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Faieta M, Falcone R, Duca S, Corsetti E, Giannico R, Gigante L, Diano L, Calugi G, Spinella F, Pizzuti F. Test performance and clinical utility of expanded non-invasive prenatal test: Experience on 71,883 unselected routine cases from one single center. Prenat Diagn 2024; 44:936-945. [PMID: 38686956 DOI: 10.1002/pd.6580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 02/29/2024] [Accepted: 04/08/2024] [Indexed: 05/02/2024]
Abstract
OBJECTIVE The balance between benefits and risks of discordant outcomes makes the Genome-Wide Non-Invasive Prenatal Test (GW-NIPT) controversial. This study aims to evaluate performance and clinical utility in a wide cohort of unselected clinical cases from a single center when a standardized protocol is applied and integrated with a secondary algorithm for data interpretation. METHOD In 2 years, over 70,000 pregnant patients underwent GW-NIPT for fetal common trisomies, sex chromosome aneuploidies, rare autosomal aneuploidies, segmental abnormalities (CNVs ≥ 7 Mb) and microdeletions (CNVs < 7 Mb). All samples were uniformly processed with Veriseq NIPT Solution v2 and analyzed using all data metrics along with a home-made algorithm for sequencing data analysis. Results were retrospectively reviewed for clinical outcomes. RESULTS Among 71,883 eligible cases including twin pregnancies, 1011 (1.4%) received a positive result and 781 were confirmed by invasive prenatal diagnosis. Clinical sensitivity ranged from 99.65% for common trisomy (T21, T18, T13) to 83.33% for microdeletions, while specificity remained high (99.98%) for each class of fetal abnormalities detected. CONCLUSIONS Integrating a standardized protocol with an internal algorithm allowed discordant results to be reduced, yielding high accuracy. Observed reliability in detecting genome-wide chromosomal conditions reinforced the expanded NIPT utility in clinical practice.
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Affiliation(s)
- Monica Faieta
- Department of NIPT, Eurofins Genoma Group, Rome, Italy
| | - Rossella Falcone
- Department of NIPT, Eurofins Genoma Group, Rome, Italy
- Department of Genetic Counselling, Eurofins Genoma Group, Rome, Italy
| | - Sara Duca
- Department of NIPT, Eurofins Genoma Group, Rome, Italy
| | | | | | - Laura Gigante
- Department of Genetic Counselling, Eurofins Genoma Group, Rome, Italy
| | - Laura Diano
- Department of Genetic Counselling, Eurofins Genoma Group, Rome, Italy
| | - Graziella Calugi
- Department of Research and Development, Eurofins Genoma Group, Rome, Italy
| | - Francesca Spinella
- Department of Research and Development, Eurofins Genoma Group, Rome, Italy
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2
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Shen S, Qi H, Yuan X, Gan J, Chen J, Huang J. The performance evaluation of NIPT for fetal chromosome microdeletion/microduplication detection: a retrospective analysis of 68,588 Chinese cases. Front Genet 2024; 15:1390539. [PMID: 38911296 PMCID: PMC11190309 DOI: 10.3389/fgene.2024.1390539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/16/2024] [Indexed: 06/25/2024] Open
Abstract
Background Chromosomal abnormalities are the main cause of birth defects in newborns. Since the inception of noninvasive prenatal testing (NIPT) technology, it has primarily been applied to the detection of common trisomy (T21, T18, T13). However, the application of NIPT in microdeletion and microduplication detection is still controversial. Methods This study retrospectively analyzed the data of 68,588 cases that underwent NIPT at Ganzhou Maternal and Child Health Hospital in China. These data were used to evaluate the performance of NIPT in fetal chromosome microdeletion/microduplication detection and to investigate the key factors affecting the NIPT performance. Results A total of 281 cases (0.41%) had positive NIPT results with copy number variants (CNVs), of which 161 were validated by karyotyping and chromosome microarray analysis (CMA). Among the 161 cases, 92 were confirmed as true positives through karyotyping or CMA, including 61 microdeletion cases and 31 microduplication cases, resulting in a positive predictive value (PPV) of 57.14%. Improvements in library construction methods increased the fraction of cell-free fetal DNA (cffDNA) from 13.76% to 18.44%, leading to a significant improvement in the detection rate (0.47% vs. 0.15%) and PPV (59.86% vs. 28.57%) of NIPT for CNVs. Conclusion This study proved the robust performance of NIPT for fetal chromosome microdeletion/microduplication detection. In addition, the cffDNA fraction is a key factor influencing NIPT, with increased cffDNA fraction improving the performance of NIPT.
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Affiliation(s)
- Shichun Shen
- Department of Medical Genetics, Ganzhou Maternal and Child Health Hospital, Ganzhou, China
| | - Haimei Qi
- Clinical Laboratory, Ganzhou Maternal and Child Health Hospital, Ganzhou, China
| | - Xianping Yuan
- Obstetrical Department, Ganzhou Maternal and Child Health Hospital, Ganzhou, China
| | - Jinhui Gan
- Department of Medical Genetics, Ganzhou Maternal and Child Health Hospital, Ganzhou, China
| | - Junkun Chen
- Department of Medical Genetics, Ganzhou Maternal and Child Health Hospital, Ganzhou, China
| | - Jungao Huang
- Department of Medical Genetics, Ganzhou Maternal and Child Health Hospital, Ganzhou, China
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Chen CP. Genetic counseling of non-invasive prenatal testing (NIPT) trisomy 7-positive pregnancies. Taiwan J Obstet Gynecol 2024; 63:293-296. [PMID: 38802190 DOI: 10.1016/j.tjog.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2024] [Indexed: 05/29/2024] Open
Abstract
Trisomy 7 is the most common observed type of rare autosomal trisomies (RATs) detected at expanded genome-wide non-invasive prenatal testing (NIPT). Genetic counseling of NIPT trisomy 7-positive pregnancies remains to be not easy because the parents may worry about the likelihood of adverse pregnancy outcomes, fetal abnormality and the necessity of invasive procedures for confirmation of fetal mosaic trisomy 7 and uniparental disomy (UPD) 7. This review provides a comprehensive information on the update issues concerning genetic counseling of NIPT trisomy 7-positive pregnancies.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medical and Health Science, Asia University, Taichung, Taiwan.
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Soster E, Mossfield T, Menezes M, Agenbag G, Dubois ML, Gekas J, Hardy T, Loggenberg K. Clinical outcomes of screen-positive genome-wide cfDNA cases for trisomy 20: results from the global expanded NIPT Consortium. Mol Cytogenet 2024; 17:9. [PMID: 38627791 PMCID: PMC11021009 DOI: 10.1186/s13039-024-00677-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/03/2024] [Indexed: 04/20/2024] Open
Abstract
Trisomy 20 has been shown to be one of the most frequent rare autosomal trisomies in patients that undergo genome-wide noninvasive prenatal testing. Here, we describe the clinical outcomes of cases that screened positive for trisomy 20 following prenatal genome-wide cell-free (cf.) DNA screening. These cases are part of a larger cohort of previously published cases. Members of the Global Expanded NIPT Consortium were invited to submit details on their cases with a single rare autosomal aneuploidy following genome-wide cfDNA screening for retrospective analysis. Clinical details including patient demographics, test indications, diagnostic testing, and obstetric pregnancy outcomes were collected. Genome-wide cfDNA screening was conducted following site-specific laboratory procedures. Cases which screened positive for trisomy 20 (n = 10) were reviewed. Clinical outcome information was available for 90% (9/10) of our screen-positive trisomy 20 cases; the case without diagnostic testing ended in a fetal demise. Of the nine cases with outcome information, one was found to have a mosaic partial duplication (duplication at 20p13), rather than a full trisomy 20. Only one case in the study cohort had placental testing; therefore, confined placental mosaicism could not be ruled out in most cases. Adverse pregnancy outcomes were seen in half of the cases, which could suggest the presence of underlying confined placental mosaicism or mosaic/full fetal trisomy 20. Based on our limited series, the likelihood of true fetal aneuploidy is low but pregnancies may be at increased risk for adverse obstetric outcomes and may benefit from additional surveillance.
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Affiliation(s)
- Erica Soster
- Labcorp, 3400 Computer Drive, Westborough, MA, 01581, USA.
| | | | - Melody Menezes
- Monash IVF Genetics, Monash IVF Group, Richmond, VIC, Australia
| | | | | | - Jean Gekas
- Department of Medical Genetics, CHU de Quebec Research and Mother and Child Center, University Hospital of Quebec, Laval University, Quebec City, QC, Canada
| | - Tristan Hardy
- SA Pathology, Adelaide, SA, 5000, Australia
- Monash IVF Group, Melbourne, Victoria, Australia
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Koukou Z, Panteris E, Manolakos E, Papadopoulos A, Papoulidis I, Relakis K, Sifakis S. Cell‑free fetal DNA at 11‑13 weeks of gestation is not altered in complicated pregnancies. Biomed Rep 2024; 20:69. [PMID: 38495346 PMCID: PMC10941718 DOI: 10.3892/br.2024.1757] [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: 06/19/2023] [Accepted: 12/13/2023] [Indexed: 03/19/2024] Open
Abstract
Non-invasive maternal cell-free fetal DNA (cffDNA) is a promising biomarker for screening common genetic syndromes. Alterations in the expression levels of cffDNA in the maternal circulation have been demonstrated in abnormal pregnancies. However, the results are conflicting. The present study aimed to investigate whether cffDNA levels are associated with pregnancy complications. The study group comprised pregnant women who presented with pregnancy complications, such as preterm birth, gestational hypertension, intrauterine growth retardation, gestational diabetes, polyhydramnios, oligohydramnios, vaginal bleeding and placental abruption. The control group comprised women who had a normal pregnancy course. Blood samples were obtained from 500 pregnant women between 11-13 weeks of gestation. cffDNA was amplified, sequenced and analyzed using the next-generation aneuploidy test of a Panorama-Natera kit. Nuchal translucency (NT) thickness as well as pregnancy associated plasma protein-A (PAPP-A) and β-human chorionic gonadotropin (β-hCG) levels were also assessed. Statistical analysis was performed in 494 out of the 500 samples collected with SPSS v.26 using non-parametric methods. The parameters were normalized by the multiples of median (MoM) method. The expression levels of PAPP-A, β-hCG, and the NT mean MoM values were significantly different between the study and control groups (P=0.005, P<0.001 and P=0.007, respectively). However, the expression levels of cffDNA and the mean MoM values were not significantly different between these two groups (P=0.687). The findings of the present study support the conclusion that cffDNA expression is not altered in a series of pregnancy complications. The prognostic value of cffDNA in predicting adverse pregnancy outcomes requires further investigation.
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Affiliation(s)
- Zoi Koukou
- School of Health Sciences, International Hellenic University (IHU), 57400 Thessaloniki, Greece
- Department of Obstetrics and Gynecology, University Hospital of Heraklion, 71500 Heraklion, Greece
| | - Eleftherios Panteris
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Emmanouel Manolakos
- Access to Genome P.C., Clinical Laboratory Genetics, 11528 Thessaloniki, Greece
| | | | - Ioannis Papoulidis
- Access to Genome P.C., Clinical Laboratory Genetics, 11528 Thessaloniki, Greece
| | - Konstantinos Relakis
- Department of Obstetrics and Gynecology, University Hospital of Heraklion, 71500 Heraklion, Greece
| | - Stavros Sifakis
- Department of Obstetrics and Gynecology, University Hospital of Heraklion, 71500 Heraklion, Greece
- Mitera Maternity Hospital, 71202 Heraklion, Greece
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6
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Ye Q, Huang G, Hu Q, Man Q, Hao X, Liu L, Zhong Q, Jin Z. Performance Evaluation of Noninvasive Prenatal Testing in Screening Chromosome Disorders: A Single-Center Observational Study of 15,304 Consecutive Cases in China. Int J Womens Health 2024; 16:563-573. [PMID: 38567087 PMCID: PMC10986408 DOI: 10.2147/ijwh.s455778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
Objective This study was to evaluate the performance of noninvasive prenatal testing (NIPT) in detecting fetal chromosome disorders in pregnant women. Methods From October 1st, 2017, to December 31th, 2022, a total of 15,304 plasma cell free DNA-NIPT samples were collected for fetal chromosome disorders screening. The results of NIPT were validated by confirmatory invasive testing or clinical outcome follow-up. Further, NIPT performance between low-risk and high-risk groups, as well as singleton pregnancy and twin pregnancy groups was compared. Besides, analysis of 111 false-positive cases was performed. Results Totally, NIPT was performed on 15,086 eligible venous blood samples, of which 179 (1.19%) showed positive NIPT results and 68 were further validated to be true positive samples via confirmatory invasive testing or follow-up of clinical outcomes. For common chromosome aneuploidies, sex chromosome abnormalities (SCA) and other chromosomal aneuploidies, the detection sensitivities of NIPT were all 100%, the specificities were 99.87%, 99.70%, and 99.68% and the positive predictive values (PPVs) were 65.45%, 31.82%, and 10.91%, respectively. No statistically significant variance in detection performance was observed among 2987 high-risk and 12,099 low-risk subjects, as well as singleton and twin pregnancy subjects. The concentration of cell-free fetal DNA of 111 false-positive cases ranged from 5.5% to 33.7%, which was higher than the minimum requirement of NIPT. Conclusion With stringent protocol, NIPT shows high sensitivity and specificity for detecting fetal chromosome disorders in a large-scale clinical service, helping improving overall pregnancy management.
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Affiliation(s)
- Qiang Ye
- Department of Clinical Laboratory, West China Second University Hospital, Southern Sichuan Women’s and Children’s Hospital, Zigong, Sichuan, 643000, People’s Republic of China
| | - Guoping Huang
- Department of Clinical Laboratory, West China Second University Hospital, Southern Sichuan Women’s and Children’s Hospital, Zigong, Sichuan, 643000, People’s Republic of China
| | - Qin Hu
- Department of Clinical Laboratory, West China Second University Hospital, Southern Sichuan Women’s and Children’s Hospital, Zigong, Sichuan, 643000, People’s Republic of China
| | - Qin Man
- Department of Prenatal Diagnosis Center, West China Second University Hospital, Southern Sichuan Women’s and Children’s Hospital, Zigong, Sichuan, 643000, People’s Republic of China
| | - Xiaoying Hao
- Department of Ultrasound, West China Second University Hospital, Southern Sichuan Women’s and Children’s Hospital, Zigong, Sichuan, 643000, People’s Republic of China
| | - Liangyan Liu
- Department of Obstetrics, West China Second University Hospital, Southern Sichuan Women’s and Children’s Hospital, Zigong, Sichuan, 643000, People’s Republic of China
| | - Qiang Zhong
- Department of Clinical Laboratory, West China Second University Hospital, Southern Sichuan Women’s and Children’s Hospital, Zigong, Sichuan, 643000, People’s Republic of China
| | - Zhao Jin
- Department of Prenatal Diagnosis Center, West China Second University Hospital, Southern Sichuan Women’s and Children’s Hospital, Zigong, Sichuan, 643000, People’s Republic of China
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7
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Bakkeren IM, Henneman L, van Vliet-Lachotzki EH, Martin L, Gitsels-van der Wal JT, Polak MG, Bekker MN, Galjaard RJH. Psychological impact of additional findings detected by genome-wide Non-Invasive Prenatal Testing (NIPT): TRIDENT-2 study. Eur J Hum Genet 2024; 32:302-308. [PMID: 38057584 PMCID: PMC10923886 DOI: 10.1038/s41431-023-01504-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/01/2023] [Accepted: 11/16/2023] [Indexed: 12/08/2023] Open
Abstract
In the Netherlands, genome-wide non-invasive prenatal testing (NIPT) is offered to all pregnant women as part of the nationwide TRIDENT-2 study. Findings other than trisomy 21, 18, or 13, which are called "additional findings", are reported only on request of the pregnant woman. This study examined: (1) women's pre-test perceptions and reasons to opt for additional findings and (2) women's experiences with- and the psychological impact of being informed about an additional finding. A questionnaire, consisting of the anxiety measure State-Trait Anxiety Inventory (STAI), distress measure Impact of Event Scale (IES) and questions developed specifically for this study, was retrospectively administered to 402 women who received an additional finding. A total of 227 (56.5%) women completed the questionnaire. Most (60.2%) chose to know additional findings because they wanted as much information as possible about the health of their fetus. Almost all (92%) stated that receiving the additional finding was unexpected, a shock, and/or they were in disbelief, for 85% it caused a lot of worry. Post-test, high anxiety (STAI) levels were reported in 15.5% of women, and 7.5% reported severe distress (IES). Women who gave birth to an affected child (n = 10) experienced most psychological impact (STAI and IES). Eighty-six percent of women with a fetal aberration would opt for additional findings again, compared to 49.2% of women whose result was confined to the placenta. Pre-test counseling should focus on explaining the different results NIPT can generate. Post-test counseling should focus on guiding pregnant women through this uncertain and anxious time.
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Affiliation(s)
- Iris M Bakkeren
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Lidewij Henneman
- Department of Human Genetics and Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | | | - Linda Martin
- Department of Midwifery Science, AVAG, Amsterdam Public Health research institute, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Janneke T Gitsels-van der Wal
- Department of Midwifery Science, AVAG, Amsterdam Public Health research institute, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Marike G Polak
- Department of Psychology, Education & Child Studies (DPECS), Erasmus University Rotterdam, Rotterdam, the Netherlands
| | - Mireille N Bekker
- Department of Obstetrics and Gynecology, Utrecht University Medical Center, Utrecht, the Netherlands
| | - Robert-Jan H Galjaard
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
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Kim H, Park JE, Kang KM, Jang HY, Go M, Yang SH, Kim JC, Lim SY, Cha DH, Choi J, Shim SH. Clinical evaluation of noninvasive prenatal testing for sex chromosome aneuploidies in 9,176 Korean pregnant women: a single-center retrospective study. BMC Pregnancy Childbirth 2024; 24:93. [PMID: 38297236 PMCID: PMC10829263 DOI: 10.1186/s12884-024-06275-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/15/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND To evaluate the clinical significance of noninvasive prenatal testing (NIPT) for detecting fetal sex chromosome aneuploidies (SCAs) in Korean pregnant women. METHODS We retrospectively analyzed NIPT data from 9,176 women with singleton pregnancies referred to the CHA Biotech genome diagnostics center. Cell-free fetal DNA (cffDNA) was extracted from maternal peripheral blood, and high-throughput massively parallel sequencing was conducted. Subsequently, the positive NIPT results for SCA were validated via karyotype and chromosomal microarray analyses. RESULTS Overall, 46 cases were SCA positive after NIPT, including 20, 12, 8, and 6 for Turner, triple X, Klinefelter, and Jacob syndromes, respectively. Among 37 women with invasive prenatal diagnosis, 19 had true positive NIPT results. The overall positive predictive value (PPV) of NIPT for detecting SCAs was 51.35%. The PPV was 18.75% for Turner, 88.89% for triple X, 71.43% for Klinefelter, and 60.00% for Jacob's syndromes. NIPT accuracy for detecting sex chromosome trisomies was higher than that for sex chromosome monosomy (P = 0.002). No significant correlation was observed between fetal SCA incidence and maternal age (P = 0.914), except for the borderline significance of Jacob's syndrome (P = 0.048). No significant differences were observed when comparing NIPT and karyotyping validation for fetal SCA according to pregnancy characteristics. CONCLUSION Our data suggest that NIPT can reliably screen for SCAs, and it performed better in predicting sex chromosome trisomies compared with monosomy X. No correlation was observed between maternal age and fetal SCA incidence, and no association was observed between different pregnancy characteristics. The accuracy of these findings requires improvements; however, our study provides an important reference for clinical genetic counseling and further management. Larger scale studies, considering confounding factors, are required for accurate evaluation.
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Affiliation(s)
- Hyunjin Kim
- Center for Genome Diagnostics, CHA Biotech Inc, Seoul, 06125, Republic of Korea
| | - Ji Eun Park
- Center for Genome Diagnostics, CHA Biotech Inc, Seoul, 06125, Republic of Korea
| | - Kyung Min Kang
- Center for Genome Diagnostics, CHA Biotech Inc, Seoul, 06125, Republic of Korea
| | - Hee Yeon Jang
- Center for Genome Diagnostics, CHA Biotech Inc, Seoul, 06125, Republic of Korea
| | - Minyeon Go
- Center for Genome Diagnostics, CHA Biotech Inc, Seoul, 06125, Republic of Korea
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, 13488, Republic of Korea
| | - So Hyun Yang
- Center for Genome Diagnostics, CHA Biotech Inc, Seoul, 06125, Republic of Korea
| | - Jong Chul Kim
- Center for Genome Diagnostics, CHA Biotech Inc, Seoul, 06125, Republic of Korea
| | - Seo Young Lim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, 13488, Republic of Korea
| | - Dong Hyun Cha
- Center for Genome Diagnostics, CHA Biotech Inc, Seoul, 06125, Republic of Korea
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul, 06135, Republic of Korea
| | - Jungah Choi
- College of Liberal Art, CHA University, Pocheon, Gyeonggi, Republic of Korea.
| | - Sung Han Shim
- Center for Genome Diagnostics, CHA Biotech Inc, Seoul, 06125, Republic of Korea.
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, 13488, Republic of Korea.
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Battese Ellis K, Sathasivam N, Bonifacio M, Benzie R. Comparison of noninvasive prenatal screening with combined first-trimester screening as a frontline screening approach for common trisomies in a public hospital in Australia. Aust N Z J Obstet Gynaecol 2023; 63:666-672. [PMID: 36048565 DOI: 10.1111/ajo.13605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 08/08/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Combined first-trimester screening (cFTS) for fetal anomalies involves maternal serum screening for biochemical markers and measurement of the nuchal translucency (NT) by ultrasound. Noninvasive prenatal screening (NIPS) analyses cell-free DNA present in a maternal blood sample for presence of fetal chromosomal aneuploidies. AIMS To compare NIPS with cFTS as frontline screening in a public hospital in Australia. MATERIALS AND METHODS Women were offered NIPS in addition to the usual cFTS routinely offered to all women at a public hospital in NSW, Australia. The cFTS sample was collected at ten weeks' gestation and the NIPS sample at 12 weeks' gestation at the ultrasound appointment. RESULTS In a low-risk population of 997 women, frontline NIPS had a screen-positive rate of 0.5% (5/997) vs 4.2% (42/997) with cFTS. cFTS correctly identified one trisomy 21 case and one trisomy 18 case; however, there were two trisomy 18 false negatives. Of five positive NIPS calls, four were correctly identified as trisomy 21 (one) and trisomy 18 (three); there were no NIPS false negatives. Overall, the false-positive rate with NIPS was 0.1% vs 4.0% by cFTS. CONCLUSIONS The lower screen-positive rate with NIPS for common trisomies was a result of the significantly lower false-positive rate with NIPS. Consequently, NIPS as first-line screening, even if funded by the hospital, may provide cost savings. We believe NIPS should be used from ten weeks' gestation in conjunction with morphology ultrasound for routine first-trimester prenatal management.
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Affiliation(s)
| | - Nalayin Sathasivam
- Perinatal Ultrasound Unit, Nepean Hospital, Penrith, New South Wales, Australia
| | | | - Ronald Benzie
- Perinatal Ultrasound Unit, Nepean Hospital, Penrith, New South Wales, Australia
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10
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Fiorentino D, Dar P. Prenatal Screening for Microdeletions and Rare Autosomal Aneuploidies. Clin Obstet Gynecol 2023; 66:579-594. [PMID: 37438896 DOI: 10.1097/grf.0000000000000799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Noninvasive prenatal screening with cell-free DNA is now considered a first-line screening for common aneuploidies. Advancements in existing laboratory techniques now allow to interrogate the entirety of the fetal genome, and many commercial laboratories have expanded their screening panels to include screening for rare autosomal aneuploidies and copy number variants. Here, we review the currently available data on the performance of fetal cell-free DNA to detect rare autosomal aneuploidies and copy number variants that are associated with clinically significant microdeletion and microduplication syndromes and the current position of medical societies on routine screening for these syndromes.
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Affiliation(s)
- Desiree Fiorentino
- Division of Fetal Medicine, Department of Obstetrics and Gynecology, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
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11
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Lannoo L, Van Camp J, Brison N, Parijs I, Vancoillie L, Van Den Bogaert K, Vermeesch JR, Devriendt K, Van Calsteren K. What helps define outcomes in persistent uninterpretable non-invasive prenatal testing: Maternal factors, fetal fraction or quality scores? Prenat Diagn 2023; 43:1333-1343. [PMID: 37592442 DOI: 10.1002/pd.6423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023]
Abstract
OBJECTIVES To assess maternal characteristics and comorbidities in patients with persistent uninterpretable non-invasive prenatal testing (NIPT) and to evaluate the association with adverse pregnancy outcome in a general risk population. METHODS A retrospective cohort study (July 2017-December 2020) was conducted of patients with persistent uninterpretable NIPT samples. Maternal characteristics and pregnancy outcomes were compared with the general Belgian obstetric population. RESULTS Of the 148 patients with persistent uninterpretable NIPT, 37 cases were due to a low fetal fraction (LFF) and 111 due to a low quality score (LQS). Both groups (LFF, LQS) showed more obesity (60.6%, 42.4%), multiple pregnancies (18.9%, 4.5%) and more obstetrical complications. In the LQS group, a high rate of maternal auto-immune disorders (30.6%) was seen and hypertensive complications (17.6%), preterm birth (17.6%) and neonatal intensive care unit (NICU) admission (22%) were significantly increased. In the LFF group hypertensive complications (21.6%), gestational diabetes (20.6%), preterm birth (27%), SGA (25.6%), major congenital malformations (11.4%), c-section rate (51.4%) and NICU admission (34.9%) were significantly increased. Chromosomal abnormalities were not increased in both groups. CONCLUSIONS Patients with persistent uninterpretable NIPT have significantly more maternal obesity, comorbidities and adverse pregnancy outcome than the general population and should receive high-risk pregnancy care. Distinguishing between LFF and LQS optimizes counseling because maternal characteristics and pregnancy outcome differ between these groups.
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Affiliation(s)
- Lore Lannoo
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Joke Van Camp
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Nathalie Brison
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Ilse Parijs
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Leen Vancoillie
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | | | - Koen Devriendt
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Kristel Van Calsteren
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
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12
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Wen L, Zhang Y, Gao J, Hu W. The predictive value of noninvasive prenatal screening for copy number variations: a cohort study and a systematic meta-analysis. Expert Rev Mol Diagn 2023; 23:713-722. [PMID: 37401569 DOI: 10.1080/14737159.2023.2233415] [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: 12/14/2022] [Revised: 06/19/2023] [Accepted: 07/03/2023] [Indexed: 07/05/2023]
Abstract
OBJECTIVE To assess the diagnostic accuracy of noninvasive prenatal screening (NIPS) in screening for copy number variations (CNVs). METHODS We conducted a systematic review and meta-analysis by combining our study results with those reported in other articles. We retrospectively collected the data of pregnant women with NIPS testing in the Hangzhou Women's Hospital from December 2019 to February 2022. Simultaneously, a systematic search of PubMed, EMBASE, and Web of Science was carried out to identify all relevant peer-reviewed publications. Statistical analysis was performed based on the random-effects model to determine a pooled estimate of the positive predictive value (PPV). RESULTS A total of 29 studies involving 2,667 women were included for analysis. The pooled PPV of NIPS in the detection of CNVs was 32.86% (95% confidence interval [24.61-41.64]). Statistical heterogeneity was high, while no significant publication bias was found in this meta-analysis. There were insufficient data to accurately determine sensitivity and specificity, as most studies only performed confirmatory tests on high-risk women. CONCLUSIONS The PPV of NIPS in screening for CNVs was approximately 33%. Cautions should be kept in mind for the pretest guidance and subsequent after-test counseling when offering such genome-wide NIPS tests.
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Affiliation(s)
- Li Wen
- Department of Prenatal Diagnosis and Screening Center, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, Zhejiang, China
| | - Yanzhen Zhang
- Department of Prenatal Diagnosis and Screening Center, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, Zhejiang, China
| | - Jiye Gao
- Department of Prenatal Diagnosis and Screening Center, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, Zhejiang, China
| | - Wensheng Hu
- Department of Obstetrics, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, Zhejiang, China
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13
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Soster E, Tynan J, Gibbons C, Meschino W, Wardrop J, Almasri E, Schwartz S, McLennan G. Laboratory performance of genome-wide cfDNA for copy number variants as compared to prenatal microarray. Mol Cytogenet 2023; 16:10. [PMID: 37301962 DOI: 10.1186/s13039-023-00642-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Noninvasive prenatal testing (NIPT) allows for screening of fetal aneuploidy and copy number variants (CNVs) from cell-free DNA (cfDNA) in maternal plasma. Professional societies have not yet embraced NIPT for fetal CNVs, citing a need for additional performance data. A clinically available genome-wide cfDNA test screens for fetal aneuploidy and CNVs larger than 7 megabases (Mb). RESULTS This study reviews 701 pregnancies with "high risk" indications for fetal aneuploidy which underwent both genome-wide cfDNA and prenatal microarray. For aneuploidies and CNVs considered 'in-scope' for the cfDNA test (CNVs ≥ 7 Mb and select microdeletions), sensitivity and specificity was 93.8% and 97.3% respectively, with positive and negative predictive values of 63.8% and 99.7% as compared to microarray. When including 'out-of-scope' CNVs on array as false negatives, the sensitivity of cfDNA falls to 48.3%. If only pathogenic out-of-scope CNVs are treated as false negatives, the sensitivity is 63.8%. Of the out-of-scope CNVs identified by array smaller than 7 Mb, 50% were classified as variants of uncertain significance (VUS), with an overall VUS rate in the study of 2.29%. CONCLUSIONS While microarray provides the most robust assessment of fetal CNVs, this study suggests that genome-wide cfDNA can reliably screen for large CNVs in a high-risk cohort. Informed consent and adequate pretest counseling are essential to ensuring patients understand the benefits and limitations of all prenatal testing and screening options.
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Affiliation(s)
| | - John Tynan
- Labcorp®, La Jolla, CA, USA
- PetDx, The Center for Novel Therapeutics, La Jolla, CA, USA
| | - Clare Gibbons
- Genetics Program, North York General Hospital, Toronto, ON, Canada
| | - Wendy Meschino
- Genetics Program, North York General Hospital, Toronto, ON, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
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14
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Acreman ML, Bussolaro S, Raymond YC, Fantasia I, Rolnik DL, Da Silva Costa F. The predictive value of prenatal cell-free DNA testing for rare autosomal trisomies: a systematic review and meta-analysis. Am J Obstet Gynecol 2023; 228:292-305.e6. [PMID: 36027954 DOI: 10.1016/j.ajog.2022.08.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022]
Abstract
OBJECTIVE The diagnostic accuracy of cell-free fetal DNA in screening for rare autosomal trisomies is uncertain. We conducted a systematic review and meta-analysis aiming to determine the predictive value of cell-free DNA in screening for rare autosomal trisomies. DATA SOURCES PubMed, Embase, and Web of Science were searched from inception to January 2022. STUDY ELIGIBILITY CRITERIA All studies that reported on the diagnostic accuracy of cell-free DNA in the detection of rare autosomal trisomies were included. Case series were included if they contained at least 10 cases with diagnostic test results or postnatal genetic testing. METHODS Study appraisal was completed using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) tool. Statistical analysis was performed using random-effects meta-analysis of double-arcsine transformed proportions of confirmed results in the fetus out of the positive tests to obtain a pooled estimate of the positive predictive value. RESULTS The search identified 7553 studies, of which 1852 were duplicates. After screening 5701 titles and abstracts, 380 studies proceeded to the full-text screen; 206 articles were retrieved for data extraction, of which another 175 articles were excluded. A total of 31 studies, with a total of 1703 women were included for analysis. The pooled positive predictive value of cell-free DNA for the diagnosis of rare autosomal trisomies was 11.46% (95% confidence interval, 7.80-15.65). Statistical heterogeneity was high (I2=82%). Sensitivity analysis restricted to 5 studies at low risk of bias demonstrated a pooled positive predictive value of 9.13% (95% confidence interval, 2.49-18.76). There were insufficient data to provide accurate ascertainment of sensitivity and specificity because most studies only offered confirmatory tests to women with high-risk results. CONCLUSION The positive predictive value of cell-free DNA in diagnosing rare autosomal trisomies is approximately 11%. Clinicians should provide this information when offering cell-free DNA for screening of conditions outside of common autosomal trisomies.
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Affiliation(s)
- Melissa L Acreman
- Department of Obstetrics and Gynaecology, Ipswich Hospital, Queensland, Australia.
| | - Sofia Bussolaro
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Yvette C Raymond
- Department of Obstetrics and Gynaecology, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Australia
| | - Ilaria Fantasia
- Obstetrics and Gynaecology Unit, San Salvatore Hospital, L'Aquila, Italy
| | - Daniel L Rolnik
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia
| | - Fabricio Da Silva Costa
- Maternal Foetal Medicine Unit, Gold Coast University Hospital and School of Medicine, Griffith University, Gold Coast, Australia
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15
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Lannoo L, van der Meij KRM, Bekker MN, De Catte L, Deckers S, Devriendt K, Roggen N, Galjaard RJH, Gitsels-van der Wal J, Macville MVE, Martin L, Sistermans EA, Van Calsteren K, Van Keirsbilck J, Crombag N, Henneman L. A cross-country comparison of pregnant women's decision-making and perspectives when opting for non-invasive prenatal testing in the Netherlands and Belgium. Prenat Diagn 2023; 43:294-303. [PMID: 36740754 DOI: 10.1002/pd.6329] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 02/07/2023]
Abstract
BACKGROUND The Netherlands and Belgium have been among the first countries to offer non-invasive prenatal testing (NIPT) as a first-tier screening test. Despite similarities, differences exist in counseling modalities and test uptake. This study explored decision-making and perspectives of pregnant women who opted for NIPT in both countries. METHODS A questionnaire study was performed among pregnant women in the Netherlands (NL) (n = 587) and Belgium (BE) (n = 444) opting for NIPT, including measures on informed choice, personal and societal perspectives on trisomy 21, 18 and 13 and pregnancy termination. RESULTS Differences between Dutch and Belgian women were shown in the level of informed choice (NL: 83% vs. BE: 59%, p < 0.001), intention to terminate the pregnancy in case of confirmed trisomy 21 (NL: 51% vs. BE: 62%, p = 0.003) and trisomy 13/18 (NL: 80% vs. BE: 73%, p = 0.020). More Belgian women considered trisomy 21 a severe condition (NL: 64% vs. BE: 81%, p < 0.001). Belgian women more frequently indicated that they believed parents are judged for having a child with trisomy 21 (BE: 42% vs. NL: 16%, p < 0.001) and were less positive about quality of care and support for children with trisomy 21 (BE: 23% vs. NL: 62%, p < 0.001). CONCLUSION Differences in women's decision-making regarding NIPT and the conditions screened for may be influenced by counseling aspects and country-specific societal and cultural contexts.
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Affiliation(s)
- Lore Lannoo
- Department of Obstetrics and Gynaecology, Fetomaternal Medicine, University Hospitals Leuven, Leuven, Belgium.,Department of Development and Regeneration, Cluster Woman and Child, Biomedical Sciences, KU Leuven, Leuven, Belgium
| | - Karuna R M van der Meij
- Department of Human Genetics, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Amsterdam, The Netherlands
| | - Mireille N Bekker
- Department of Obstetrics and Gynaecology, Utrecht University Medical Center, Utrecht, The Netherlands
| | - Luc De Catte
- Department of Obstetrics and Gynaecology, Fetomaternal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Sarah Deckers
- Department of Obstetrics and Gynaecology, Fetomaternal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Koenraad Devriendt
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Nele Roggen
- Department of Obstetrics and Gynaecology, AZ Imelda, Bonheiden, Belgium
| | - Robert-Jan H Galjaard
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Janneke Gitsels-van der Wal
- Department of Midwifery Science, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Amsterdam Public Health Research Institute, Quality of Care, Amsterdam, The Netherlands
| | - Merryn V E Macville
- Department of Clinical Genetics, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Linda Martin
- Department of Midwifery Science, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Midwifery Academy Amsterdam Groningen, InHolland, Amsterdam, The Netherlands
| | - Erik A Sistermans
- Department of Human Genetics, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Amsterdam, The Netherlands
| | - Kristel Van Calsteren
- Department of Obstetrics and Gynaecology, Fetomaternal Medicine, University Hospitals Leuven, Leuven, Belgium.,Department of Development and Regeneration, Cluster Woman and Child, Biomedical Sciences, KU Leuven, Leuven, Belgium
| | | | - Neeltje Crombag
- Department of Development and Regeneration, Cluster Woman and Child, Biomedical Sciences, KU Leuven, Leuven, Belgium.,Department of Obstetrics and Gynaecology, Utrecht University Medical Center, Utrecht, The Netherlands
| | - Lidewij Henneman
- Department of Human Genetics, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Amsterdam, The Netherlands
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16
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Prenatal Diagnosis of Uniparental Disomy in Cases of Rare Autosomal Trisomies Detected Using Noninvasive Prenatal Test: A Case of Prader-Willi Syndrome. Diagnostics (Basel) 2023; 13:diagnostics13040580. [PMID: 36832068 PMCID: PMC9955094 DOI: 10.3390/diagnostics13040580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
Rare autosomal trisomies (RATs) other than common aneuploidies can be detected using noninvasive prenatal testing (NIPT). However, conventional karyotyping is insufficient for evaluating diploid fetuses with uniparental disomy (UPD) due to trisomy rescue. Using the diagnostic process for Prader-Willi syndrome (PWS), we aim to describe the need for additional prenatal diagnostic testing for confirming UPD in fetuses diagnosed with RATs via NIPT and its clinical implications. NIPT was performed using the massively parallel sequencing (MPS) method, and all pregnant women with RATs underwent amniocentesis. After confirming the normal karyotype, short tandem repeat (STR) analysis, methylation-specific PCR (MS-PCR), and methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) were performed to detect UPD. Overall, six cases were diagnosed with RATs. There was a suspicion of trisomies of chromosomes 7, 8, and 15 in two cases each. However, these cases were confirmed to have a normal karyotype using amniocentesis. In one of six cases, PWS caused by maternal UPD 15 was diagnosed using MS-PCR and MS-MLPA. We propose that in cases where RAT is detected by NIPT, UPD should be considered following trisomy rescue. Even if amniocentesis confirms a normal karyotype, UPD testing (such as MS-PCR and MS-MLPA) should be recommended for accurate assessment, as an accurate diagnosis can lead to appropriate genetic counseling and improved overall pregnancy management.
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17
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Zou Y, Feng C, Qin J, Wang X, Huang T, Yang Y, Xie K, Yuan H, Huang S, Yang B, Lu W, Liu Y. Performance of expanded non-invasive prenatal testing for fetal aneuploidies and copy number variations: A prospective study from a single center in Jiangxi province, China. Front Genet 2023; 13:1073851. [PMID: 36712884 PMCID: PMC9880269 DOI: 10.3389/fgene.2022.1073851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/27/2022] [Indexed: 01/14/2023] Open
Abstract
To evaluate the performance of expanded non-invasive prenatal testing (expanded noninvasive prenatal testing, NIPT-Plus) in screening for fetal chromosomal abnormalities includes aneuploidies and copy number variations, a total of 23,116 pregnant women with a singleton pregnancy were recruited for NIPT-Plus. Screening positive results were verified by karyotype analysis and chromosomal microarray analysis after amniocentesis. A total of 264 pregnancies (1.14%) were positive results as predicted by NIPT-Plus, including 233 aneuploidies and 31 copy number variations. Following genetic counseling, 233 (88.26%) pregnant women underwent invasive prenatal diagnosis and 136 were verified as true positives, comprising 72 common trisomies (T21, T18, T13), 47 sex chromosomal abnormalities two rare autosomal aneuploidies (RATs) and 15 copy number variations The positive predictive value for common trisomies, SCAs, RATs and CNVs were 68.57%, 68.12%, 6.67% and 51.72%, respectively. Pregnant women with screen-positive results for common trisomies have higher rates of invasive prenatal diagnosis and pregnancy termination than those with positive results for SCAs, RATs, and CNVs. NIPT-Plus showed a good performance in detecting common trisomies, SCAs and also contributed to detecting pathogenic CNVs, but higher accuracy was required in the detection of RATs. In summary, this study provides a reference for the clinical application of NIPT-Plus for screening fetal chromosomal abnormalities in this region. Therefore, we suggest that NIPT-Plus could be widely used in clinical screening for fetal chromosomal abnormalities in combination with prenatal diagnosis and genetic counseling.
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Affiliation(s)
- Yongyi Zou
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China,Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Chuanxin Feng
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China,Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Jiawei Qin
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China,Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Xinrong Wang
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Tingting Huang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China,Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Yan Yang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China,Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Kang Xie
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China,Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Huizhen Yuan
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China,Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Shuhui Huang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China,Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Bicheng Yang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China,Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Wan Lu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China,Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China,*Correspondence: Wan Lu, ; Yanqiu Liu,
| | - Yanqiu Liu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China,Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China,*Correspondence: Wan Lu, ; Yanqiu Liu,
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18
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Xiang L, Zhu J, Deng K, Li Q, Tao J, Li M, Wang Y, Yuan X, Yao Y, Li X. Non-invasive prenatal testing for the detection of trisomies 21, 18, and 13 in pregnant women with various clinical indications: A multicenter observational study of 1,854,148 women in China. Prenat Diagn 2023. [PMID: 36639250 DOI: 10.1002/pd.6312] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/29/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
OBJECTIVE This study aimed to evaluate the performance of noninvasive prenatal testing (NIPT) for detecting three common trisomies (T21, T18, and T13) in pregnant women with diverse clinical indications. METHODS Frequencies of NIPT, of high chance of having one of the three trisomies, and of confirmed trisomies were determined for women with each of seven clinical indications in a national cross-sectional survey of approximately 300 prenatal diagnosis centers. Data were collected for the period from October 1, 2016 to September 30, 2018 using the Prenatal Diagnosis Technology Management On-line Information System. The performance of NIPT for detecting the three trisomies in pregnant women with different clinical indications was assessed in terms of sensitivity, specificity, positive predictive value (PPV), negative predictive value, and the corresponding 95% confidence intervals. RESULTS A total of 5766 true positive cases for T21, T18, and T13 were detected among 1,854,148 samples, giving an overall detection rate of 0.31% (95% CI: 0.30%-0.32%). Most positive cases were associated with "NT thickening" (1.18%) and "advanced maternal age" (0.51%). The detection sensitivities of NIPT were 99.60% for T21, 99.14% for T18, and 100% for T13, while the corresponding specificities were 99.90%, 99.94%, and 99.95%. The corresponding PPVs were 69.77%, 47.24%, and 22.36%. NIPT showed high sensitivity and specificity, regardless of clinical indication. In contrast, PPV for three trisomies varied widely between 9.09% and 66.46% depending on the clinical indication. Across seven clinical indications, PPV ranged from 50.62% to 73.09% for T21, 20.00%-58.33% for T18, and 4.17%-47.37% for T13. The highest PPVs were 73.09% for T21 in pregnancies involving "advanced maternal age", 58.33% for T18 in pregnancies with "NT thickening", and 47.37% for T13 in pregnancies with "NT thickening". CONCLUSIONS NIPT shows high sensitivity and specificity for detecting T21, T18, and T13 in pregnant women with different clinical indications. However, PPV depends strongly on clinical indication, highlighting the need to strengthen education and genetic counseling about prenatal screening.
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Affiliation(s)
- Liangcheng Xiang
- National Office for Maternal and Child Health Surveillance of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jun Zhu
- National Center for Birth Defect Monitoring of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Kui Deng
- National Office for Maternal and Child Health Surveillance of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Qi Li
- National Office for Maternal and Child Health Surveillance of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jing Tao
- National Office for Maternal and Child Health Surveillance of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mingrong Li
- National Office for Maternal and Child Health Surveillance of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yanping Wang
- National Center for Birth Defect Monitoring of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xuelian Yuan
- National Office for Maternal and Child Health Surveillance of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yongna Yao
- National Center for Birth Defect Monitoring of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiaohong Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China.,Sichuan Birth Defects Clinical Research Center, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
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19
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Hu R, Huang W, Zhou W, Luo X, Ren C, Huang H, Hou Y, Guo L, He W, Lu J. Phenotypic findings and pregnancy outcomes of fetal rare autosomal aneuploidies detected using chromosomal microarray analysis. Hum Genomics 2022; 16:64. [PMID: 36457118 PMCID: PMC9714082 DOI: 10.1186/s40246-022-00438-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Aneuploidies are the most common chromosomal abnormality and the main genetic cause of adverse pregnancy outcomes. Since numerous studies have focused on common trisomies, relatively little is known about the association between phenotypic findings and rare autosomal aneuploidies (RAAs). We conducted a retrospective study of 48,904 cases for chromosomal microarray analysis in a large tertiary referral center and reported the overall frequencies, clinical manifestations, and outcomes of prenatal RAAs. RESULTS A total of 90 RAAs were detected, of which 83 cases were mosaic trisomies and 7 were non-mosaic trisomies. Chromosomes 16, 22, and 9 were identified as the major chromosomes involving RAAs. The four predominant indications for prenatal diagnosis in our RAA cases were RAA-positive in noninvasive prenatal screening, advanced maternal age, ultrasound abnormalities, and high-risk for serum prenatal screening. Cardiovascular defects were the most frequently observed structural abnormalities, followed by musculoskeletal anomalies. Increased nuchal translucency and persistent left superior vena cava, the major soft marker abnormalities involved, were also observed in our RAA cases. Clinical outcomes were available for all RAAs, with 63 induced abortions and 27 live births recorded. CONCLUSIONS Variable phenotypes and outcomes were observed, which were highly heterogeneous in cases of prenatal RAAs. Thus, a cautious and comprehensive strategy should be implemented during prenatal counseling for RAAs.
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Affiliation(s)
- Rong Hu
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Weiwei Huang
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Weining Zhou
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Xiaohui Luo
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Congmian Ren
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Huajie Huang
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Yaping Hou
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Li Guo
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Wei He
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Jian Lu
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
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20
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Genome-Wide Cell-Free DNA Test for Fetal Chromosomal Abnormalities and Variants: Unrestricted Versus Restricted Reporting. Diagnostics (Basel) 2022; 12:diagnostics12102439. [PMID: 36292129 PMCID: PMC9600475 DOI: 10.3390/diagnostics12102439] [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: 08/18/2022] [Revised: 09/19/2022] [Accepted: 09/28/2022] [Indexed: 11/23/2022] Open
Abstract
This study aimed to compare the screening performance of genome-wide cfDNA testing for chromosomal abnormalities between two periods where additional findings were reported and not reported. Data were obtained from consecutive pregnant women with a singleton pregnancy at ≥10 weeks who requested cfDNA testing during 2015–2019. The performance of screening of the cfDNA test was determined by calculating the concordance rate, detection rate, and false-positive rate. Data from 3981 women were included. The no-result rates were similar between the two reporting periods (2.04% vs. 2.08%). Concordance rates for trisomy 21 and 18 were 100% and 100%, respectively. There were two cases tested high risk for trisomy 13, with a concordance rate of 0%. In total, 12 cases were high risk for any sex chromosome aneuploidy with an overall concordance of 75%, and 15 cases tested high risk for any rare autosomal trisomy, with a 13.3% concordance rate. The detection rates for trisomy 21 and 18 were 100% and 100%, respectively. For any SCA, the detection rate was 90%. For the two reporting periods, the combined false-positive rates were 0.93% and 0.17%, which were significantly different (p = 0.002). Restricting the reporting of additional findings from genome-wide cfDNA analysis has reduced the false-positive rate but without a reduction in the no-result rate.
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21
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Zheng Y, Li J, Zhang J, Yang H. The accuracy and feasibility of noninvasive prenatal testing in a consecutive series of 20,626 pregnancies with different clinical characteristics. J Clin Lab Anal 2022; 36:e24660. [PMID: 36099005 PMCID: PMC9550972 DOI: 10.1002/jcla.24660] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND To evaluate the accuracy and feasibility of noninvasive prenatal testing (NIPT) according to the results of NIPT and pregnancy outcomes with different indications. METHODS Between October 2014 and December 2020, 20,626 pregnant women who received NIPT were included in this study. The positive predictive value (PPV) of trisomy 21, 18, and 13 (T21, T18, T13), sex chromosome abnormalities (SCAs), other chromosomal aneuploidies, and chromosomal microdeletion/microduplication were calculated. The positive results of NIPT were confirmed by amniocentesis, Karyotype analysis, and chromosome microarray analysis (CMA). RESULTS In total, 263 positive cases (263/20,626, 1.28%) were detected by NIPT, of which T21, T18, and T13 were 69, 26, and 9 cases, respectively. Sex chromosome abnormalities (SCAs), other chromosomal aneuploidies, and copy number variants (CNVs) were 69, 12, and 38 cases, respectively. There were true positive in 49 of T21, 13 of T18, 1 of T13, 32 of SCAs, 1 of other chromosomal aneuploidies, and 15 of CNVs. The NIPT sensitivity of T21, T18, T13, SCAs, other chromosomal aneuploidies, and CNVs was all 100%, the specialty was 99.90%, 99.94%, 99.96%, 99.82%, 99.95%, 99.89%, and the PPV was 71.01%, 50.00%, 11.11%, 46.38%, 8.33%, 39.47%, respectively. The PPV was high in T21, moderate in T18 and SCAs, and low in T13 and other chromosomal abnormalities. CONCLUSION NIPT has high accuracy, specificity and and can effectively avoid the occurrence of birth defects, but it cannot replace prenatal diagnosis. The accuracy, specificity, and sensitivity of NIPT in detecting sex chromosomes, chromosome microdeletion/microduplication, and other chromosomal abnormalities should be improved.
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Affiliation(s)
- Yunyun Zheng
- Department of Obstetrics and GynecologyXiJing Hospital of Air Force Medical UniversityXi'anChina
| | - Jia Li
- Department of Obstetrics and GynecologyXiJing Hospital of Air Force Medical UniversityXi'anChina
| | - Jianfang Zhang
- Department of Obstetrics and GynecologyXiJing Hospital of Air Force Medical UniversityXi'anChina
| | - Hong Yang
- Department of Obstetrics and GynecologyXiJing Hospital of Air Force Medical UniversityXi'anChina
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22
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Kleinfinger P, Brechard M, Luscan A, Trost D, Boughalem A, Mylene Valduga, Serero DR S, Costa JM, Lohmann L. Case Report: How whole-genome sequencing-based cell-free DNA prenatal testing can help identify a marker mhromosome. Front Genet 2022; 13:926290. [PMID: 36226188 PMCID: PMC9549001 DOI: 10.3389/fgene.2022.926290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022] Open
Abstract
A supernumerary marker chromosome (SMC) is a structurally abnormal chromosome that cannot be characterized by conventional banding cytogenetics. Marker chromosomes are present in 0.075% of prenatal cases. They are associated with variable phenotypes, ranging from normal to severely abnormal, and the prognosis is largely dependent on the results of further cytogenomic analysis. Here, we report the identification and characterization of a marker chromosome following prenatal screening in a 39-year-old pregnant patient. The patient had a normal first trimester ultrasound but was high-risk for fetal chromosome anomalies based on the results of maternal serum parameters. Chorionic villus sampling was performed, and analysis of chorionic villi revealed the presence of two identical marker chromosomes. In the interest of a rapid identification of the markers, we performed noninvasive prenatal testing (NIPT) together with chorionic villus sampling. A pericentromeric 29 Mb duplication of chromosome 20: dup (20) (p13q11.21) was identified and thereafter confirmed by targeted metaphasic FISH. Whole-genome sequencing-based NIPT was instrumental in rapid characterization of the SMCs and allowed us to obviate the need for multiple expensive and time-consuming FISH analyses.
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23
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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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24
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Positive predictive value estimates for noninvasive prenatal testing from data of a prenatal diagnosis laboratory and literature review. Mol Cytogenet 2022; 15:29. [PMID: 35794576 PMCID: PMC9261060 DOI: 10.1186/s13039-022-00607-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022] Open
Abstract
Objective Since 2011, noninvasive prenatal testing (NIPT) has undergone rapid expansion, with both utilization and coverage. However, conclusive data regarding the clinical validity and utility of this testing tool are lacking. Thus, there is a continued need to educate clinicians and patients about the current benefits and limitations in order to inform pre- and post-test counseling, pre/perinatal decision making, and medical risk assessment/management. Methods This retrospective study included women referred for invasive prenatal diagnosis to confirm positive NIPT results between January 2017 and December 2020. Prenatal diagnosis testing, including karyotyping, chromosomal microarray analysis (CMA) were performed. Positive predictive values (PPVs) were calculated. Results In total, 468 women were recruited. The PPVs for trisomies 21, 18, and 13 were 86.1%, 57.8%, and 25.0%, respectively. The PPVs for rare chromosomal abnormalities (RCAs) and copy number variants (CNVs) were 17.0% and 40.4%, respectively. The detection of sex chromosomal aneuploidies (SCAs) had a PPV of 20% for monosomy X, 23.5% for 47,XXX, 68.8% for 47,XXY, and 62.5% for 47,XYY. The high-risk groups had a significant increase in the number of true positive cases compared to the low- and moderate-risk groups. Conclusions T13, monosomy X, and RCA were associated with lower PPVs. The improvement of cell-free fetal DNA screening technology and continued monitoring of its performance are important.
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25
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Zaninović L, Bašković M, Ježek D, Katušić Bojanac A. Validity and Utility of Non-Invasive Prenatal Testing for Copy Number Variations and Microdeletions: A Systematic Review. J Clin Med 2022; 11:jcm11123350. [PMID: 35743413 PMCID: PMC9224664 DOI: 10.3390/jcm11123350] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/31/2022] [Accepted: 06/08/2022] [Indexed: 02/07/2023] Open
Abstract
Valid data on prenatal cell-free DNA-based screening tests for copy number variations and microdeletions are still insufficient. We aimed to compare different methodological approaches concerning the achieved diagnostic accuracy measurements and positive predictive values. For this systematic review, we searched the Scopus and PubMed databases and backward citations for studies published between 2013 and 4 February 2022 and included articles reporting the analytical and clinical performance of cfDNA screening tests for CNVs and microdeletions. Of the 1810 articles identified, 32 met the criteria. The reported sensitivity of the applied tests ranged from 20% to 100%, the specificity from 81.62% to 100%, and the PPV from 3% to 100% for cases with diagnostic or clinical follow-up information. No confirmatory analysis was available in the majority of cases with negative screening results, and, therefore, the NPVs could not be determined. NIPT for CNVs and microdeletions should be used with caution and any developments regarding new technologies should undergo strict evaluation before their implementation into clinical practice. Indications for testing should be in correlation with the application guidelines issued by international organizations in the field of prenatal diagnostics.
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Affiliation(s)
- Luca Zaninović
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia; (L.Z.); (D.J.); (A.K.B.)
- Children’s Hospital Zagreb, Ulica Vjekoslava Klaića 16, 10 000 Zagreb, Croatia
| | - Marko Bašković
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia; (L.Z.); (D.J.); (A.K.B.)
- Children’s Hospital Zagreb, Ulica Vjekoslava Klaića 16, 10 000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-1-3636-379
| | - Davor Ježek
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia; (L.Z.); (D.J.); (A.K.B.)
- Department of Histology and Embryology, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia
- Department of Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Kišpatićeva 12, 10 000 Zagreb, Croatia
| | - Ana Katušić Bojanac
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia; (L.Z.); (D.J.); (A.K.B.)
- Department of Medical Biology, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia
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Battese Ellis K. Effectiveness of alternative prenatal genetic counselling methods in a cohort of pregnant women from a low socio-economic population. Aust N Z J Obstet Gynaecol 2022; 62:674-680. [PMID: 35531789 DOI: 10.1111/ajo.13522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/02/2022] [Accepted: 03/14/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND There are concerns about the capacity of healthcare providers to adequately counsel women on the implications of noninvasive prenatal screening (NIPS). Studies suggest that more resource-efficient counselling methods are needed for broad adoption. AIMS We prospectively examined the effectiveness of alternative methods of prenatal counselling on a patient's knowledge and understanding of prenatal testing choices, with a focus on NIPS. We also evaluated prenatal test choice and emotional well-being after making this decision. METHODS Women from a low socio-economic population were offered NIPS at no additional cost along with typical prenatal screening and diagnosis. Study participants underwent prenatal counselling via a web-based video consultation or a telephone consultation with a genetic counsellor. Participants were asked to complete pre-counselling and post-counselling questionnaires. RESULTS Of 1000 women enrolled, 600 completed both surveys in full and were included in the analysis. Of these, 354 (59%) underwent counselling via a telephone consultation and 246 (41%) via the web-based video consultation. Both counselling methods led to a significant increase in patient knowledge (P < 0.01). NIPS uptake was equivalent between groups. Patients expressed a high level (90%) of satisfaction with their prenatal screen choice, with no significant difference (P > 0.10) between telephone and web participants. CONCLUSIONS Alternative methods of counselling such as a web-based education portal can be highly effective and should be considered to enable informed decision-making prior to undergoing prenatal screening such as NIPS. Further, web-based education tools could be beneficial for those in rural areas with limited access to healthcare providers and non-native speakers.
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27
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Mayo S, Gómez-Manjón I, Atencia G, Moreno-Izquierdo A, Escribano D, Fernández-Martínez FJ. Noninvasive prenatal testing: How far can we reach detecting fetal copy number variations. Eur J Obstet Gynecol Reprod Biol 2022; 272:150-155. [PMID: 35313136 DOI: 10.1016/j.ejogrb.2022.03.027] [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: 09/20/2021] [Revised: 02/14/2022] [Accepted: 03/11/2022] [Indexed: 11/27/2022]
Abstract
Non-invasive prenatal testing (NIPT) is currently the best screening test for fetal chromosome abnormalities with the highest sensitivity and specificity and can be done from 10 weeks gestation. We report a detection of 44.7 Mb duplication at 11p15.5-p11.2 by NIPT with a fetal fraction (FF) of only 3%. This chromosome abnormality was confirmed after amniocentesis by karyotyping and array comparative genomic hybridization (aCGH) on cultured fetal cells. Further parental investigation showed that the fetal chromosome abnormality was inherited from the mother who was a carrier of a balanced translocation 46,XX,t(11;X)(p11.2;q28). This case highlights the importance of expanded NIPT in the detection of fetal segmental aneuploidy. NIPT together with complementary studies can lead to the detection of parental chromosome rearrangement despite a low FF, which can impact the couple's reproductive plans. We also reviewed other cases with chromosome rearrangement, detected by NIPT, derived from a parental reciprocal translocation.
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Affiliation(s)
- Sonia Mayo
- Genetics and Inheritance Research Group, Instituto de Investigación Sanitaria Hospital, 12 de Octubre (imas12), 28041 Madrid, Spain.
| | - Irene Gómez-Manjón
- Genetics and Inheritance Research Group, Instituto de Investigación Sanitaria Hospital, 12 de Octubre (imas12), 28041 Madrid, Spain; Department of Genetics, Hospital Universitario, 12 de Octubre, 28041 Madrid, Spain
| | - Gabriela Atencia
- Genetics and Inheritance Research Group, Instituto de Investigación Sanitaria Hospital, 12 de Octubre (imas12), 28041 Madrid, Spain
| | - Ana Moreno-Izquierdo
- Genetics and Inheritance Research Group, Instituto de Investigación Sanitaria Hospital, 12 de Octubre (imas12), 28041 Madrid, Spain; Department of Genetics, Hospital Universitario, 12 de Octubre, 28041 Madrid, Spain
| | - David Escribano
- Fetal Medicine Unit, Department of Obstetrics and Gynaecology, Hospital Universitario, 12 de Octubre, 28041 Madrid, Spain
| | - Fco Javier Fernández-Martínez
- Genetics and Inheritance Research Group, Instituto de Investigación Sanitaria Hospital, 12 de Octubre (imas12), 28041 Madrid, Spain; Department of Genetics, Hospital Universitario, 12 de Octubre, 28041 Madrid, Spain
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28
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Harasim T, Neuhann T, Behnecke A, Stampfer M, Holinski-Feder E, Abicht A. Initial Clinical Experience with NIPT for Rare Autosomal Aneuploidies and Large Copy Number Variations. J Clin Med 2022; 11:jcm11020372. [PMID: 35054066 PMCID: PMC8777675 DOI: 10.3390/jcm11020372] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVE Amniocentesis, chorionic villi sampling and first trimester combined testing are able to screen for common trisomies 13, 18, and 21 and other atypical chromosomal anomalies (ACA). The most frequent atypical aberrations reported are rare autosomal aneuploidies (RAA) and copy number variations (CNV), which are deletions or duplications of various sizes. We evaluated the clinical outcome of non-invasive prenatal testing (NIPT) results positive for RAA and large CNVs to determine the clinical significance of these abnormal results. METHODS Genome-wide NIPT was performed on 3664 eligible patient samples at a single genetics center. For patients with positive NIPT reports, the prescribing physician was asked retrospectively to provide clinical follow-up information using a standardized questionnaire. RESULTS RAAs and CNVs (>7 Mb) were detected in 0.5%, and 0.2% of tested cases, respectively. Follow up on pregnancies with an NIPT-positive result for RAA revealed signs of placental insufficiency or intra-uterine death in 50% of the cases and normal outcome at the time of birth in the other 50% of cases. We showed that CNV testing by NIPT allows for the detection of unbalanced translocations and relevant maternal health conditions. CONCLUSION NIPT for aneuploidies of all autosomes and large CNVs of at least 7 Mb has a low "non-reportable"-rate (<0.2%) and allows the detection of additional conditions of clinical significance.
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29
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Bevilacqua E, Jani JC, Chaoui R, Suk EA, Palma‐Dias R, Ko T, Warsof S, Stokowski R, Jones KJ, Grati FR, Schmid M. Performance of a targeted cell-free DNA prenatal test for 22q11.2 deletion in a large clinical cohort. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 58:597-602. [PMID: 34090308 PMCID: PMC8518527 DOI: 10.1002/uog.23699] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/10/2021] [Accepted: 05/21/2021] [Indexed: 05/17/2023]
Abstract
OBJECTIVE 22q11.2 deletion is more common than trisomies 18 and 13 combined, yet no routine approach to prenatal screening for this microdeletion has been established. This study evaluated the clinical sensitivity and specificity of a targeted cell-free DNA (cfDNA) test to screen for fetal 22q11.2 deletion in a large cohort, using blinded analysis of prospectively enrolled pregnancies and stored clinical samples. METHODS In order to ensure that the analysis included a meaningful number of cases with fetal 22q11.2 deletion, maternal plasma samples were obtained by prospective, multicenter enrolment of pregnancies with a fetal cardiac abnormality and from stored clinical samples from a research sample bank. Fetal genetic status, as evaluated by microarray analysis, karyotyping with fluorescence in-situ hybridization or a comparable test, was available for all cases. Samples were processed as described previously for the Harmony prenatal test, with the addition of DANSR (Digital Analysis of Selected Regions) assays targeting the 3.0-Mb region of 22q11.2 associated with 22q11.2 deletion syndrome. Operators were blinded to fetal genetic status. Sensitivity and specificity of the cfDNA test for 22q11.2 deletion were calculated based on concordance between the cfDNA result and fetal genotype. RESULTS The final study group consisted of 735 clinical samples, including 358 from prospectively enrolled pregnancies and 377 stored clinical samples. Of 46 maternal plasma samples from pregnancies with a 22q11.2 deletion, ranging in size from 1.25 to 3.25 Mb, 32 had a cfDNA result indicating a high probability of 22q11.2 deletion (sensitivity, 69.6% (95% CI, 55.2-80.9%)). All 689 maternal plasma samples without a 22q11.2 deletion were classified correctly by the cfDNA test as having no evidence of a 22q11.2 deletion (specificity, 100% (95% CI, 99.5-100%)). CONCLUSIONS The results of this large-scale prospective clinical evaluation of the sensitivity and specificity of a targeted cfDNA test for fetal 22q11.2 deletion demonstrate that this test can detect the common and smaller, nested 22q11.2 deletions with a low (0-0.5%) false-positive rate. Although the positive predictive value (PPV) observed in this study population was 100%, the expected PPV in the general pregnant population is estimated to be 12.2% at 99.5% specificity and 41.1% at 99.9% specificity. The use of this cfDNA test to screen for 22q11.2 deletion could enhance identification of pregnancies at risk for 22q11.2 deletion syndrome without significantly increasing the likelihood of maternal anxiety and unnecessary invasive procedures related to a false-positive result. © 2021 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- E. Bevilacqua
- Department of Obstetrics and Gynecology, University Hospital BrugmannUniversité Libre de BruxellesBrusselsBelgium
| | - J. C. Jani
- Department of Obstetrics and Gynecology, University Hospital BrugmannUniversité Libre de BruxellesBrusselsBelgium
| | - R. Chaoui
- Prenatal Diagnosis and Human GeneticsBerlinGermany
| | - E.‐K. A. Suk
- Prenatal Diagnosis and Human GeneticsBerlinGermany
| | - R. Palma‐Dias
- The Royal Women's HospitalUniversity of MelbourneParkvilleVICAustralia
| | - T.‐M. Ko
- Genephile Bioscience Laboratory, Ko's Obstetrics & Gynecology ClinicTaipei CityTaiwan
| | - S. Warsof
- Eastern Virginia Medical SchoolNorfolkVAUSA
| | | | - K. J. Jones
- Roche Sequencing Solutions, Inc.San JoseCAUSA
| | - F. R. Grati
- TOMA Advanced Biomedical Assays S.p.A, Impact Lab.Busto ArsizioItaly
| | - M. Schmid
- Roche Sequencing Solutions, Inc.San JoseCAUSA
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30
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Srebniak MI, Jehee FS, Joosten M, Boter M, de Valk WG, van der Helm R, Sistermans EA, Voorhoeve E, Bhola S, Hoffer MJV, den Hollander N, Macville MVE, Van Opstal D. Non-invasive prenatal diagnosis for translocation carriers-YES please or NO go? Acta Obstet Gynecol Scand 2021; 100:2036-2043. [PMID: 34472080 DOI: 10.1111/aogs.14256] [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: 05/04/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 11/28/2022]
Abstract
INTRODUCTION The presence of an unbalanced familial translocation can be reliably assessed in the cytotrophoblast of chorionic villi. However, carriers of a balanced translocation often decline invasive testing. This study aimed to investigate whether an unbalanced translocation can also be diagnosed in cell free DNA by whole-genome non-invasive prenatal screening (NIPS). MATERIAL AND METHODS Pregnant women carrying a fetus with an unbalanced familial translocation, for whom NIPS as well as microarray data were available, were included in this retrospective assessment. NIPS was performed in the course of the TRIDENT study. RESULTS In 12 cases, both NIPS and microarray data were available. In 10 of 12 cases the unbalanced translocation was correctly identified by NIPS without prior knowledge on parental translocation. One was missed because the fetal fraction was too low. One was missed because of technical restrictions in calling 16p gains. CONCLUSIONS This study supports the hypothesis that routine NIPS may be used for prenatal diagnosis of unbalanced inheritance of familial translocations, especially with prior knowledge of the translocation allowing focused examination of the involved chromosomal regions. Our study showed that routine shallow sequencing designed for aneuploidy detection in cell free DNA may be sufficient for higher resolution NIPS, if specialized copy number software is used and if sufficient fetal fraction is present.
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Affiliation(s)
| | - Fernanda S Jehee
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marieke Joosten
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marjan Boter
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Walter G de Valk
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Robert van der Helm
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Erik A Sistermans
- Department of Clinical Genetics and Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Els Voorhoeve
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Shama Bhola
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mariette J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Merryn V E Macville
- Department of Clinical Genetics, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Diane Van Opstal
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
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Shi P, Wang Y, Liang H, Hou Y, Chen D, Zhao G, Dai P, Xia Y, Feng Y, Cram DS, Kong X. The potential of expanded noninvasive prenatal screening for detection of microdeletion and microduplication syndromes. Prenat Diagn 2021; 41:1332-1342. [PMID: 34181751 DOI: 10.1002/pd.6002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 11/10/2022]
Abstract
OBJECTIVES To evaluate the clinical potential of a higher resolution noninvasive prenatal screening (NIPS-Plus) test for detection of microdeletion/microduplication syndromes (MMS) in addition to common aneuploidies. METHODS In a multicenter prospective study, 37,002 pregnant women with unremarkable first-trimester ultrasound scans had a NIPS-Plus test. Ultrasound screen positive women were not included in this study. RESULTS Of 36,970 ultrasound negative women there were 291 NIPS-Plus screen positive results indicating 237 aneuploidies and 54 MMS. Following amniocentesis, 171 (72%) were confirmed as genuine, comprising 3 T13s, 10 T18s, 61 T21s, 70 SCAs and 27 MMS. The PPV for MMS with unremarkable ultrasound findings was 50%. Routine clinical examination of children born from NIPS-Plus negative pregnancies revealed no obvious signs of chromosome disease syndromes at one year of age. CONCLUSIONS NIPS-Plus has the potential for clinical utility not only for routine aneuploid screening but also for MMS that do not show overt signs during early pregnancy ultrasound screening. We suggest that ultrasound with NIPS-Plus in combination with appropriate counselling could be considered as a comprehensive first-tier prenatal screening approach for all pregnant women.
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Affiliation(s)
- Panlai Shi
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuan Wang
- Berry Genomics Corporation, Beijing, China
| | | | - Yaqin Hou
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Duo Chen
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ganye Zhao
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Peng Dai
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanjie Xia
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yin Feng
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | | | - Xiangdong Kong
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Pertile MD, Flowers N, Vavrek D, Andrews D, Kalista T, Craig A, Deciu C, Duenwald S, Meier K, Bhatt S. Performance of a Paired-End Sequencing-Based Noninvasive Prenatal Screening Test in the Detection of Genome-Wide Fetal Chromosomal Anomalies. Clin Chem 2021; 67:1210-1219. [PMID: 34077512 DOI: 10.1093/clinchem/hvab067] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/13/2021] [Indexed: 12/29/2022]
Abstract
BACKGROUND Noninvasive prenatal tests (NIPTs) detect fetal chromosomal anomalies with high clinical sensitivity and specificity. We examined the performance of a paired-end sequencing-based NIPT in the detection of genome-wide fetal chromosomal anomalies including common trisomies, sex chromosomal aneuploidies (SCA), rare autosomal aneuploidies (RAAs), and partial deletions/duplications ≥7 Mb. METHODS Frozen plasma samples from pregnant women were tested using the VeriSeq NIPT Solution v2 assay. All samples were previously tested with a laboratory-developed NIPT and had known clinical outcomes. Individuals performing the sequencing were blinded to clinical outcome data. Clinical sensitivity and specificity were determined for basic (chromosomes 21, 18, 13, X, and Y) and genome-wide screening modes. RESULTS Of 2335 samples that underwent genome-wide analysis, 28 did not meet QC requirements, resulting in a first-pass assay failure rate of 1.2%. Basic screening analysis, excluding known mosaics, correctly classified 130/130 trisomy 21 samples (sensitivity >99.9%, 95% confidence interval [CI] 97.1%-100%), 41/41 trisomy 18 samples (sensitivity >99.9%, 95% CI 91.4%-100%), and 26/26 trisomy 13 samples (sensitivity >99.9%, 95% CI 87.1%-100%) with 6 false-positive results; specificities ≥99.90% were reported for all 3 trisomies. Concordance for SCAs ranged from 90.5%-100%. Genome-wide screening analysis including known mosaics correctly classified 27/28 RAAs and 20/27 partial deletions/duplications with a specificity of 99.80% for both anomalies, and an overall genome-wide specificity for all anomalies of 99.34%. CONCLUSIONS The VeriSeq NIPT Solution v2 assay enables accurate identification of fetal aneuploidy, allowing detection of genome-wide fetal chromosomal anomalies with high clinical sensitivities and specificities and a low assay failure rate.Clinical Trial Notification [CTN] identification number [ID]: CT-2018-CTN-01585-1 v1, Protocol: NIPT T05 002.
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Affiliation(s)
- Mark D Pertile
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Nicola Flowers
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Darcy Vavrek
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Daniel Andrews
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Tasha Kalista
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Andrew Craig
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Cosmin Deciu
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Sven Duenwald
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Kristen Meier
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Sucheta Bhatt
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
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Christiaens L, Chitty LS, Langlois S. Current controversies in prenatal diagnosis: Expanded NIPT that includes conditions other than trisomies 13, 18, and 21 should be offered. Prenat Diagn 2021; 41:1316-1323. [PMID: 33829520 DOI: 10.1002/pd.5943] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/06/2021] [Accepted: 03/22/2021] [Indexed: 11/11/2022]
Abstract
Non-invasive prenatal testing (NIPT) based on analysis of cell free DNA circulating in the maternal plasma has been available clinically to screen for chromosomal abnormalities since 2011. There is significant evidence to suggest that NIPT has revolutionised prenatal screening for the common trisomies 13, 18, and 21. However, the evidence in favour of its extended use to screen for conditions other than these trisomies remains a topic of debate with no national or international organisation supporting clinical implementation for these indications. In the debate presented here - "Expanded NIPT that includes conditions other than trisomies 13, 18, and 21 should be offered" - we will see the pros and cons of screening for a wider range of chromosomal problems. The discussion presented swung the vote from 65% in favour and 35% against before the arguments were voiced to 41% in favour and 59% against. This significant swing in the vote indicates that the majority of our community feel more evidence is required before clinical implementation of extended NIPT.
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Affiliation(s)
- Lieve Christiaens
- Illumina Inc., San Diego, California, USA.,University Hospital of Utrecht, Utrecht, Netherlands
| | - Lyn S Chitty
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,The UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sylvie Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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34
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Lai Y, Zhu X, He S, Dong Z, Tang Y, Xu F, Chen Y, Meng L, Tao Y, Yi S, Su J, Huang H, Luo J, Leung TY, Wei H. Performance of Cell-Free DNA Screening for Fetal Common Aneuploidies and Sex Chromosomal Abnormalities: A Prospective Study from a Less Developed Autonomous Region in Mainland China. Genes (Basel) 2021; 12:478. [PMID: 33806256 PMCID: PMC8067030 DOI: 10.3390/genes12040478] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/01/2021] [Accepted: 03/19/2021] [Indexed: 12/24/2022] Open
Abstract
To evaluate the performance of noninvasive prenatal screening (NIPS) in the detection of common aneuploidies in a population-based study, a total of 86,262 single pregnancies referred for NIPS were prospectively recruited. Among 86,193 pregnancies with reportable results, follow-up was successfully conducted in 1160 fetuses reported with a high-risk result by NIPS and 82,511 cases (95.7%) with a low-risk result. The screen-positive rate (SPR) of common aneuploidies and sex chromosome abnormalities (SCAs) provided by NIPS were 0.7% (586/83,671) and 0.6% (505/83,671), respectively. The positive predictive values (PPVs) for Trisomy 21, Trisomy 18, Trisomy 13 and SCAs were calculated as 89.7%, 84.0%, 52.6% and 38.0%, respectively. In addition, less rare chromosomal abnormalities, including copy number variants (CNVs), were detected, compared with those reported by NIPS with higher read-depth. Among these rare abnormalities, only 23.2% (13/56) were confirmed by prenatal diagnosis. In total, four common trisomy cases were found to be false negative, resulting in a rate of 0.48/10,000 (4/83,671). In summary, this study conducted in an underdeveloped region with limited support for the new technology development and lack of cost-effective prenatal testing demonstrates the importance of implementing routine aneuploidy screening in the public sector for providing early detection and precise prognostic information.
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Affiliation(s)
- Yunli Lai
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
- Guangxi Clinical Research Center for Fetal Diseases, Nanning 530000, China
| | - Xiaofan Zhu
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; (X.Z.); (Z.D.); (T.Y.L.)
- Genetics and Prenatal Diagnosis Center, The First Affiliation Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Sheng He
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Zirui Dong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; (X.Z.); (Z.D.); (T.Y.L.)
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518000, China
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Yanqing Tang
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Fuben Xu
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Yun Chen
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Lintao Meng
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Yuli Tao
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Shang Yi
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Jiasun Su
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Hongqian Huang
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Jingsi Luo
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; (X.Z.); (Z.D.); (T.Y.L.)
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518000, China
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Hongwei Wei
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Guangxi Clinical Research Center for Fetal Diseases, Nanning 530000, China
- Department of Obstetrics and Gynaecology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
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35
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Levy B, Hoffmann ER, McCoy RC, Grati FR. Chromosomal mosaicism: Origins and clinical implications in preimplantation and prenatal diagnosis. Prenat Diagn 2021; 41:631-641. [PMID: 33720449 DOI: 10.1002/pd.5931] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/03/2021] [Accepted: 03/06/2021] [Indexed: 12/18/2022]
Abstract
The diagnosis of chromosomal mosaicism in the preimplantation and prenatal stage is fraught with uncertainty and multiple factors need to be considered in order to gauge the likely impact. The clinical effects of chromosomal mosaicism are directly linked to the type of the imbalance (size, gene content, and copy number), the timing of the initial event leading to mosaicism during embryogenesis/fetal development, the distribution of the abnormal cells throughout the various tissues within the body as well as the ratio of normal/abnormal cells within each of those tissues. Additional factors such as assay noise and culture artifacts also have an impact on the significance and management of mosaic cases. Genetic counseling is an important part of educating patients about the likelihood of having a liveborn with a chromosome abnormality and these risks differ according to the time of ascertainment and the tissue where the mosaic cells were initially discovered. Each situation needs to be assessed on a case-by-case basis and counseled accordingly. This review will discuss the clinical impact of finding mosaicism through: embryo biopsy, chorionic villus sampling, amniocentesis, and noninvasive prenatal testing using cell-free DNA.
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Affiliation(s)
- Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Eva R Hoffmann
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Francesca R Grati
- Research and Development, Cytogenetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays, S.p.A. (Impact Lab), Busto Arsizio, Varese, Italy
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36
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Familiari A, Boito S, Rembouskos G, Ischia B, Accurti V, Fabietti I, Volpe P, Persico N. Cell-free DNA analysis of maternal blood in prenatal screening for chromosomal microdeletions and microduplications: a systematic review. Prenat Diagn 2021; 41:1324-1331. [PMID: 33710639 DOI: 10.1002/pd.5928] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 02/20/2021] [Accepted: 02/23/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIM OF THE STUDY Scientific Societies do not recommend the use of cell-free DNA (cfDNA) testing as a first-tier screening for microdeletion and microduplication syndromes (MMs). The aim of this study was to review the current available literature on the performance of cell-free DNA as a screening for MMs. METHODS Medline, Embase and the Cochrane Library were searched electronically from 2000 to January 2020 and articles reporting the diagnostic performance of cfDNA screening for MMs in large (>5000 cases) series were included. Between-study heterogeneity and random effect model for screen positive rate (SPR), false positive rate (FPR) and positive predictive value (PPV) were calculated. RESULTS We identified 42 papers, seven included, for a total of 474,189 pregnancies and 210 cases of MMs. Diagnostic verification of positive cases was available overall in 486 (71.68 %) of 678 cases. The weighted pooled SPR, FPR and PPV were 0.19% (95% CI = 0.09-0.33), 0.07 (95% CI = 0.02-0.15) and 44.1 (95% CI = 31.49-63.07). In conclusion, the pooled PPV of cfDNA testing in screening for MMs was about 40%, ranging from 29% to 91%, for an overall FPR <0.1%. CONCLUSIONS No confirmatory analysis was available in cases that did not undergo invasive testing, which were the vast majority of cases with a negative test, and therefore, the DR and the negative predictive value cannot be determined.
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Affiliation(s)
- Alessandra Familiari
- High Risk Pregnancy Unit, Children and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Simona Boito
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Benedetta Ischia
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Veronica Accurti
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Isabella Fabietti
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Paolo Volpe
- Fetal Medicine Unit, Di Venere and Sarcone Hospitals, Bari, Italy
| | - Nicola Persico
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.,Department of Clinical Science and Community Health, University of Milan, Italy
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37
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Zhu X, Chen M, Wang H, Guo Y, Chau MHK, Yan H, Cao Y, Kwok YKY, Chen J, Hui ASY, Zhang R, Meng Z, Zhu Y, Leung TY, Xiong L, Kong X, Choy KW. Clinical utility of expanded non-invasive prenatal screening and chromosomal microarray analysis in high-risk pregnancy. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 57:459-465. [PMID: 32198896 DOI: 10.1002/uog.22021] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/27/2020] [Accepted: 03/13/2020] [Indexed: 06/10/2023]
Abstract
OBJECTIVE To evaluate the utility of expanded non-invasive prenatal screening (NIPS), compared with chromosomal microarray analysis (CMA), for the detection of chromosomal abnormalities in high-risk pregnancies. METHODS This was a multicenter retrospective study of singleton pregnancies at high risk for chromosomal abnormality. Patients who underwent expanded NIPS and CMA sequentially during pregnancy from 2015 to 2019 were included in the analysis. Pregnancies with a positive result for sex chromosome aneuploidy were excluded as the full details could not be retrieved. The utility of expanded NIPS and CMA for detection of chromosomal abnormalities in this cohort was compared by assessing the concordance between the results. RESULTS Of the 774 included high-risk pregnancies, 550 (71.1%) had a positive NIPS result, while a positive CMA result was detected in 308 (39.8%) cases. The rate of full or partial concordance between NIPS and CMA was 82.2%, 59.6% and 25.0% for trisomies 21, 18 and 13, respectively. For rare aneuploidies and segmental imbalances, NIPS and CMA results were fully or partially concordant in 7.5% and 33.3% of cases, respectively. Copy-number variants < 5 Mb were detected more often by CMA, with an incidence of 7.9% (61/774) compared with 3.1% (24/774) by NIPS. A genetic aberration was detected by CMA in 1 in 17 (5.8%) high-risk pregnancies that had a negative or non-reportable NIPS result. CONCLUSION CMA allows for comprehensive detection of genome-wide chromosomal abnormalities in high-risk pregnancies. CMA should be offered instead of expanded NIPS for high-risk pregnancies. Copyright © 2020 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- X Zhu
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - M Chen
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - H Wang
- Department of Central Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Guangdong, China
| | - Y Guo
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - M H K Chau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - H Yan
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Y Cao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
- The Chinese University of Hong Kong, Baylor College of Medicine Joint Center for Medical Genetics, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Y K Y Kwok
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - J Chen
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - A S Y Hui
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - R Zhang
- Department of Central Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Guangdong, China
| | - Z Meng
- Department of Central Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Guangdong, China
| | - Y Zhu
- Department of Central Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Guangdong, China
| | - T Y Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- The Chinese University of Hong Kong, Baylor College of Medicine Joint Center for Medical Genetics, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - L Xiong
- Department of Central Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Guangdong, China
| | - X Kong
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - K W Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- The Chinese University of Hong Kong, Baylor College of Medicine Joint Center for Medical Genetics, The Chinese University of Hong Kong, Hong Kong, SAR, China
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38
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Davidson L, Boland MR. Towards deep phenotyping pregnancy: a systematic review on artificial intelligence and machine learning methods to improve pregnancy outcomes. Brief Bioinform 2021; 22:6065792. [PMID: 33406530 PMCID: PMC8424395 DOI: 10.1093/bib/bbaa369] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 10/13/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022] Open
Abstract
Objective Development of novel informatics methods focused on improving pregnancy outcomes remains an active area of research. The purpose of this study is to systematically review the ways that artificial intelligence (AI) and machine learning (ML), including deep learning (DL), methodologies can inform patient care during pregnancy and improve outcomes. Materials and methods We searched English articles on EMBASE, PubMed and SCOPUS. Search terms included ML, AI, pregnancy and informatics. We included research articles and book chapters, excluding conference papers, editorials and notes. Results We identified 127 distinct studies from our queries that were relevant to our topic and included in the review. We found that supervised learning methods were more popular (n = 69) than unsupervised methods (n = 9). Popular methods included support vector machines (n = 30), artificial neural networks (n = 22), regression analysis (n = 17) and random forests (n = 16). Methods such as DL are beginning to gain traction (n = 13). Common areas within the pregnancy domain where AI and ML methods were used the most include prenatal care (e.g. fetal anomalies, placental functioning) (n = 73); perinatal care, birth and delivery (n = 20); and preterm birth (n = 13). Efforts to translate AI into clinical care include clinical decision support systems (n = 24) and mobile health applications (n = 9). Conclusions Overall, we found that ML and AI methods are being employed to optimize pregnancy outcomes, including modern DL methods (n = 13). Future research should focus on less-studied pregnancy domain areas, including postnatal and postpartum care (n = 2). Also, more work on clinical adoption of AI methods and the ethical implications of such adoption is needed.
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Affiliation(s)
- Lena Davidson
- MS degree at College of St. Scholastica, Duluth, MN, USA
| | - Mary Regina Boland
- Department of Biostatistics, Epidemiology, and Informatics at the University of Pennsylvania
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Clinical Significance of Non-Invasive Prenatal Screening for Trisomy 7: Cohort Study and Literature Review. Genes (Basel) 2020; 12:genes12010011. [PMID: 33374124 PMCID: PMC7824243 DOI: 10.3390/genes12010011] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/09/2020] [Accepted: 12/21/2020] [Indexed: 12/24/2022] Open
Abstract
Trisomy 7 is the most frequently observed type of rare autosomal trisomies in genome-wide non-invasive prenatal screening (NIPS). Currently, the clinical significance of trisomy 7 NIPS-positive results is still unknown. We reviewed two independent cohorts from two laboratories where similar NIPS metrics were applied. A total of 70,441 singleton cases who underwent genome-wide NIPS were analyzed, among which 39 pregnancies were positive for trisomy 7, yielding a screen-positive rate of 0.055% (39/70,441). There were 28 cases with invasive testing results available; the positive predictive value (PPV) was 3.6% (1/28). We then searched the published NIPS studies to generate a large cohort of 437,873 pregnancies and identified 247 cases (0.056%) that were screened positive for trisomy 7. The overall PPV was 3.4% (4/118) in the combined data. The presence of uniparental disomy 7 was not detected in the NIPS trisomy 7-positive pregnancies with normal fetal karyotype. Among the 85 cases with pregnancy outcome available in combined data, 88.2% were normal live births, 14.1% had intrauterine growth restriction, preterm birth or low birth weight, 3.5% presented with ultrasound abnormality, and no fetal loss was observed. Our data provide valuable information for counseling and management of trisomy 7-positive NIPS pregnancies.
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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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Flowers NJ, Burgess T, Giouzeppos O, Shi G, Love CJ, Hunt CE, Scarff KL, Archibald AD, Pertile MD. Genome-wide noninvasive prenatal screening for carriers of balanced reciprocal translocations. Genet Med 2020; 22:1944-1955. [PMID: 32807973 DOI: 10.1038/s41436-020-0930-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Balanced reciprocal translocation carriers are at increased risk of producing gametes with unbalanced forms of the translocation leading to miscarriage, fetal anomalies, and birth defects. We sought to determine if genome-wide cell-free DNA based noninvasive prenatal screening (gw-NIPS) could provide an alternative to prenatal diagnosis for carriers of these chromosomal rearrangements. METHODS This pilot series comprises a retrospective analysis of gw-NIPS and clinical outcome data from 42 singleton pregnancies where one parent carried a balanced reciprocal translocation. Gw-NIPS was performed between August 2015 and March 2018. Inclusion criteria required at least one translocation segment to be ≥15 Mb in size. RESULTS Forty samples (95%) returned an informative result; 7 pregnancies (17.5%) were high risk for an unbalanced translocation and confirmed after diagnostic testing. The remaining 33 informative samples were low risk and confirmed after diagnostic testing or normal newborn physical exam. Test sensitivity of 100% (95% confidence interval [CI]: 64.6-100%) and specificity of 100% (95% CI: 89.6-100%) were observed for this pilot series. CONCLUSION We demonstrate that gw-NIPS is a potential option for a majority of reciprocal translocation carriers. Further confirmation of this methodology could lead to adoption of this noninvasive alternative.
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Affiliation(s)
- Nicola Jane Flowers
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Trent Burgess
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Olivia Giouzeppos
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Grace Shi
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Clare Jane Love
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Clare Elizabeth Hunt
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Katrina Louise Scarff
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Alison Dalton Archibald
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Mark Domenic Pertile
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia. .,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.
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Persico N, Boito S, Volpe P, Ischia B, Gentile M, Ronzoni L, De Robertis V, Fabietti I, Olivieri C, Periti E, Ficarella R, Silipigni R, Rembouskos G. Incidence of chromosomal abnormalities in fetuses with first trimester ultrasound anomalies and a low-risk cell-free DNA test for common trisomies. Prenat Diagn 2020; 40:1474-1481. [PMID: 33034897 DOI: 10.1002/pd.5799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 11/09/2022]
Abstract
OBJECTIVE To examine the incidence and type of chromosomal abnormalities in fetuses with first trimester ultrasound anomalies and a low-risk cfDNA test for common trisomies. METHODS In 486 singleton pregnancies undergoing invasive testing after combined screening, a detailed first trimester ultrasound assessment was carried out and a maternal blood sample was sent for cfDNA analysis. Ultrasound and cfDNA data were analyzed in relation to fetal karyotype. RESULTS Invasive testing demonstrated a chromosomal abnormality in 157 (32.3%) of 486 fetuses. In 348 cases with a low-risk cfDNA test for common trisomies, NT ≥ 3.5 mm and/or a major structural defect were observed in 92 (26.4%) fetuses. A chromosomal abnormality was found in 17 (18.5%; 95%CI 10.55-26.41) of these pregnancies, including 1 (1.1%) case of trisomy 21 and 16 (17.4%) fetuses with abnormalities different from common trisomies. The respective incidence in the 256 cases with a low-risk cfDNA test result and no ultrasound anomalies was 2.3% (95% CI 0.49-4.20; n = 6). CONCLUSIONS In fetuses with first trimester ultrasound anomalies and a low-risk cfDNA result for trisomy 21, 18 and 13, diagnostic testing should be offered with the main objective to detect chromosomal abnormalities beyond common trisomies.
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Affiliation(s)
- Nicola Persico
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.,Department of Clinical Science and Community Health, University of Milan, Milan, Italy
| | - Simona Boito
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Paolo Volpe
- Fetal Medicine Unit, Di Venere and Sarcone Hospitals, Bari, Italy
| | - Benedetta Ischia
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Luisa Ronzoni
- Medical Genetics Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Isabella Fabietti
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Enrico Periti
- Fetal Medicine Unit, Palagi Hospital, Florence, Italy
| | | | - Rosamaria Silipigni
- Laboratory of Medical Genetics, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
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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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Zheng J, Lu H, Li M, Guan Y, Yang F, Xu M, Dong J, Zhang Q, An N, Zhou Y. The Clinical Utility of Non-invasive Prenatal Testing for Pregnant Women With Different Diagnostic Indications. Front Genet 2020; 11:624. [PMID: 32695138 PMCID: PMC7339964 DOI: 10.3389/fgene.2020.00624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/26/2020] [Indexed: 12/17/2022] Open
Abstract
Background Our aim was to evaluate the clinical utility of non-invasive prenatal testing for pregnant women with different diagnostic indications. Methods In eight counties and districts of Yancheng, we studied 13,149 pregnant women with different indications who were offered NIPT for fetal screening, including for sex chromosomal aneuploidies (SCAs), rare autosomal trisomies (RATs), and subchromosomal copy number variations (CNVs). The purpose was to compare the detection of positive predictive values (PPVs) of different indications with the use of NIPT. The results were validated by karyotyping, chromosomal microarray analysis (CMA), or follow-up of pregnancy outcomes. Results 13,149 maternal plasma samples were sequenced, among which 28 samples (0.2%) failed the sequencing quality control. The remaining 13,121 samples were analyzed, and birth follow-up missed 2,192 samples (16.7%). The PPVs of NIPT results for trisomy 21 (T21) and trisomy 18 (T18) and SCAs were 96.67, 63.64, and 31.34%, respectively. Among the advanced maternal age (AMA), serum screening high risk (SSHR), serum screening intermediate risk (SSIR), and voluntary screening (VS) groups, the PPVs for the common trisomies were 81.25, 85.71, 100, and 70%, respectively; the PPVs for total chromosomal abnormalities were 55.82, 65.22, 23.08, and 36.59%, respectively. Conclusion NIPT for T21 and T18 and SCAs screening were ideal, and the PPVs for trisomy 13 (T13), RATs, and CNVs were low. For the AMA and VS groups, NIPT could be used as a first-line screening program; for SSHR and SSIR groups, NIPT could be used as a second-line supplementary screening program.
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Affiliation(s)
- Jianli Zheng
- Department of Prenatal Diagnosis, Center of Medical Genetics, Yancheng Maternity and Child Health Care Hospital, Yancheng, China
| | - Haiyan Lu
- Department of Prenatal Diagnosis, Center of Medical Genetics, Yancheng Maternity and Child Health Care Hospital, Yancheng, China
| | - Min Li
- Department of Prenatal Diagnosis, Center of Medical Genetics, Yancheng Maternity and Child Health Care Hospital, Yancheng, China
| | - Yongjuan Guan
- Department of Prenatal Diagnosis, Center of Medical Genetics, Yancheng Maternity and Child Health Care Hospital, Yancheng, China
| | - Fangfang Yang
- Department of Prenatal Diagnosis, Center of Medical Genetics, Yancheng Maternity and Child Health Care Hospital, Yancheng, China
| | - Mengjun Xu
- Department of Prenatal Diagnosis, Center of Medical Genetics, Yancheng Maternity and Child Health Care Hospital, Yancheng, China
| | - Jingjing Dong
- Department of Prenatal Diagnosis, Center of Medical Genetics, Yancheng Maternity and Child Health Care Hospital, Yancheng, China
| | - Qinge Zhang
- Department of Prenatal Diagnosis, Center of Medical Genetics, Yancheng Maternity and Child Health Care Hospital, Yancheng, China
| | - Ning An
- Department of Prenatal Diagnosis, Center of Medical Genetics, Yancheng Maternity and Child Health Care Hospital, Yancheng, China
| | - Yun Zhou
- Department of Prenatal Diagnosis, Center of Medical Genetics, Yancheng Maternity and Child Health Care Hospital, Yancheng, China
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Qi Y, Yang J, Hou Y, Hu R, Wang D, Peng H, Yin A. Potential influence of parental copy number variations on noninvasive prenatal testing (NIPT): two case reports. Mol Cytogenet 2020; 13:18. [PMID: 32508984 PMCID: PMC7249382 DOI: 10.1186/s13039-020-00485-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/15/2020] [Indexed: 11/10/2022] Open
Abstract
Background Small subchromosomal deletions and duplications caused by copy number variants (CNVs) can now be detected with noninvasive prenatal testing (NIPT) technology. However, the clinical utility and validity of this screening for CNVs are still unknown. Here, we discuss some special conditions in which both cases simultaneously exhibited false positives caused by maternal CNVs and false negatives due to limitations of the technology. Case presentation In case 1, NIPT indicated a 1.1 Mb deletion at 21q21.1, but the umbilical cord for array CGH (aCGH) revealed a 422 kb deletion at 15q13.3. Peripheral blood of the parents for aCGH showed a 1.1 Mb deletion at 21q21.1 in the mother’s sample, and the same deletion at 15q13.3 was detected in the father’s blood. In case 2, NIPT showed a 1.5 Mb deletion at 22q11.21, but aCGH of amniocytes revealed a 1.377 Mb duplication rather than a 1.5 Mb deletion at 22q11.21. Furthermore, aCGH analysis of the parental blood revealed a 647 kb deletion at 22q11.21 in the mother and a 2.8 Mb duplication of 22q11.21 in the father. Conclusions Our findings not only highlight the significance of diagnostic testing following a positive cfDNA sequencing result but also the necessity for additional analytical and clinical validation before routine use in practice.
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Affiliation(s)
- Yiming Qi
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Jiexia Yang
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Yaping Hou
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Rong Hu
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Dongmei Wang
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Haishan Peng
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Aihua Yin
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
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Oneda B, Sirleto P, Baldinger R, Taralczak M, Joset P, Zweier M, Niedrist D, Azzarello-Burri S, Britschgi C, Breymann C, Ochsenbein-Kölble N, Burkhardt T, Wisser J, Zimmermann R, Steindl K, Rauch A. Genome-wide non-invasive prenatal testing in single- and multiple-pregnancies at any risk: Identification of maternal polymorphisms to reduce the number of unnecessary invasive confirmation testing. Eur J Obstet Gynecol Reprod Biol 2020; 252:19-29. [PMID: 32619881 DOI: 10.1016/j.ejogrb.2020.05.070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Non-invasive prenatal testing by targeted or genome-wide copy number profiling (cnNIPT) has the potential to outperform standard NIPT targeting the common trisomies 13, 18, and 21, only. Nevertheless, prospective results and outcome data on cnNIPT are still scarce and there is increasing evidence for maternal copy number variants (CNVs) interfering with results of both, standard and cnNIPT. STUDY DESIGN We assessed the performance of cnNIPT in 3053 prospective and 116 retrospective cases with special consideration of maternal CNVs in singleton and multiple gestational pregnancies at any risk, as well as comprehensive follow-up. RESULTS A result was achieved in 2998 (98.2%) of total prospective cases (89.2% analyzed genome-wide). Confirmed fetal chromosomal abnormalities were detected in 45 (1.5%) cases, of which five (11%) would have remained undetected in standard NIPTs. Additionally, we observed 4 likely fetal trisomies without follow-up and a likely phenotype associated placental partial trisomy 16. Moreover, we observed clinically relevant confirmed maternal CNVs in 9 (0.3%) cases and likely maternal clonal hematopoiesis in 3 (0.1%). For common fetal trisomies we prospectively observed a very high sensitivity (100% [95% CI: 91.96-100%]) and specificity (>99.9% [95% CI: 99.8-100%]), and positive predictive value (PPV) (97.8% [95% CI: 86.1-99.7%]), but our retrospective control cases demonstrated that due to cases of fetal restricted mosaicism the true sensitivity of NIPT is lower. After showing that 97.3% of small CNVs prospectively observed in 8.3% of genome-wide tests were mostly benign maternal variants, sensitivity (75.0% [95% CI: 19.4%-99.4%]), specificity (99.7% [99.5%-99.9%]) and PPV (30.0% [14.5%-52.1%]) for relevant fetal CNVs were relatively high, too. Maternal autoimmune disorders and medication, such as dalteparin, seem to impair assay quality. CONCLUSION When maternal CNVs are recognized as such, cnNIPT showed a very high sensitivity, specificity and PPV for common trisomies in single and multiple pregnancies at any risk and very good values genome-wide. We found that the resolution for segmental aberrations is generally comparable to standard karyotyping, and exceeds the latter if the fetal fraction is above 10%, which allows detection of the 2.5 Mb 22q11.2 microdeletion associated with the velocardiofacial syndrome, even if the mother is not a carrier.
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Affiliation(s)
- Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland.
| | - Pietro Sirleto
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Rosa Baldinger
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | | | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Dunja Niedrist
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | | | - Christian Britschgi
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | | | - Nicole Ochsenbein-Kölble
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Tilo Burkhardt
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Josef Wisser
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Roland Zimmermann
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
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Chau MHK, Lam DYM, Zhu X, Kwok YKY, Ting YH, Chan WP, Shi M, Cheung SWH, Lau TK, Ville Y, Leung TY, Choy KW. The utility of genome-wide cell-free DNA screening in the prenatal diagnosis of Pallister-Killian syndrome. Prenat Diagn 2020; 40:1005-1012. [PMID: 32350887 DOI: 10.1002/pd.5721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 12/22/2022]
Abstract
OBJECTIVE To report genome-wide cell-free DNA (cfDNA) screening facilitating the diagnosis of Pallister-Killian syndrome (PKS). METHODS This is a retrospective cohort analysis of positive genome-wide cfDNA screening results showing increased signal from chromosome 12 and the detection of PKS. The genome-wide cfDNA screening results and the subsequent investigations were reviewed. RESULTS Three singleton pregnancies (3/29007) from 2016 to 2017 yielded positive results indicating large gains on the entire p-arm of chromosome 12. In two cases, multiple structural abnormalities were detected by prenatal ultrasound and the couples opted for termination of pregnancy. Chromosomal microarray performed on fetal skin tissues of the two abortuses detected mosaic tetrasomy 12p, consistent with PKS. In the third case, karyotype and chromosomal microarray performed on an amniotic fluid sample also showed mosaic tetrasomy 12p. In each of the three cases, genome-wide cfDNA screening revealed a large gain on chromosome 12p; subsequent prenatal or postnatal diagnostic testing confirmed the diagnosis of PKS. CONCLUSION We report the ability of genome-wide cfDNA screening to provide early suspicion and facilitate the subsequent genetic diagnosis of PKS. As genome-wide cfDNA screening becomes increasingly available, incidental diagnosis of partial aneuploidies is expected to increase.
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Affiliation(s)
- Matthew Hoi Kin Chau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Xiaofan Zhu
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yvonne Ka Yin Kwok
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, Shatin, Hong Kong, China
| | - Yuen Ha Ting
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wan Pang Chan
- Obstetrics & Gynaecology Centre, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Mengmeng Shi
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Tze Kin Lau
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, Shatin, Hong Kong, China.,Fetal Medicine Centre, Paramount Medical Centre, Hong Kong, China
| | - Yves Ville
- EA 73-28, Faculté de Médecine de l'Université René Descartes, Paris, France
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, The Chinese University of Hong Kong, Hong Kong, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, The Chinese University of Hong Kong, Hong Kong, China
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Current Status of Noninvasive Prenatal Testing and Counselling Considerations: An Indian Perspective. JOURNAL OF FETAL MEDICINE 2020. [DOI: 10.1007/s40556-019-00228-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Lin Y, Liang D, Wang Y, Li H, Liu A, Hu P, Xu Z. Analyzing false-negative results detected in low-risk non-invasive prenatal screening cases. Mol Genet Genomic Med 2020; 8:e1185. [PMID: 32067421 PMCID: PMC7196474 DOI: 10.1002/mgg3.1185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 01/14/2020] [Accepted: 01/31/2020] [Indexed: 01/03/2023] Open
Abstract
Background The non‐invasive prenatal screening (NIPS) has been introduced into clinical practice with a high sensitivity and specificity. Although the false‐negative results are inevitable and important, limited false‐negative NIPS results have been reported and studied previously. In this study, we aim to report and analyze false‐negative results detected in the NIPS cases with a low‐risk result. Methods NIPS was performed using whole‐genome massively parallel shotgun sequencing for screening common trisomies, rare autosomal aneuploidies, and subchromosome copy number variants. All the NIPS cases with a low‐risk result performed in our center in 2017 were followed‐up using medical records and telephone interview at 3 months after delivery. Fetal ultrasound results and available genetic diagnostic testing results were collected for pregnancies with adverse outcomes. The genetic diagnostic testing referred to chromosomal microarray analysis or fluorescent in situ hybridization on amniotic fluid cells, fetal skin tissue, neonatal peripheral blood, or available placental biopsies. Results By following‐up 10,975 low‐risk results, we found 166 NIPS cases with adverse pregnancy outcomes, in which eight cases had diagnostic testing. Among them, four false‐negative cases were confirmed, including one trisomy 18 caused by placental mosaicism, one mosaic tetrasomy 12p, and 2 microdeletion/microduplication cases. Conclusion Our results revealed that mosaicism contributes to a major cause of false negative in NIPS, and highlighted the importance of ultrasound in identifying these false‐negative results.
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Affiliation(s)
- Ying Lin
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province, China
| | - Dong Liang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province, China
| | - Yan Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province, China
| | - Hang Li
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province, China
| | - An Liu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province, China
| | - Ping Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province, China
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province, China
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van der Meij KR, Sistermans EA, Macville MV, Stevens SJ, Bax CJ, Bekker MN, Bilardo CM, Boon EM, Boter M, Diderich KE, de Die-Smulders CE, Duin LK, Faas BH, Feenstra I, Haak MC, Hoffer MJ, den Hollander NS, Hollink IH, Jehee FS, Knapen MF, Kooper AJ, van Langen IM, Lichtenbelt KD, Linskens IH, van Maarle MC, Oepkes D, Pieters MJ, Schuring-Blom GH, Sikkel E, Sikkema-Raddatz B, Smeets DF, Srebniak MI, Suijkerbuijk RF, Tan-Sindhunata GM, van der Ven AJE, van Zelderen-Bhola SL, Henneman L, Galjaard RJH, Van Opstal D, Weiss MM. TRIDENT-2: National Implementation of Genome-wide Non-invasive Prenatal Testing as a First-Tier Screening Test in the Netherlands. Am J Hum Genet 2019; 105:1091-1101. [PMID: 31708118 DOI: 10.1016/j.ajhg.2019.10.005] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/02/2019] [Indexed: 12/30/2022] Open
Abstract
The Netherlands launched a nationwide implementation study on non-invasive prenatal testing (NIPT) as a first-tier test offered to all pregnant women. This started on April 1, 2017 as the TRIDENT-2 study, licensed by the Dutch Ministry of Health. In the first year, NIPT was performed in 73,239 pregnancies (42% of all pregnancies), 7,239 (4%) chose first-trimester combined testing, and 54% did not participate. The number of trisomies 21 (239, 0.33%), 18 (49, 0.07%), and 13 (55, 0.08%) found in this study is comparable to earlier studies, but the Positive Predictive Values (PPV)-96% for trisomy 21, 98% for trisomy 18, and 53% for trisomy 13-were higher than expected. Findings other than trisomy 21, 18, or 13 were reported on request of the pregnant women; 78% of women chose to have these reported. The number of additional findings was 207 (0.36%); these included other trisomies (101, 0.18%, PPV 6%, many of the remaining 94% of cases are likely confined placental mosaics and possibly clinically significant), structural chromosomal aberrations (95, 0.16%, PPV 32%,) and complex abnormal profiles indicative of maternal malignancies (11, 0.02%, PPV 64%). The implementation of genome-wide NIPT is under debate because the benefits of detecting other fetal chromosomal aberrations must be balanced against the risks of discordant positives, parental anxiety, and a potential increase in (invasive) diagnostic procedures. Our first-year data, including clinical data and laboratory follow-up data, will fuel this debate. Furthermore, we describe how NIPT can successfully be embedded into a national screening program with a single chain for prenatal care including counseling, testing, and follow-up.
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