenatal screening for trisomy 21 and to explore the potential implementation strategies in China compared with those in developing countries. METHODS Searches of the Cochrane Library, Medline, EMBASE, Web of Science, Biosis Previews, and three major Chinese databases were performed to identify all the peer-reviewed articles published between 1 January 2011 and 15 October 2016. We also reviewed and discussed the potential challenges and risks in the future promotion of MPS technology in China compared with those in developing countries. RESULTS The weighted pooled sensitivity and specificity of MPS technology for the prenatal detection of trisomy 21 were 99.7% (95% CI 98.3-99.9%) and 100.0% (95% CI 99.9-100.0%), respectively, based on a meta-analysis of 44 included studies. An additional meta-analysis was conducted based on the 25 included studies that were performed in medical/genetic sequencing institutions in mainland China, showing a weighted pooled sensitivity and specificity of MPS technology as 99.5% (95% CI 98.7-99.8%) and 100% (95% CI 99.9-100%), respectively. CONCLUSION MPS technology offers effective screening performance for trisomy 21 but should be cautiously promoted due to its clinical limitations and challenges that stem from the ethics and business aspects. © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Jiajie Jin
- School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Health Technology Assessment, National Health and Family Planning Committee (Fudan University), Shanghai, China
| | - Junwen Yang
- School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Health Technology Assessment, National Health and Family Planning Committee (Fudan University), Shanghai, China
| | - Yingyao Chen
- School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Health Technology Assessment, National Health and Family Planning Committee (Fudan University), Shanghai, China
| | - Jiayan Huang
- School of Public Health, Fudan University, Shanghai, China.,Key Laboratory of Health Technology Assessment, National Health and Family Planning Committee (Fudan University), Shanghai, China
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Skrzypek H, Hui L. Noninvasive prenatal testing for fetal aneuploidy and single gene disorders. Best Pract Res Clin Obstet Gynaecol 2017; 42:26-38. [DOI: 10.1016/j.bpobgyn.2017.02.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/21/2017] [Indexed: 01/16/2023]
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50
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Scott FP, Menezes M, Palma-Dias R, Nisbet D, Schluter P, da Silva Costa F, McLennan AC. Factors affecting cell-free DNA fetal fraction and the consequences for test accuracy. J Matern Fetal Neonatal Med 2017; 31:1865-1872. [DOI: 10.1080/14767058.2017.1330881] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Fergus Perry Scott
- Sydney Ultrasound for Women, Bondi Junction, Australia
- Department of Obstetrics and Gynaecology, University of New South Wales, Sydney, Australia
| | - Melody Menezes
- Monash Ultrasound for Women, The Epworth Centre, Richmond, Australia
| | - Ricardo Palma-Dias
- Women’s Ultrasound Melbourne, Parkville, Australia
- Pregnancy Research Centre, Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Australia
| | - Debbie Nisbet
- Women’s Ultrasound Melbourne, Parkville, Australia
- Department of Medicine and Radiology, University of Melbourne, Melbourne, Australia
| | - Philip Schluter
- School of Health Sciences, University of Canterbury, Christchurch, New Zealand
- School of Nursing, Midwifery and Social Work, University of Queensland, Brisbane, Australia
| | - Fabricio da Silva Costa
- Monash Ultrasound for Women, The Epworth Centre, Richmond, Australia
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Australia
| | - Andrew Cameron McLennan
- Sydney Ultrasound for Women, Bondi Junction, Australia
- Discipline of Obstetrics, Gynaecology and Neonatology, University of Sydney, Sydney, Australia
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