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Wang Y, He Y, Shi Y, Qian DC, Gray KJ, Winn R, Martin AR. Aspiring toward equitable benefits from genomic advances to individuals of ancestrally diverse backgrounds. Am J Hum Genet 2024; 111:809-824. [PMID: 38642557 PMCID: PMC11080611 DOI: 10.1016/j.ajhg.2024.04.002] [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: 10/05/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/22/2024] Open
Abstract
Advancements in genomic technologies have shown remarkable promise for improving health trajectories. The Human Genome Project has catalyzed the integration of genomic tools into clinical practice, such as disease risk assessment, prenatal testing and reproductive genomics, cancer diagnostics and prognostication, and therapeutic decision making. Despite the promise of genomic technologies, their full potential remains untapped without including individuals of diverse ancestries and integrating social determinants of health (SDOHs). The NHGRI launched the 2020 Strategic Vision with ten bold predictions by 2030, including "individuals from ancestrally diverse backgrounds will benefit equitably from advances in human genomics." Meeting this goal requires a holistic approach that brings together genomic advancements with careful consideration to healthcare access as well as SDOHs to ensure that translation of genetics research is inclusive, affordable, and accessible and ultimately narrows rather than widens health disparities. With this prediction in mind, this review delves into the two paramount applications of genetic testing-reproductive genomics and precision oncology. When discussing these applications of genomic advancements, we evaluate current accessibility limitations, highlight challenges in achieving representativeness, and propose paths forward to realize the ultimate goal of their equitable applications.
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Affiliation(s)
- Ying Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
| | - Yixuan He
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Yue Shi
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Reproductive Medicine Center, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - David C Qian
- Department of Thoracic Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kathryn J Gray
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Robert Winn
- Virginia Commonwealth University Massey Cancer Center, Richmond, VA, USA
| | - Alicia R Martin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
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Roberts AW, Maisenbacher MK, Parmar S, Wilkinson J, Poll S, Faulkner N, Prakash SK. Maternal Sex Chromosome Aneuploidy Identified through Noninvasive Prenatal Screening: Clinical Profile and Patient Experience. Am J Perinatol 2024; 41:e2574-e2581. [PMID: 37433314 DOI: 10.1055/a-2126-7476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
OBJECTIVE Noninvasive prenatal screening (NIPS) may incidentally identify maternal aneuploidies that have health implications. We evaluated patients' experience with counseling and follow-up diagnostic testing after NIPS flags a potential maternal sex chromosome aneuploidy (SCA). STUDY DESIGN Patients who underwent NIPS at two reference laboratories between 2012 and 2021 and had test results that were consistent with possible or probable maternal SCA were contacted with a link to an anonymous survey. Survey topics included demographics, health history, pregnancy history, counseling, and follow-up testing. RESULTS A total of 269 patients responded to the anonymous survey, and 83 of these individuals also completed one follow-up survey. Most received pretest counseling. A total of 80% were offered fetal genetic testing during the pregnancy, and 35% of patients completed diagnostic maternal testing. Monosomy X-related phenotypes such as short stature or hearing loss prompted follow-up testing that led to a diagnosis of monosomy X in 14 (6%) cases. CONCLUSION Follow-up counseling and testing after a high-risk NIPS result suggestive of maternal SCA is heterogenous in this cohort and may be frequently incomplete. Health outcomes may be affected by these results and additional research could improve the provision, delivery, and quality of posttest counseling. KEY POINTS · NIPS results showing potential SCA could have maternal health implications.. · Variations in counseling and testing after NIPS were observed for women with suspected SCA.. · Comprehensive counseling and diagnostic testing strategies are critical for these patients..
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Affiliation(s)
- Aaron W Roberts
- Department of Obstetrics and Gynecology, The University of Texas Health Science Center at Houston, Houston, Texas
| | | | | | | | - Sarah Poll
- Invitae, Inc., San Francisco, California
| | | | - Siddharth K Prakash
- Department of Internal Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
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Zhang B, Zhang LX, Yi J, Wang CH, Zhao Y. Selection of prenatal screening with nuchal translucency > 95th centile and below 99th centile: a 4-year observational study with real-world data. Arch Gynecol Obstet 2024:10.1007/s00404-024-07500-7. [PMID: 38625542 DOI: 10.1007/s00404-024-07500-7] [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: 01/07/2024] [Accepted: 03/26/2024] [Indexed: 04/17/2024]
Abstract
OBJECTIVE We sought to analyze the genetic outcomes of fetuses with nuchal translucency (NT) > 95th centile, and determine whether prenatal genetic counseling, chromosomal microarray analysis (CMA) or non-invasive prenatal testing (NIPT) are truly beneficial for the outcomes of fetuses with increased NT > 95th centile and below 99th centile. MATERIALS AND METHODS A total of 535 pregnant women were included in this study, with a fetal NT > 95th centile at 11-13+6 weeks of gestation from January 2017 to December 2020. 324 pregnant women with fetal NT > 95th centile and below 99th centile combined with other risk factors and NT > 99th centile received prenatal diagnostic karyotype analysis and CMA, and 211 pregnant women with fetal isolated increased NT > 95th centile and below 99th centile were selected to carry out NIPT. RESULTS A total of 211 pregnant women who underwent NIPT were included in the study, NIPT results showed that 8 high-risk cases were confirmed by prenatal diagnosis. Overall, the detection rate of NIPT was 3.79%. A total of 324 pregnant women with fetal NT > 95th centile and below 99th centile, along with other risk factors, and those with fetal NT > 99th centile, received karyotype analysis and CMA for prenatal diagnosis. Among them, a total of 73 genetic abnormalities were detected, including 45 cases of chromosomal aneuploidy, 7 cases of structural abnormalities, and 21 cases of copy number variations (CNVs) with a size of less than 10 Mb. In addition, the 73 women with genetic abnormalities are divided into three groups based on the NT measurement (Group 1: Fetuses with NT > 95th centile and below 99th centile, Group 2: Fetuses with NT > 99th centile, and Group 3: Fetuses with NT > 99th centile). 13.11% (8/61) of pathogenic genetic abnormalities (6 chromosomal aneuploidy, 1 structural abnormality, and 1 likely pathogenic CNV) will be missed if genetic counseling and prenatal genetic testing were not conducted in fetuses with increased NT > 95th centile and below 99th centile combined with other risks. Pathogenic CNVs were the most common abnormalities in group 3, and one likely pathogenic CNV was detected in group 1 and group 3, respectively, and a total of 14 CNVs of unknown clinical significance (VOUS) were detected. CONCLUSIONS Through this study, we demonstrated that the critical value of NT > 95th centile for invasive detection or NIPT. Invasive testing combined with CMA may be recommended for fetuses with NT > 95th centile and below 99th centile and with other risks. But when isolated NT > 95th centile and below 99th centile, NIPT would be appropriate.
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Affiliation(s)
- Bin Zhang
- Department of Science and Education, Maternal and Child Medical Centre, Anhui Medical University, Hefei Maternal and Child Health Hospital, Hefei, 230001, Anhui, China
| | - Long-Xiu Zhang
- Department of Imaging Centre, The Fifth Clinical School of Anhui Medical University, Children's Medical Centre of Anhui Medical University, Anhui Children's Hospital, Hefei, 230041, Anhui, China
- Teaching and Research Section of Nuclear Medicine, Department of School of Basic Medical Sciences, Teaching and Research Section of Nuclear Medicine of Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Jiao Yi
- Department of Obstetrics and Gynecology, Maternal and Child Medical Centre of Anhui Medical University, Hefei, 230001, Anhui, China
| | - Chao-Hong Wang
- Clinical Genetics CenterMaternal and Child Medical Centre, Anhui Medical University, Hefei, 230001, Anhui, China.
| | - Ye Zhao
- Teaching and Research Section of Nuclear Medicine, Department of School of Basic Medical Sciences, Teaching and Research Section of Nuclear Medicine of Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China.
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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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Eiben B, Glaubitz R, Winkler T, Teubert A, Borth H. Clinical Experience with Noninvasive Prenatal Testing in Twin Pregnancy Samples at a Single Center in Germany. J Lab Physicians 2023; 15:590-595. [PMID: 37780866 PMCID: PMC10539069 DOI: 10.1055/s-0043-1770066] [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] [Indexed: 10/03/2023] Open
Abstract
In this study we wanted to determine the performance of a paired-end sequencing-based noninvasive prenatal testing (NIPT) assay in the detection of common fetal trisomies in twin pregnancy samples. Samples from patients with a twin pregnancy were collected from at least 10 weeks of gestation and analyzed at a single prenatal center in Germany. Results of Anomaly Detected (i.e., high risk) or No Anomaly Detected (i.e., low risk) for trisomy 21, trisomy 18, or trisomy 13 were reported. Follow-up confirmatory outcomes were requested for all cases. A total of 1,658 patients with twin pregnancies submitted samples during the study period; only two of these samples failed resulting in a low failure rate of 0.12%. Of the remaining 1,656 cases, there were 1,625 (98.1%) low-risk and 31 (1.9%) high-risk NIPT samples in our cohort. Of these, follow-up information was available for 301 (18.5%) of the low-risk samples and 19 (61.3%) of the high-risk samples. All of the low-risk cases with follow-up were determined to be true negatives giving an estimated negative predictive value of 100%. Seventeen of the 19 high-risk samples with follow-up were true positives, resulting in an overall positive predictive value of 89.5%. Sensitivities of > 99.9% were noted for both trisomy 21 and trisomy 18, with high specificities of ≥ 99.7% observed for all three trisomies. In conclusion, our study showed strong performance of the NIPT assay in the detection of common fetal trisomies in twin pregnancy samples, with high sensitivities, specificities, and positive predictive values observed based on known clinical outcomes along with a low failure rate.
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Affiliation(s)
- Bernd Eiben
- Amedes Institut für Labormedizin und Klinische Genetik Rhein/Ruhr, Essen, Germany
| | | | - Thomas Winkler
- Amedes Institut für Labormedizin und Klinische Genetik Rhein/Ruhr, Essen, Germany
| | | | - Heike Borth
- Amedes Institut für Labormedizin und Klinische Genetik Rhein/Ruhr, Essen, Germany
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Zhu S, Jia C, Hao S, Zhang Q, He J, Wang X, Lin P, Guo Y, Li Y, Feng X. Evaluation of the clinical effects of non-invasive prenatal screening for diseases associated with aneuploidy and copy number variation. Mol Genet Genomic Med 2023; 11:e2200. [PMID: 37354111 PMCID: PMC10496052 DOI: 10.1002/mgg3.2200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 11/09/2022] [Accepted: 05/04/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND To explore and compare the clinical effects of high-resolution non-invasive prenatal screening (NIPS-Plus) for common/uncommon chromosomal aneuploidy and microdeletion/microduplication syndromes (MMS). METHODS The current prospective study included a total of 25,380 pregnant women who performed NIPS-Plus, and amniocentesis was performed on women with MMS with the screening results to diagnose patients with suspected MMS. RESULTS There were 415 samples with positive results for NIPS-Plus, included 275 with aneuploidy and 140 with MMS. After diagnosis by amniocentesis, 188 cases were confirmed as true positive, included46 cases of T21, 9 cases of T18, 1 case of T13, 34 cases of SCA, 41 cases of other chromosomal euploidy and 57 cases of MMS. In addition, no false negative cases were found, MMS was classified with 5 Mb with the cutoff value, and the PPV of different fragment size was counted, respectively. CONCLUSION We found that the corresponding PPV was 44.66% with the fragment of copy number variation (CNV) being less than or equal to 5 Mb, and when it was greater than 5 Mb, the PPV was 29.73%, which suggested that NIPS-Plus was more suitable for screening the PPV of small fragment abnormalities. NIPS-Plus has a good application effect in routine aneuploidy screening and had the best detection effect for T21; moreover, it performed well in screening of MMS and had better detection effect on MMS with CNV fragment length less than 5 Mb. Based on the current results, we suggested that NIPS-Plus should be used as a comprehensive elementary prenatal screening method for all pregnant women, but for MMS caused by abnormal large fragment CNV, the detection method and efficiency still need to be improved.
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Affiliation(s)
- Shaohua Zhu
- Medical Genetic Centre, Gansu Maternity and Child‐Care HospitalLanzhouChina
- Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Chunyang Jia
- Medical Genetic Centre, Gansu Maternity and Child‐Care HospitalLanzhouChina
| | - Shengju Hao
- Medical Genetic Centre, Gansu Maternity and Child‐Care HospitalLanzhouChina
- Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Qinghua Zhang
- Medical Genetic Centre, Gansu Maternity and Child‐Care HospitalLanzhouChina
- Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Jing He
- Medical Genetic Centre, Gansu Maternity and Child‐Care HospitalLanzhouChina
| | - Xing Wang
- Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Pengwu Lin
- Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Yuanyuan Guo
- Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Yigang Li
- Gansu Provincial Clinical Research Center for Birth Defects and Rare DiseasesLanzhouChina
| | - Xuan Feng
- Medical Genetic Centre, Gansu Maternity and Child‐Care HospitalLanzhouChina
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Dunn TM, Subramaniam A. Updates in Genetic Screening for the General Obstetrician. Obstet Gynecol Clin North Am 2023; 50:493-507. [PMID: 37500212 DOI: 10.1016/j.ogc.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The number of prenatal genetic screening options, including aneuploidy screening and carrier screening, has drastically increased with rapid advancements in DNA sequencing technologies. Noninvasive prenatal screening analyzing cell-free DNA has quickly been integrated into routine prenatal care as it is the most sensitive and specific screening method for pregnancies at increased and average risk of fetal aneuploidy. The aim of this article is to outline current recommendations for cell-free DNA screening and carrier screening, important aspects of pretest and posttest counseling for obstetric providers, and which patients should be referred to a genetic specialist.
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Affiliation(s)
- Taylor M Dunn
- Department of Genetics, University of Alabama at Birmingham, 1720 2nd Avenue South, VH1L108B, Birmingham, AL 35294-0019, USA.
| | - Akila Subramaniam
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, University of Alabama at Birmingham, 1700 6th Avenue South, Women and Infants Center, 10270, Birmingham, AL 35249, USA
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8
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De Falco L, Pelo E, Qi Z, Novelli A. Editorial: Unravelling the basis of non-invasive prenatal screening results. Front Genet 2023; 14:1247764. [PMID: 37529782 PMCID: PMC10390063 DOI: 10.3389/fgene.2023.1247764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/05/2023] [Indexed: 08/03/2023] Open
Affiliation(s)
- Luigia De Falco
- AMES, Centro Polidiagnostico Strumentale, srl, Naples, Italy
| | - Elisabetta Pelo
- SOD Diagnostica Genetica, Azienda Ospedaliero Universitaria Careggi, Florence, Italy
| | - Zhongxia Qi
- Medical Center, Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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Bussolaro S, Raymond YC, Acreman ML, Guido M, Da Silva Costa F, Rolnik DL, Fantasia I. The accuracy of prenatal cell-free DNA screening for sex chromosome abnormalities: A systematic review and meta-analysis. Am J Obstet Gynecol MFM 2023; 5:100844. [PMID: 36572107 DOI: 10.1016/j.ajogmf.2022.100844] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/26/2022] [Accepted: 12/20/2022] [Indexed: 12/26/2022]
Abstract
OBJECTIVE Although cell-free DNA screening for sex chromosome abnormalities is increasingly used in clinical practice, its diagnostic accuracy and clinical utility remain unclear. This systematic review and meta-analysis aimed to determine the performance of cell-free DNA in the detection of sex chromosome abnormalities. DATA SOURCES Medline and PubMed, Embase, and Web of Science were searched from inception to January 2022 for articles relating to cell-free DNA screening for sex chromosome abnormalities. STUDY ELIGIBILITY CRITERIA Original articles, randomized control trials, conference abstracts, cohort and case-control studies, and case series with more than 10 cases with diagnostic confirmation were considered for inclusion. METHODS Quality assessment of each included publication was performed using the Quality Assessment of Diagnostic Accuracy Studies 2 tool. The positive predictive value was calculated as the proportion of true positive cases among those who tested positive and underwent diagnostic testing. Sensitivity and specificity were pooled, and a summary receiver operating characteristic curve was produced using bivariate models that included studies that had diagnostic confirmation for high- and low-risk women. RESULTS The search identified 7553 results. Of these, 380 proceeded to the full-text screening, of which 94 articles were included in the meta-analysis with a total of 1,531,240 women tested. All studies reported a confirmatory genetic test. The pooled positive predictive value was 49.4% (95% confidence interval, 45.8-53.1). The pooled positive predictive value was 32.0% (95% confidence interval, 27.0%-37.3%) for monosomy X, 67.6% (95% confidence interval, 62.5%-72.5%) for XXY, 57.5% (95% confidence interval, 51.7%-63.1%) for XXX, and 70.9% (95% confidence interval, 63.9%-77.1%) for XYY. The pooled sensitivity and specificity of cell-free DNA for sex chromosome abnormalities were 94.1% (95% confidence interval, 90.8%-96.3%) and 99.5% (95% confidence interval, 99.0%-99.7%), respectively, with an area under the summary receiver operating characteristic curve of 0.934 (95% confidence interval, 0.907-0.989). CONCLUSION Although the sensitivity and specificity of cell-free DNA for sex chromosome abnormalities are high, the positive predictive value was approximately 50%. The positive predictive value was higher for sex chromosome abnormalities with a supernumerary Y chromosome and lower for monosomy X. Clinicians should inform couples about these findings when offering cell-free DNA for sex chromosome abnormalities.
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Affiliation(s)
- Sofia Bussolaro
- Department of Medicine, Surgery, and Health Sciences, University of Trieste, Trieste, Italy (Dr Bussolaro)
| | - Yvette C Raymond
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Australia (Ms Raymond and Dr Rolnik)
| | - Melissa L Acreman
- Department of Obstetrics and Gynaecology, Ipswich Hospital, Queensland, Australia (Dr Acreman)
| | - Maurizio Guido
- Obstetrics and Gynaecology Unit, San Salvatore Hospital, L'Aquila, Italy (XX Guido and Dr Fantasia); Department of Life, Health, and Environmental Sciences, University of L'Aquila, L'Aquila, Italy (XX Guido)
| | - Fabricio Da Silva Costa
- Maternal Fetal Medicine Unit, Gold Coast University Hospital, Gold Coast, Queensland, Australia (Dr Da Silva Costa); School of Medicine, Griffith University, Gold Coast, Queensland, Australia (Dr Da Silva Costa)
| | - Daniel L Rolnik
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Australia (Ms Raymond and Dr Rolnik); Monash Women's, Monash Health, Clayton, Australia (Dr Rolnik)
| | - Ilaria Fantasia
- Obstetrics and Gynaecology Unit, San Salvatore Hospital, L'Aquila, Italy (XX Guido and Dr Fantasia).
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Wang H, Liang B, Wang Y, Huang H, Lin N, Xu L. Retrospective analysis of the sex chromosomal copy number variations in 186 fetuses using single nucleotide polymorphism arrays. Front Genet 2022; 13:997757. [DOI: 10.3389/fgene.2022.997757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Sex chromosomal abnormalities are associated with multiple defects. However, the types of sex chromosomal abnormalities during pregnancy in Fujian Province, China, are not recorded. In this retrospective analysis, we showed the sex chromosomal abnormalities of 186 fetuses, including 162 cases of X chromosomal abnormalities and 22 cases of Y chromosomal abnormalities in Fujian Province. We detected 73 cases of Turner syndrome, 24 cases of triple X syndrome, 37 cases of Klinefelter syndrome, and 14 cases of XYY syndrome. It was observed that 67.3% fetuses with classic Turner syndrome had their growth arrested. Moreover, we found 21 cases of mosaic Turner syndrome, 3 cases of mosaic Triple X syndrome, 2 cases of mosaic Klinefelter syndrome, and 1 case of mosaic XYY syndrome. Furthermore, 37 cases of large scales of sex chromosomal deletions/duplications were detected, including 30 cases of X chromosomal deletions/duplications and 7 cases of Y chromosomal deletions/duplications. Parent-of-origins of five cases of sex chromosomal deletions/duplications were determined. One case was with de novo X chromosomal variations, while the sex chromosomal deletions/duplications in other four cases were inherited from their parents. Overall, our results presented a detailed manifestation of sex chromosomal abnormalities of 186 fetuses in Fujian Province and suggested the important roles of single nucleotide polymorphism (SNP) array analysis in the prenatal diagnosis of sex chromosomal abnormalities. Also, determining the parent-of-origins of the deletions/duplications was critical for the prenatal diagnosis of sex chromosomal abnormalities.
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Xu C, Li J, Chen S, Cai X, Jing R, Qin X, Pan D, Zhao X, Ma D, Xu X, Liu X, Wang C, Yang B, Zhang L, Li S, Chen Y, Pan N, Tang P, Song J, Liu N, Zhang C, Zhang Z, Qiu X, Lu W, Ying C, Li X, Xu C, Wang Y, Wu Y, Huang HF, Zhang J. Genetic deconvolution of fetal and maternal cell-free DNA in maternal plasma enables next-generation non-invasive prenatal screening. Cell Discov 2022; 8:109. [PMID: 36229437 PMCID: PMC9562363 DOI: 10.1038/s41421-022-00457-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/09/2022] [Indexed: 11/09/2022] Open
Abstract
Current non-invasive prenatal screening (NIPS) analyzes circulating fetal cell-free DNA (cfDNA) in maternal peripheral blood for selected aneuploidies or microdeletion/duplication syndromes. Many genetic disorders are refractory to NIPS largely because the maternal genetic material constitutes most of the total cfDNA present in the maternal plasma, which hinders the detection of fetus-specific genetic variants. Here, we developed an innovative sequencing method, termed coordinative allele-aware target enrichment sequencing (COATE-seq), followed by multidimensional genomic analyses of sequencing read depth, allelic fraction, and linked single nucleotide polymorphisms, to accurately separate the fetal genome from the maternal background. Analytical confounders including multiple gestations, maternal copy number variations, and absence of heterozygosity were successfully recognized and precluded for fetal variant analyses. In addition, fetus-specific genomic characteristics, including the cfDNA fragment length, meiotic error origins, meiotic recombination, and recombination breakpoints were identified which reinforced the fetal variant assessment. In 1129 qualified pregnancies tested, 54 fetal aneuploidies, 8 microdeletions/microduplications, and 8 monogenic variants were detected with 100% sensitivity and 99.3% specificity. Using the comprehensive cfDNA genomic analysis tools developed, we found that 60.3% of aneuploidy samples had aberrant meiotic recombination providing important insights into the mechanism underlying meiotic nondisjunctions. Altogether, we show that the genetic deconvolution of the fetal and maternal cfDNA enables thorough and accurate delineation of fetal genome which paves the way for the next-generation prenatal screening of essentially all types of human genetic disorders.
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Affiliation(s)
- Chenming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Jianli Li
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Songchang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaoqiang Cai
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Ruilin Jing
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiaomei Qin
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Dong Pan
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xin Zhao
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Dongyang Ma
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiufeng Xu
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiaojun Liu
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Can Wang
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Bingxin Yang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lanlan Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuyuan Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yiyao Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Nina Pan
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Tang
- Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang, China
| | - Jieping Song
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Nian Liu
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Chen Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiwei Zhang
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiang Qiu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Weiliang Lu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chunmei Ying
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xiaotian Li
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Congjian Xu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yanlin Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanting Wu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.
| | - He-Feng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China. .,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China.
| | - Jinglan Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,Beijing BioBiggen Technology Co., Ltd, Beijing, China.
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12
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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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13
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Mossfield T, Soster E, Menezes M, Agenbag G, Dubois ML, Gekas J, Hardy T, Jurkowska M, Kleinfinger P, Loggenberg K, Marchili P, Sirica R. Multisite assessment of the impact of cell-free DNA-based screening for rare autosomal aneuploidies on pregnancy management and outcomes. Front Genet 2022; 13:975987. [PMID: 36105088 PMCID: PMC9465083 DOI: 10.3389/fgene.2022.975987] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022] Open
Abstract
Cell-free (cf) DNA screening is a noninvasive prenatal screening approach that is typically used to screen for common fetal trisomies, with optional screening for sex chromosomal aneuploidies and fetal sex. Genome-wide cfDNA screening can screen for a wide variety of additional anomalies, including rare autosomal aneuploidies (RAAs) and copy number variants. Here, we describe a multi-cohort, global retrospective study that looked at the clinical outcomes of cases with a high-risk cfDNA screening result for a RAA. Our study cohort included a total of 109 cases from five different sites, with diagnostic outcome information available for 68% (74/109) of patients. Based on confirmatory diagnostic testing, we found a concordance rate of 20.3% for presence of a RAA (15/74) in our study population. Pregnancy outcome was also available for 77% (84/109) of cases in our cohort. Many of the patients experienced adverse pregnancy outcomes, including intrauterine fetal demise, fetal growth restriction, and preterm birth. These adverse outcomes were observed both in patients with fetal or placental confirmation of the presence of a RAA, as well as patients that did not undergo fetal and/or placental diagnostic testing. In addition, we have proposed some suggestions for pregnancy management and counseling considerations for situations where a RAA is noted on a cfDNA screen. In conclusion, our study has shown that genome-wide cfDNA screening for the presence of rare autosomal aneuploidies can be beneficial for both patients and their healthcare practitioners. This can provide a possible explanation for an adverse pregnancy outcome or result in a change in pregnancy management, such as increased monitoring for adverse outcomes.
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Affiliation(s)
| | - Erica Soster
- Labcorp Women’s Health and Genetics, Laboratory Corporation of America, San Diego, CA, United States
| | - Melody Menezes
- Monash IVF Genetics, Monash IVF Group, Richmond, VIC, Australia
| | | | | | - Jean Gekas
- CHU de Quebec Research and Mother and Child Center, Department of Medical Genetics, University Hospital of Quebec, Laval University, Quebec City, QC, Canada
| | - Tristan Hardy
- Monash IVF Genetics, Monash IVF Group, Richmond, VIC, Australia
| | | | | | | | | | - Roberto Sirica
- AMES, Centro Polidiagnostico Strumentale, Srl, Naples, Italy
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14
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Genovese G, Mello CJ, Loh PR, Handsaker RE, Kashin S, Whelan CW, Bayer-Zwirello LA, McCarroll SA. Chromosomal phase improves aneuploidy detection in non-invasive prenatal testing at low fetal DNA fractions. Sci Rep 2022; 12:12025. [PMID: 35835769 PMCID: PMC9283487 DOI: 10.1038/s41598-022-14049-5] [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: 01/20/2022] [Accepted: 05/31/2022] [Indexed: 11/09/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) to detect fetal aneuploidy by sequencing the cell-free DNA (cfDNA) in maternal plasma is being broadly adopted. To detect fetal aneuploidies from maternal plasma, where fetal DNA is mixed with far-larger amounts of maternal DNA, NIPT requires a minimum fraction of the circulating cfDNA to be of placental origin, a level which is usually attained beginning at 10 weeks gestational age. We present an approach that leverages the arrangement of alleles along homologous chromosomes—also known as chromosomal phase—to make NIPT analyses more conclusive. We validate our approach with in silico simulations, then re-analyze data from a pregnant mother who, due to a fetal DNA fraction of 3.4%, received an inconclusive aneuploidy determination through NIPT. We find that the presence of a trisomy 18 fetus can be conclusively inferred from the patient’s same molecular data when chromosomal phase is incorporated into the analysis. Key to the effectiveness of our approach is the ability of homologous chromosomes to act as natural controls for each other and the ability of chromosomal phase to integrate subtle quantitative signals across very many sequence variants. These results show that chromosomal phase increases the sensitivity of a common laboratory test, an idea that could also advance cfDNA analyses for cancer detection.
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Affiliation(s)
- Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Curtis J Mello
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Po-Ru Loh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Robert E Handsaker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Seva Kashin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Christopher W Whelan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lucy A Bayer-Zwirello
- Steward St. Elizabeth's Medical Center, Tufts University School of Medicine, Boston, MA, 02135, USA
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
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15
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Li J, Lu J, Su F, Yang J, Ju J, Lin Y, Xu J, Qi Y, Hou Y, Wu J, He W, Yang Z, Wu Y, Tang Z, Huang Y, Zhang G, Yang Y, Long Z, Cheng X, Liu P, Xia J, Zhang Y, Wang Y, Chen F, Zhang J, Zhao L, Jin X, Gao Y, Yin A. Non-Invasive Prenatal Diagnosis of Monogenic Disorders Through Bayesian- and Haplotype-Based Prediction of Fetal Genotype. Front Genet 2022; 13:911369. [PMID: 35846127 PMCID: PMC9283829 DOI: 10.3389/fgene.2022.911369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 06/13/2022] [Indexed: 12/02/2022] Open
Abstract
Background: Non-invasive prenatal diagnosis (NIPD) can identify monogenic diseases early during pregnancy with negligible risk to fetus or mother, but the haplotyping methods involved sometimes cannot infer parental inheritance at heterozygous maternal or paternal loci or at loci for which haplotype or genome phasing data are missing. This study was performed to establish a method that can effectively recover the whole fetal genome using maternal plasma cell-free DNA (cfDNA) and parental genomic DNA sequencing data, and validate the method’s effectiveness in noninvasively detecting single nucleotide variations (SNVs), insertions and deletions (indels). Methods: A Bayesian model was developed to determine fetal genotypes using the plasma cfDNA and parental genomic DNA from five couples of healthy pregnancy. The Bayesian model was further integrated with a haplotype-based method to improve the inference accuracy of fetal genome and prediction outcomes of fetal genotypes. Five pregnancies with high risks of monogenic diseases were used to validate the effectiveness of this haplotype-assisted Bayesian approach for noninvasively detecting indels and pathogenic SNVs in fetus. Results: Analysis of healthy fetuses led to the following accuracies of prediction: maternal homozygous and paternal heterozygous loci, 96.2 ± 5.8%; maternal heterozygous and paternal homozygous loci, 96.2 ± 1.4%; and maternal heterozygous and paternal heterozygous loci, 87.2 ± 4.7%. The respective accuracies of predicting insertions and deletions at these types of loci were 94.6 ± 1.9%, 80.2 ± 4.3%, and 79.3 ± 3.3%. This approach detected pathogenic single nucleotide variations and deletions with an accuracy of 87.5% in five fetuses with monogenic diseases. Conclusions: This approach was more accurate than methods based only on Bayesian inference. Our method may pave the way to accurate and reliable NIPD.
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Affiliation(s)
- Jia Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Shijiazhuang BGI Genomics, Shijiazhuang, China
| | - Jiaqi Lu
- Medical Genetics Centre, Guangdong Women and Children’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Fengxia Su
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
| | - Jiexia Yang
- Prenatal Diagnosis Centre, Guangdong Women and Children’s Hospital, Guangzhou, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children’s Hospital, Guangzhou, China
| | - Jia Ju
- BGI-Shenzhen, Shenzhen, China
| | - Yu Lin
- BGI-Shenzhen, Shenzhen, China
| | | | - Yiming Qi
- Prenatal Diagnosis Centre, Guangdong Women and Children’s Hospital, Guangzhou, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children’s Hospital, Guangzhou, China
| | - Yaping Hou
- Prenatal Diagnosis Centre, Guangdong Women and Children’s Hospital, Guangzhou, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children’s Hospital, Guangzhou, China
| | - Jing Wu
- Prenatal Diagnosis Centre, Guangdong Women and Children’s Hospital, Guangzhou, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children’s Hospital, Guangzhou, China
| | - Wei He
- Prenatal Diagnosis Centre, Guangdong Women and Children’s Hospital, Guangzhou, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children’s Hospital, Guangzhou, China
| | - Zhengtao Yang
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Yujing Wu
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
| | - Zhuangyuan Tang
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
| | - Yingping Huang
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
| | - Guohong Zhang
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
| | - Ying Yang
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
| | | | | | | | - Jun Xia
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | - Jianguo Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Shijiazhuang BGI Genomics, Shijiazhuang, China
| | - Lijian Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Shijiazhuang BGI Genomics, Shijiazhuang, China
- College of Medical Technology, Hebei Medical University, Shijiazhuang, China
- *Correspondence: Lijian Zhao, ; Xin Jin, ; Ya Gao, ; Aihua Yin,
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, China
- *Correspondence: Lijian Zhao, ; Xin Jin, ; Ya Gao, ; Aihua Yin,
| | - Ya Gao
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
- *Correspondence: Lijian Zhao, ; Xin Jin, ; Ya Gao, ; Aihua Yin,
| | - Aihua Yin
- Prenatal Diagnosis Centre, Guangdong Women and Children’s Hospital, Guangzhou, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children’s Hospital, Guangzhou, China
- *Correspondence: Lijian Zhao, ; Xin Jin, ; Ya Gao, ; Aihua Yin,
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16
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Mohan P, Lemoine J, Trotter C, Rakova I, Billings P, Peacock S, Kao C, Wang Y, Xia F, Eng CM, Benn P. Clinical experience with non-invasive prenatal screening for single-gene disorders. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2022; 59:33-39. [PMID: 34358384 PMCID: PMC9302116 DOI: 10.1002/uog.23756] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 05/10/2023]
Abstract
OBJECTIVE To assess the performance of a non-invasive prenatal screening test (NIPT) for a panel of dominant single-gene disorders (SGD) with a combined population incidence of 1 in 600. METHODS Cell-free fetal DNA isolated from maternal plasma samples accessioned from 14 April 2017 to 27 November 2019 was analyzed by next-generation sequencing, targeting 30 genes, to look for pathogenic or likely pathogenic variants implicated in 25 dominant conditions. The conditions included Noonan spectrum disorders, skeletal disorders, craniosynostosis syndromes, Cornelia de Lange syndrome, Alagille syndrome, tuberous sclerosis, epileptic encephalopathy, SYNGAP1-related intellectual disability, CHARGE syndrome, Sotos syndrome and Rett syndrome. NIPT-SGD was made available as a clinical service to women with a singleton pregnancy at ≥ 9 weeks' gestation, with testing on maternal and paternal genomic DNA to assist in interpretation. A minimum of 4.5% fetal fraction was required for test interpretation. Variants identified in the mother were deemed inconclusive with respect to fetal carrier status. Confirmatory prenatal or postnatal diagnostic testing was recommended for all screen-positive patients and follow-up information was requested. The screen-positive rates with respect to the clinical indication for testing were evaluated. RESULTS A NIPT-SGD result was available for 2208 women, of which 125 (5.7%) were positive. Elevated test-positive rates were observed for referrals with a family history of a disorder on the panel (20/132 (15.2%)) or a primary indication of fetal long-bone abnormality (60/178 (33.7%)), fetal craniofacial abnormality (6/21 (28.6%)), fetal lymphatic abnormality (20/150 (13.3%)) or major fetal cardiac defect (4/31 (12.9%)). For paternal age ≥ 40 years as a sole risk factor, the test-positive rate was 2/912 (0.2%). Of the 125 positive cases, follow-up information was available for 67 (53.6%), with none classified as false-positive. No false-negative cases were identified. CONCLUSIONS NIPT can assist in the early detection of a set of SGD, particularly when either abnormal ultrasound findings or a family history is present. Additional clinical studies are needed to evaluate the optimal design of the gene panel, define target populations and assess patient acceptability. NIPT-SGD offers a safe and early prenatal screening option. © 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)
| | | | | | | | | | | | | | - Y. Wang
- Baylor GeneticsHoustonTXUSA
- Baylor College of MedicineHoustonTXUSA
| | - F. Xia
- Baylor GeneticsHoustonTXUSA
- Baylor College of MedicineHoustonTXUSA
| | - C. M. Eng
- Baylor GeneticsHoustonTXUSA
- Baylor College of MedicineHoustonTXUSA
| | - P. Benn
- Department of Genetics and Genome SciencesUniversity of Connecticut Health CenterFarmingtonCTUSA
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17
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Wang C, Tang J, Tong K, Huang D, Tu H, Li Q, Zhu J. Expanding the application of non-invasive prenatal testing in the detection of foetal chromosomal copy number variations. BMC Med Genomics 2021; 14:292. [PMID: 34895207 PMCID: PMC8666043 DOI: 10.1186/s12920-021-01131-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
Purpose The aim of this study was to assess the detection efficiency and clinical application value of non-invasive prenatal testing (NIPT) for foetal copy number variants (CNVs) in clinical samples from 39,002 prospective cases. Methods A total of 39,002 pregnant women who received NIPT by next-generation sequencing (NGS) with a sequencing depth of 6 M reads in our centre from January 2018 to April 2020 were enrolled. Chromosomal microarray analysis (CMA) was further used to diagnose suspected chromosomal aneuploidies and chromosomal microdeletion/microduplication for consistency assessment. Results A total of 473 pregnancies (1.213%) were positive for clinically significant foetal chromosome abnormalities by NIPT. This group comprised 99 trisomy 21 (T21, 0.254%), 30 trisomy 18 (T18, 0.077%), 25 trisomy 13 (T13, 0.064%), 155 sex chromosome aneuploidy (SCA, 0.398%), 69 rare trisomy (0.177%), and 95 microdeletion/microduplication syndrome (MMS, 0.244%) cases. Based on follow-up tests, the positive predictive values (PPVs) for the T21, T18, T13, SCA, rare trisomy, and MMS cases were calculated to be 88.89%, 53.33%, 20.00%, 40.22%, 4.88%, and 49.02%, respectively. In addition, the PPVs of CNVs of < 5 Mb, 5–10 Mb, and > 10 Mb were 54.55%, 38.46%, and 40.00%, respectively. Among the 95 cases with suspected CNVs, 25 were diagnosed as true positive and 26 cases as false positive; follow-up prenatal diagnosis by CMA was not performed for 44 cases. Moreover, among the 25 true positive cases, 10 were pathogenic, 3 were likely pathogenic, and 12 were of uncertain significance. Conclusion NIPT is not only suitable for screening T21, T18, T13, and SCA but also has potential significance for CNV detection. As combined with ultrasound, extended NIPT is effective for screening MMS. However, NIPT should not be recommended for whole-chromosome aneuploidy screening.
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Affiliation(s)
- Chaohong Wang
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Junxiang Tang
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Keting Tong
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Daoqi Huang
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Huayu Tu
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Qingnan Li
- Beijing Genomics Institute, Beijing, China
| | - Jiansheng Zhu
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Maternity and Child Health Hospital of Anhui Province, Hefei, China.
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18
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Jeppesen LD, Hatt L, Singh R, Schelde P, Andreasen L, Markholt S, Lildballe DL, Vogel I. Screening for Fetal Aneuploidy and Sex Chromosomal Anomalies in a Pregnant Woman With Mosaicism for Turner Syndrome-Applications and Advantages of Cell-Based NIPT. Front Genet 2021; 12:741752. [PMID: 34594364 PMCID: PMC8476991 DOI: 10.3389/fgene.2021.741752] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Cell-free NIPT and cell-based NIPT are risk-free testing options using maternal blood samples to screen for fetal aneuploidies, but the methods differ. For cell-free NIPT, the fetal fraction of cell-free DNA in plasma is analyzed with a high background of maternal DNA. In contrast, for cell-based NIPT, a limited number of the rare, intact fetal cells are isolated for the genetic analysis. This case demonstrates the differences regarding testing for fetal sex-chromosomes anomalies (SCAs) between these two tests. Materials and Methods: A pregnant woman with mosaicism for Turner syndrome opted for NIPT in first trimester. For the cell-free NIPT analysis, DNA extraction, genome-wide massive parallel sequencing, and data analysis were carried out as described by the kit manufacturer (Illumina©, San Diego, CA, USA). For cell-based NIPT, the first sample gave no result, but the woman consented to repeat cell-based NIPT. After whole genome amplification and STR analysis, fetal DNA from three individual fetal cells was subjected to chromosomal microarray (aCGH, Agilent oligoarray, 180 kb). Results: Fetal fraction was 7%, and cell-free NIPT showed 2 copies of chromosomes 13, 18, and 21 and a decreased proportion of chromosome X, suggestive of fetal Turner syndrome. In contrast, the cell-based NIPT result showed no aneuploidy and two X-chromosomes in the fetus. Conclusion: cell-based NIPT may provide a non-invasive testing option to screen for SCAs in women with mosaicism for monosomy-X in blood, where cell-free NIPT cannot discriminate whether the X-loss is maternal or fetal.
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Affiliation(s)
- Line Dahl Jeppesen
- ARCEDI Biotech, Vejle, Denmark.,Department of Clinical Medicine, Center for Fetal Diagnostics, Aarhus University, Aarhus, Denmark
| | | | | | | | - Lotte Andreasen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Sara Markholt
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Dorte L Lildballe
- Department of Clinical Medicine, Center for Fetal Diagnostics, Aarhus University, Aarhus, Denmark.,Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Ida Vogel
- Department of Clinical Medicine, Center for Fetal Diagnostics, Aarhus University, Aarhus, Denmark.,Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
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19
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Calculation of Fetal Fraction for Non-Invasive Prenatal Testing. BIOTECH 2021; 10:biotech10030017. [PMID: 35822771 PMCID: PMC9245487 DOI: 10.3390/biotech10030017] [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: 06/13/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/05/2022] Open
Abstract
Estimating the fetal fraction of DNA in a pregnant mother’s blood is a risk-free, non-invasive way of predicting fetal aneuploidy. It is a rapidly developing field of study, offering researchers a plethora of different complementary methods. Such methods include examining the differences in methylation profiles between the fetus and the mother. Others include calculating the average allele frequency based on the difference in genotype of a number of single-nucleotide polymorphisms. Differences in the length distribution of DNA fragments between the mother and the fetus as well as measuring the proportion of DNA reads mapping to the Y chromosome also constitute fetal fraction estimation methods. The advantages and disadvantages of each of these main method types are discussed. Moreover, several well-known fetal fraction estimation methods, such as SeqFF, are described and compared with other methods. These methods are amenable to not only the estimation of fetal fraction but also paternity, cancer, and transplantation monitoring studies. NIPT is safe, and should aneuploidy be detected, this information can help parents prepare mentally and emotionally for the birth of a special needs child.
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Luo Y, Hu H, Zhang R, Ma Y, Pan Y, Long Y, Hu B, Yao H, Liang Z. An assessment of the analytical performance of non-invasive prenatal testing (NIPT) in detecting sex chromosome aneuploidies: 34,717-patient sample in a single prenatal diagnosis Centre in China. J Gene Med 2021; 23:e3362. [PMID: 33973298 DOI: 10.1002/jgm.3362] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/29/2021] [Accepted: 04/21/2021] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVE The present study aimed to evaluate the efficacy of a non-invasive prenatal test (NIPT) in the detection of the sex chromosome aneuploidies (SCAs) at our prenatal diagnosis centre. METHODS Among a cohort of 34,717 pregnancies, maternal plasma samples from our prenatal diagnosis centre were subject to analysis of SCAs using NIPT detection. Pregnant women with NIPT positive results of SCAs were recommended to undergo an invasive prenatal diagnosis (i.e. karyotyping and fluorescence in situ hybridization) to validate the prediction value of NIPT. RESULTS From 34,717 clinical pregnancies, 229 (0.66%) pregnancies were identified with SCAs. Of these, 78 (34.1%) cases were positive for 45,X and 151 (65.9%) cases comprised a sex chromosome trisomy. Of the 229 positive NIPT results, 193 (84.3%) cases had accepted an invasive diagnosis involving karyotyping analysis of the amniotic fluid, which confirmed 67 cases (34.7%) as true positive, as well as 126 cases (65.3%) as false positive. The positive predictive values were 23.07%, 50%, 36% and 27.27% respectively. The remaining 36 (15.7%) cases declined a prenatal diagnosis. The termination rates of 45,X, 47,XXY, 47,XXX and 47,XYY were 20.5%,46%,12.9% and 11.5% respectively. CONCLUSIONS NIPT demonstrated a lower accuracy in predicting monosomy X than sex chromosome trisomies. After invasive testing, the fetal chromosome with 45,X and 47,XXY were terminated more often than those with 47,XXX, 47,XYY. Because NIPT is a screening test, false positive/negative cases exist, and pre- and post-test counselling is essential for informing patients about the benefits and limitations of the test. Confirmatory testing of abnormal results is recommended prenatally or after birth, and the importance of confirmatory testing and benefits of early diagnosis should be addressed.
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Affiliation(s)
- Yanmei Luo
- Department of Gynecology & Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Huamei Hu
- Department of Gynecology & Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Rong Zhang
- Department of Gynecology & Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yongyi Ma
- Department of Gynecology & Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yan Pan
- Department of Gynecology & Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yang Long
- Department of Gynecology & Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Bin Hu
- Department of Gynecology & Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Hong Yao
- Department of Gynecology & Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhiqing Liang
- Department of Gynecology & Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
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Ge Y, Li J, Zhuang J, Zhang J, Huang Y, Tan M, Li W, Chen J, Zhou Y. Expanded noninvasive prenatal testing for fetal aneuploidy and copy number variations and parental willingness for invasive diagnosis in a cohort of 18,516 cases. BMC Med Genomics 2021; 14:106. [PMID: 33853619 PMCID: PMC8045328 DOI: 10.1186/s12920-021-00955-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/01/2021] [Indexed: 12/05/2022] Open
Abstract
Background Noninvasive prenatal testing (NIPT) has been wildly used to screen for common aneuplodies. In recent years, the test has been expanded to detect rare autosomal aneuploidies (RATs) and copy number variations (CNVs). This study was performed to investigate the performance of expanded noninvasive prenatal testing (expanded NIPT) in screening for common trisomies, sex chromosomal aneuploidies (SCAs), rare autosomal aneuploidies (RATs), and copy number variations (CNVs) and parental willingness for invasive prenatal diagnosis in a Chinese prenatal diagnosis center. Methods A total of 24,702 pregnant women were retrospectively analyzed at the Women and Children’s Hospital from January 2013 to April 2019, among which expanded NIPT had been successfully conducted in 24,702 pregnant women. The high-risk expanded NIPT results were validated by karyotype analysis and chromosomal microarray analysis. All the tested pregnant women were followed up for pregnancy outcomes. Results Of the 24,702 cases, successful follow-up was conducted in 98.77% (401/446) of cases with common trisomies and SCAs, 91.95% (80/87) of RAT and CNV cases, and 76.25% (18,429/24,169) of cases with low-risk screening results. The sensitivity of expanded NIPT was 100% (95% confidence interval[CI], 97.38–100%), 96.67%(95%CI, 82.78–99.92%), and 100%(95%CI, 66.37–100.00%), and the specificity was 99.92%(95%CI, 99.87–99.96%), 99.96%(95%CI, 99.91–99.98%), and 99.88% (95%CI, 99.82–99.93%) for the detection of trisomies 21, 18, and 13, respectively. Expanded NIPT detected 45,X, 47,XXX, 47,XXY, XYY syndrome, RATs, and CNVs with positive predictive values of 25.49%, 75%, 94.12%, 76.19%, 6.45%, and 50%, respectively. The women carrying fetuses with Trisomy 21/Trisomy 18/Trisomy 13 underwent invasive prenatal diagnosis and terminated their pregnancies at higher rates than those at high risk for SCAs, RATs, and CNVs. Conclusions Our study demonstrates that the expanded NIPT detects fetal trisomies 21, 18, and 13 with high sensitivity and specificity. The accuracy of detecting SCAs, RATs, and CNVs is still relatively poor and needs to be improved. With a high-risk expanded NIPT result, the women at high risk for common trisomies are more likely to undergo invasive prenatal diagnosis procedures and terminate their pregnancies than those with unusual chromosome abnormalities. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-00955-6.
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Affiliation(s)
- Yunsheng Ge
- Prenatal Diagnosis Center, Women and Children's Hospital, School of Medicine, Xiamen University, 10 Zhenhai Road, Xiamen, 361003, Fujian Province, China
| | - Jia Li
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong Province, China
| | - Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian Province, China
| | - Jian Zhang
- Prenatal Diagnosis Center, Women and Children's Hospital, School of Medicine, Xiamen University, 10 Zhenhai Road, Xiamen, 361003, Fujian Province, China
| | - Yanru Huang
- Prenatal Diagnosis Center, Women and Children's Hospital, School of Medicine, Xiamen University, 10 Zhenhai Road, Xiamen, 361003, Fujian Province, China
| | - Meihua Tan
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong Province, China
| | - Wei Li
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong Province, China
| | - Jiayan Chen
- Prenatal Diagnosis Center, Women and Children's Hospital, School of Medicine, Xiamen University, 10 Zhenhai Road, Xiamen, 361003, Fujian Province, China
| | - Yulin Zhou
- Prenatal Diagnosis Center, Women and Children's Hospital, School of Medicine, Xiamen University, 10 Zhenhai Road, Xiamen, 361003, Fujian Province, China.
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22
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Soukkhaphone B, Lindsay C, Langlois S, Little J, Rousseau F, Reinharz D. Non-invasive prenatal testing for the prenatal screening of sex chromosome aneuploidies: A systematic review and meta-analysis of diagnostic test accuracy studies. Mol Genet Genomic Med 2021; 9:e1654. [PMID: 33755350 PMCID: PMC8172189 DOI: 10.1002/mgg3.1654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 10/31/2020] [Accepted: 02/19/2021] [Indexed: 12/19/2022] Open
Abstract
Background There is little evidence on the performance of non‐invasive prenatal testing (NIPT) for the detection of fetal sex chromosomal imbalances. In this review, we aimed to appraise and synthesize the literature on the performance of NIPT for the prenatal detection of fetal sex chromosome aneuploidies. Methods We performed our literature search in PubMed, Embase, Cochrane Library, Web of Science, and CADTH. Study selection and data extraction were performed by two reviewers independently. There were no restrictions on the study population. Meta‐analyses were performed with “R” software. Pooled sensitivities and specificities with their 95% CI were estimated using a random‐effects model. Heterogeneity between studies was assessed by a Q test. Results Based on 11 studies in high prior risk pregnancies, including 116 affected fetuses in aggregate, Massively Parallel Shotgun Sequencing (MPSS) had a sensitivity of 93.9% (95% CI 84.1%, 97.8%) and a specificity of 99.6% (95% CI 98.7%, 99.9%) for the detection of 45,X. Based on four studies in high‐risk pregnancies, with 83 affected fetuses in aggregate, Targeted Massively Parallel Sequencing (TMPS) had a sensitivity of 83.2% (95% CI 49.6%, 96.2%) and specificity was 99.8% (95% CI 98.3%, 100%) for the detection of 45,X. In mixed‐risk pregnancies, the sensitivity of TMPS for the detection of 45,X was 90.9% (2 studies; 95% CI 70%, 97.7%) and specificity 99.9% (2 studies; 95% CI 99.4%, 100%); MPSS data were not available in such pregnancies. Based on smaller numbers of studies, and small numbers of affected fetuses in either high‐risk or mixed‐risk pregnancies (using either MPSS or TMPS), the sensitivities and specificities were equal to or greater than 76.2% for 47,XXX, 47,XXY and 47, XYY. The test failures for SCAs were 0.2% (95% CI 0%, 13.6%) for MPSS and 5.6% (95% CI 3.7%, 8.4%) for TMPS. Conclusion High‐quality studies are still desirable in order to estimate the performance of NIPT for the detection of sex chromosome imbalances.
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Affiliation(s)
| | - Carmen Lindsay
- CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada
| | | | | | - Francois Rousseau
- Laval University, Quebec City, QC, Canada.,Hôpital Saint-François d'Assise, Quebec, QC, Canada
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23
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Riggan KA, Gross B, Close S, Weinberg A, Allyse MA. Prenatal Genetic Diagnosis of a Sex Chromosome Aneuploidy: Parent Experiences. J Genet Couns 2021; 30:1407-1417. [PMID: 33723878 DOI: 10.1002/jgc4.1407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 02/06/2023]
Abstract
Sex chromosome aneuploidies (SCAs) occur in 1 in every 400 births. SCAs are highly variable and have uncertain prognoses, complicating the delivery of prenatal cell-free DNA (cfDNA) results or diagnosis following amniocentesis or chorionic villus sampling. Using a mixed-methods approach, we explored the experiences of parents receiving a prenatal diagnosis of a fetus with SCA. Responses to open-ended questions were qualitatively analyzed. Of the 323 parents who completed the survey, 122 received a prenatal diagnosis and answered at least one open-ended question. Most parents did not recall being informed that cfDNA screening or amniocentesis could reveal the presence of a SCA prior to testing and described feeling unprepared for a positive result. Variation was found between parents who were delivered a diagnosis by a genetic professional versus other clinical specialties. Many parents expressed that the diagnosis was delivered in a way that emphasized the negative attributes of the SCA and that they were provided limited support materials. Parents who received a prenatal diagnosis of a SCA expressed a desire for more supportive delivery of prenatal diagnosis that focuses on parental education and nuanced discussion of potential phenotypes. Genetic counselors should be aware of the range of parental experiences when receiving a SCA diagnosis from non-genetic providers. Prenatal SCA diagnoses are predicted to increase as prenatal cfDNA screening becomes more widely used. Collaborations for greater provider education and comprehensive materials on SCAs are essential to facilitate the delivery of SCA diagnoses and improve parent understanding and support.
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Affiliation(s)
- Kirsten A Riggan
- Biomedical Ethics Research Program, Mayo Clinic, Rochester, MN, USA
| | - Brianna Gross
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sharron Close
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, USA
| | | | - Megan A Allyse
- Biomedical Ethics Research Program, Mayo Clinic, Rochester, MN, USA
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24
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Choe SA, Seol HJ, Kwon JY, Park CW, Kim M, Lee JY, Kim MA, Hwang HS, Na S, Shim JY, Kim K, Ryu HM. Clinical Practice Guidelines for Prenatal Aneuploidy Screening and Diagnostic Testing from Korean Society of Maternal-Fetal Medicine: (1) Prenatal Aneuploidy Screening. J Korean Med Sci 2021; 36:e27. [PMID: 33496086 PMCID: PMC7834900 DOI: 10.3346/jkms.2021.36.e27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/11/2020] [Indexed: 01/06/2023] Open
Abstract
In 2019, the Korean Society of Maternal-Fetal Medicine developed the first Korean clinical practice guidelines for prenatal aneuploidy screening and diagnostic testing. These guidelines were developed by adapting established clinical practice guidelines in other countries that were searched systematically, and the guidelines aim to assist in decision making of healthcare providers providing prenatal care and to be used as a source for education and communication with pregnant women in Korea. This article delineates clinical practice guidelines specifically for maternal serum screening for fetal aneuploidy and cell-free DNA (cfDNA) screening. A total of 19 key questions (12 for maternal serum and 7 for cfDNA screening) were defined. The main recommendations are: 1) Pregnant women should be informed of common fetal aneuploidy that can be detected, risks for chromosomal abnormality according to the maternal age, detection rate and false positive rate for common fetal aneuploidy with each screening test, limitations, as well as the benefits and risks of invasive diagnostic testing, 2) It is ideal to give counseling about prenatal aneuploidy screening and diagnostic testing at the first prenatal visit, and counseling is recommended to be given early in pregnancy, 3) All pregnant women should be informed about maternal serum screening regardless of their age, 4) cfDNA screening can be used for the screening of trisomy 21, 18, 13 and sex-chromosome aneuploidy. It is not recommended for the screening of microdeletion, 5) The optimal timing of cfDNA screening is 10 weeks of gestation and beyond, and 6) cfDNA screening is not recommended for women with multiple gestations. The guideline was reviewed and approved by the Korean Academy of Medical Sciences.
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Affiliation(s)
- Seung Ah Choe
- Department of Preventive Medicine, Korea University College of Medicine, Seoul, Korea
| | - Hyun Joo Seol
- Department of Obstetrics and Gynecology, Kyung Hee University Hospital at Gangdong, Kyung Hee University College of Medicine, Seoul, Korea
| | - Ji Young Kwon
- Department of Obstetrics and Gynecology, College of Medicine,The Catholic University of Korea, Seoul, Korea
| | - Chan Wook Park
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Minhyoung Kim
- Department of Obstetrics and Gynecology, MizMedi Hospital, Seoul, Korea
| | - Ji Yeon Lee
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Korea
| | - Min A Kim
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Han Sung Hwang
- Department of Obstetrics and Gynecology, Research Institute of Medical Science, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
| | - Sunghun Na
- Department of Obstetrics and Gynecology, Kangwon National University Hospital, School of Medicine Kangwon National University, Chuncheon, Korea
| | - Jae Yoon Shim
- Mirae & Heemang Obstetrics and Gynecology Clinic, Seoul, Korea
| | | | - Hyun Mee Ryu
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Korea.
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25
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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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26
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Zitzmann M, Aksglaede L, Corona G, Isidori AM, Juul A, T'Sjoen G, Kliesch S, D'Hauwers K, Toppari J, Słowikowska-Hilczer J, Tüttelmann F, Ferlin A. European academy of andrology guidelines on Klinefelter Syndrome Endorsing Organization: European Society of Endocrinology. Andrology 2020; 9:145-167. [PMID: 32959490 DOI: 10.1111/andr.12909] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 09/13/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND Knowledge about Klinefelter syndrome (KS) has increased substantially since its first description almost 80 years ago. A variety of treatment options concerning the spectrum of symptoms associated with KS exists, also regarding aspects beyond testicular dysfunction. Nevertheless, the diagnostic rate is still low in relation to prevalence and no international guidelines are available for KS. OBJECTIVE To create the first European Academy of Andrology (EAA) guidelines on KS. METHODS An expert group of academicians appointed by the EAA generated a consensus guideline according to the GRADE (Grading of Recommendations, Assessment, Development and Evaluation) system. RESULTS Clinical features are highly variable among patients with KS, although common characteristics are severely attenuated spermatogenesis and Leydig cell impairment, resulting in azoospermia and hypergonadotropic hypogonadism. In addition, various manifestations of neurocognitive and psychosocial phenotypes have been described as well as an increased prevalence of adverse cardiovascular, metabolic and bone-related conditions which might explain the increased morbidity/mortality in KS. Moreover, compared to the general male population, a higher prevalence of dental, coagulation and autoimmune disorders is likely to exist in patients with KS. Both genetic and epigenetic effects due to the supernumerary X chromosome as well as testosterone deficiency contribute to this pathological pattern. The majority of patients with KS is diagnosed during adulthood, but symptoms can already become obvious during infancy, childhood or adolescence. The paediatric and juvenile patients with KS require specific attention regarding their development and fertility. CONCLUSION These guidelines provide recommendations and suggestions to care for patients with KS in various developmental stages ranging from childhood and adolescence to adulthood. This advice is based on recent research data and respective evaluations as well as validations performed by a group of experts.
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Affiliation(s)
- Michael Zitzmann
- Center for Reproductive Medicine and Andrology/Clinical and Surgical Andrology, University Hospital of Münster, Münster, Germany
| | - Lise Aksglaede
- Rigshospitalet, Department of Growth and Reproduction, University of Copenhagen, Copenhagen, Denmark
| | - Giovanni Corona
- Medical Department, Endocrinology Unit, Maggiore Bellaria Hospital, Azienda Usl, Bologna, Italy
| | - Andrea M Isidori
- Department of Experimental Medicine, Advanced Endocrine Diagnostics Unit, Policlinico Umberto I Hospital, Sapienza University of Rome, Rome, Italy
| | - Anders Juul
- Rigshospitalet, Department of Growth and Reproduction, University of Copenhagen, Copenhagen, Denmark
| | - Guy T'Sjoen
- Department of Endocrinology and Center for Sexology and Gender, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Sabine Kliesch
- Center for Reproductive Medicine and Andrology/Clinical and Surgical Andrology, University Hospital of Münster, Münster, Germany
| | - Kathleen D'Hauwers
- Department of Urology, Radboud University Medical Centre Nijmegen, Nijmegen, The Netherlands
| | - Jorma Toppari
- Department of Pediatrics, Institute of Biomedicine, Research Centre for Integrated Physiology and Pharmacology and Centre for Population Health Research, University Hospital, University of Turku, Turku, Finland
| | | | - Frank Tüttelmann
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - Alberto Ferlin
- Department of Clinical and Experimental Sciences, Unit of Endocrinology and Metabolism, University of Brescia and ASST Spedali Civili Brescia, Brescia, Italy
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27
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Smet ME, Scott FP, McLennan AC. Discordant fetal sex on NIPT and ultrasound. Prenat Diagn 2020; 40:1353-1365. [PMID: 32125721 DOI: 10.1002/pd.5676] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 12/21/2022]
Abstract
Prenatal diagnosis of sex discordance is a relatively new phenomenon. Prior to cell-free DNA testing, the diagnosis of a disorder of sexual differentiation was serendipitous, either through identification of ambiguous genitalia at the midtrimester morphology ultrasound or discovery of genotype-phenotype discordance in cases where preimplantation genetic diagnosis or invasive prenatal testing had occurred. The widespread integration of cfDNA testing into modern antenatal screening has made sex chromosome assessment possible from 10 weeks of gestation, and discordant fetal sex is now more commonly diagnosed prenatally, with a prevalence of approximately 1 in 1500-2000 pregnancies. Early detection of phenotype-genotype sex discordance is important as it may indicate an underlying genetic, chromosomal or biochemical condition and it also allows for time-critical postnatal treatment. The aim of this article is to review cfDNA and ultrasound diagnosis of fetal sex, identify possible causes of phenotype-genotype discordance and provide a systematic approach for clinicians when counseling and managing couples in this circumstance.
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Affiliation(s)
- Maria-Elisabeth Smet
- Sydney Ultrasound for Women, Chatswood, New South Wales, Australia.,Department of Obstetrics and Gynaecology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Fergus P Scott
- Sydney Ultrasound for Women, Chatswood, New South Wales, Australia.,Department of Obstetrics and Gynaecology, Royal Hospital for Women, Randwick, New South Wales, Australia
| | - Andrew C McLennan
- Sydney Ultrasound for Women, Chatswood, New South Wales, Australia.,Department of Obstetrics and Gynaecology, Royal North Shore Hospital, St Leonards, New South Wales, Australia.,Discipline of Obstetrics, Gynaecology and Neonatology, The University of Sydney Camperdown, Sydney, New South Wales, Australia
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28
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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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29
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A retrospective analysis the clinic data and follow-up of non-invasive prenatal test in detection of fetal chromosomal aneuploidy in more than 40,000 cases in a single prenatal diagnosis center. Eur J Med Genet 2020; 63:104001. [PMID: 32622960 DOI: 10.1016/j.ejmg.2020.104001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/22/2020] [Accepted: 06/28/2020] [Indexed: 01/07/2023]
Abstract
OBJECTIVE To evaluate the efficacy of non-invasive prenatal test (NIPT) in the detection of chromosomal aneuploidy according to the follow-up information from a single prenatal diagnosis center. METHODS A total of 40,311 cases were retrospectively reviewed. The screening was performed using a BGI protocol, pre-test and post-test genetic counseling was provided, and the pregnancy outcomes were recorded. The results of NIPT and clinical follow-up data were analyzed together with the pregnancy outcomes, confirmatory testing results, and ultrasound findings. RESULTS Of the 40,311cases were includes in the study, successful follow-up was conducted in 468 (1.16%) cases with high risk, 225 (0.56%) cases with rare autosomal trisomy (RAT) and copy number variation (CNV). 39,572 (98.17%) cases with low risk and 623 (1.57%) cases of which were confirmed with adverse pregnancy outcomes. 46 (0.1%) cases with failed tests. Among them, 398 (84.7%) cases with high-risk results chose invasive testing, revealing 198 true positive cases. In cases with RAT and CNV results, 189 cases underwent invasive testing, revealing 5 cases RAT and 4 pathogenic CNVs. CONCLUSIONS NIPT appears to be effective in detecting the fetal chromosomal aneuploidies T21, T18 and SCAs, but it exist false positive/negative cases, unconfirmed high-risk cfDNA results, and the high false positive rate in cases with RAT and CNV results implied the limitations of this screening method. Our study showed the importance to associate cfDNA screening results with clinical follow-up data and provided information that may help with result interpretation, genetic counseling and the decision making in clinic.
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Samura O. Update on noninvasive prenatal testing: A review based on current worldwide research. J Obstet Gynaecol Res 2020; 46:1246-1254. [PMID: 32558079 DOI: 10.1111/jog.14268] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 04/11/2020] [Indexed: 12/25/2022]
Abstract
Eight years have passed since noninvasive prenatal testing (NIPT) was clinically evaluated and data on NIPT for trisomy 21, 18 and 13 were collected. The data revealed that NIPT is more accurate than conventional first-trimester screening. However, there is still insufficient data regarding the clinical use of NIPT results in detecting sex chromosome aneuploidies or whole-genome regions. NIPT is already being used as a clinical screening method globally. However, it is an unconfirmed diagnostic test and the results must be interpreted with caution as they may yield false negatives, false positives or inconclusive results. Therefore, the aim of this review is to highlight the current status of information, including the different methodologies, shortcomings and implications, regarding NIPT after its adoption worldwide. It is important to include genetic counseling when implementing NIPT. Going forward, the knowledge obtained to date, including the associated shortcomings, must be considered in evaluating the effectiveness of NIPT in detecting genetic abnormalities.
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Affiliation(s)
- Osamu Samura
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo, Japan
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Zitzmann M, Rohayem J. Gonadal dysfunction and beyond: Clinical challenges in children, adolescents, and adults with 47,XXY Klinefelter syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:302-312. [PMID: 32415901 DOI: 10.1002/ajmg.c.31786] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 12/12/2022]
Abstract
Klinefelter syndrome (KS) is the most frequent sex chromosomal aneuploidy. The karyotype 47,XXY originates from either paternal or maternal meiotic nondisjunction during gametogenesis. KS males are very likely to exhibit marked gonadal dysfunctions, presenting both in severely attenuated spermatogenesis as well as hypergonadotropic hypogonadism. In addition, neurocognitive and psychosocial impairments, as well as cardiovascular, metabolic and bone disorders are often found in KS and might explain for an increased morbidity/mortality. All conditions in KS are likely to be induced by both gene overdosage effects resulting from supernumerary X-chromosomal genes as well as testosterone deficiency. Notwithstanding, the clinical features are highly variable between KS men. Symptoms can become obvious at infancy, childhood, or adolescence. However, the majority of KS subjects is diagnosed during adulthood. KS adolescents require specific attention regarding pubertal development, in order to exploit their remaining fertility potential and allow for timely and tailored testosterone replacement. The chances for sperm retrieval might decline with age and could be hampered by testosterone replacement; therefore, cryostorage of spermatozoa is an option during adolescence, before the decompensation of endocrine and exocrine testicular functions becomes more overt. Sperm from semen or surgically retrieved, in combination with intracytoplasmic sperm injection enables KS males to become biological fathers of healthy children. The aim of this article is to present the current knowledge on KS, to guide clinical care and to highlight research needs.
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Affiliation(s)
- Michael Zitzmann
- Center for Reproductive Medicine and Andrology/Clinical Andrology, University Clinics Muenster, Muenster, Germany
| | - Julia Rohayem
- Center for Reproductive Medicine and Andrology/Clinical Andrology, University Clinics Muenster, Muenster, Germany
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Panchalee T, Poungvarin N, Amornrit W, Pooliam J, Taluengjit P, Wataganara T. Clinical performance of DNA-based prenatal screening using single-nucleotide polymorphisms approach in Thai women with singleton pregnancy. Mol Genet Genomic Med 2020; 8:e1256. [PMID: 32329244 PMCID: PMC7336763 DOI: 10.1002/mgg3.1256] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/22/2020] [Accepted: 03/24/2020] [Indexed: 12/20/2022] Open
Abstract
Background To review the performance of noninvasive prenatal screening (NIPS) using targeted single‐nucleotide polymorphisms (SNPs) approach in mixed‐risk Thai women. Methods Retrospective analysis of data for detection of trisomy 21 (T21), 18 (T18), 13 (T13), monosomy X (XO), other sex chromosome aneuploidies (SCA), and triploidy/vanishing twins (VT) from a single commercial laboratory. Results Mean (±SD) gestational age and maternal weight were 13.2 (±2.1) weeks and 125.7 (±22.4) pounds, respectively (n = 8,572). From 462/8,572 (5.4%) no‐calls; 1/462 (0.2%) was uninformative SNPs, and 1/462 chose amniocentesis. Redraw settled 323/460 (70%) samples with low fetal fraction (FF); and 8,434/8,572 (98.4%) were finally reportable, with 131 high risks (1.6%). The median (min‐max) FF of reportable (n = 8,434) and unreportable samples (n = 137) samples were 10.5% (2.6–37.9) and 3.8% (1–14.1), respectively (p < .05). Fetal karyotypes were available in 106/131 (80.9%) and 52/138 (37.7%) high risk and repeated no‐calls, respectively. The positive predictive values (PPVs) for T21 (n = 47), T18 (n = 15), T13 (n = 7), XO (n = 8), other SCA (n = 7), and triploidy/VT were 94%, 100%, 58.3%, 66.7%, 70%, and 57.1%, respectively. None of repeated no‐calls had aneuploidies. Conclusion SNP‐based NIPS has high PPVs for T21 and T18. Although the proprietary SNPs library is not population‐specific, uninformative SNPs are uncommon.
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Affiliation(s)
- Tachjaree Panchalee
- Department of Obstetrics and Gynecology, Mahidol University, Bangkok, Thailand
| | | | | | - Julaporn Pooliam
- Division of Clinical Epidemiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Tuangsit Wataganara
- Department of Obstetrics and Gynecology, Mahidol University, Bangkok, Thailand
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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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Zhang B, Zhou Q, Chen Y, Shi Y, Zheng F, Liu J, Yu B. High false‐positive non‐invasive prenatal screening results for sex chromosome abnormalities: Are maternal factors the culprit? Prenat Diagn 2020; 40:463-469. [PMID: 31318441 DOI: 10.1002/pd.5529] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 07/03/2019] [Accepted: 07/15/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Bin Zhang
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| | - Qin Zhou
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| | - Yingping Chen
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| | - Ye Shi
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| | - Fangxiu Zheng
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| | - Jianbing Liu
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
| | - Bin Yu
- Department of Prenatal Diagnosis CenterChangzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University Changzhou China
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Pan M, Yang D, He Y, Han J, Zhen L, Yang YD, Li DZ. Early prenatal detection of triploidy: a 9-year experience in mainland China. J Matern Fetal Neonatal Med 2019; 34:4072-4076. [PMID: 31852294 DOI: 10.1080/14767058.2019.1702963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Objective: In this study, we report the indications for prenatal cytogenetic diagnosis of triploid cases, in an attempt to identify clues to early diagnosis.Study design: This was a retrospective analysis of prenatal cases of triploidy during a 9-year period at mainland China. Clinical data were reviewed for these cases, including maternal demographics, indications for invasive testing, fetal ultrasound findings, and pregnancy outcomes.Results: A total of 22 singleton pregnancies affected with triploid fetuses were detected. The fetal karyotype included 69,XXX (72.7%) and 69,XXY (27.3%). Eighteen cases were identified by the first trimester screening program. One case was missed by maternal cell-free DNA testing, but detected by second trimester anatomy scan. Three cases escaped the first trimester screening and were detected by second trimester anatomy scan.Conclusions: The present study demonstrates that most triploid cases can be diagnosed prenatally during the first trimester. The early asymmetrical fetal growth restriction, structural anomalies, and extremely high risk serum screening result for trisomy 21 or 18 should alert the physicians to the investigation of triploidy.Key Message: Ultrasound-based first-trimester screening plays a major role in early diagnosis of fetal triploidy. Future replacement of routine first-trimester screening by cell-DNA testing might miss the chance of early diagnosis and management of triploid pregnancies.
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Affiliation(s)
- Min Pan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Dan Yang
- Capitalbio Genomics Co., Ltd, Dongguan, China
| | - Yi He
- Prenatal Diagnosis Center, Dongguan Women and Children Healthcare Hospital, Dongguan, China
| | - Jin Han
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Li Zhen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yan-Dong Yang
- Department of Ultrasound, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
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Ioannides M, Achilleos A, Kyriakou S, Kypri E, Loizides C, Tsangaras K, Constantinou L, Koumbaris G, Patsalis PC. Development of a new methylation-based fetal fraction estimation assay using multiplex ddPCR. Mol Genet Genomic Med 2019; 8:e1094. [PMID: 31821748 PMCID: PMC7005606 DOI: 10.1002/mgg3.1094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/17/2019] [Indexed: 01/12/2023] Open
Abstract
Background Non‐invasive prenatal testing (NIPT) for fetal aneuploidies has rapidly been incorporated into clinical practice. Current NGS‐based methods can reliably detect fetal aneuploidies non‐invasively with fetal fraction of at least 4%. Inaccurate fetal fraction assessment can compromise the accuracy of the test as affected samples with low fetal fraction have an increased risk for misdiagnosis. Using a novel set of fetal‐specific differentially methylated regions (DMRs) and methylation sensitive restriction digestion (MSRD), we developed a multiplex ddPCR assay for accurate detection of fetal fraction in maternal plasma. Methods We initially performed MSRD followed by methylation DNA immunoprecipitation (MeDIP) and NGS on fetal and non‐pregnant female tissues to identify fetal‐specific DMRs. DMRs with the highest methylation difference between the two tissues were selected for fetal fraction estimation employing MSRD and multiplex ddPCR. Chromosome Y multiplex ddPCR assay (YMM) was used as a reference standard, to develop our fetal fraction estimation model in male pregnancy samples. Additional 123 samples were tested to examine whether the model is sex dependent and/or ploidy dependent. Results In all, 93 DMRs were identified of which seven were selected for fetal fraction estimation. Statistical analysis resulted in the final model which included four DMRs (FFMM). High correlation with YMM‐based fetal fractions was observed using 85 male pregnancies (r = 0.86 95% CI: 0.80–0.91). The model was confirmed using an independent set of 53 male pregnancies. Conclusion By employing a set of well‐characterized DMRs, we developed a SNP‐, sex‐ and ploidy‐independent methylation‐based multiplex ddPCR assay for accurate fetal fraction estimation.
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Samango-Sprouse CA, Counts DR, Tran SL, Lasutschinkow PC, Porter GF, Gropman AL. Update On The Clinical Perspectives And Care Of The Child With 47,XXY (Klinefelter Syndrome). Appl Clin Genet 2019; 12:191-202. [PMID: 31695472 PMCID: PMC6815760 DOI: 10.2147/tacg.s180450] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
47,XXY (Klinefelter syndrome [KS]) is the most common sex chromosomal aneuploidy (1:660), yet, despite this, only 25% of the males are ever diagnosed. Males with 47,XXY present with characteristic symptoms throughout their lifetime with typical physical and neurodevelopmental manifestations focused in growth, cognitive development, endocrine function, and reproduction. Studies have demonstrated that optimal outcomes are dependent on early detection combined with consistent and targeted neurodevelopmental treatment throughout the lifespan. During infancy and into the preschool years, individuals with 47,XXY commonly face deficits in growth and development in the areas of early hormonal, motor, speech, and behavioral development. As they transition into school, the primary neurodevelopmental concerns include language difficulty, executive dysfunction, behavior, and learning and reading deficits. Adults with 47,XXY often present with taller than average height, low levels of fertility, azoospermia, and elevated gonadotropin levels. These presentations may persist from early childhood through adulthood but can be mitigated by appropriate interventions. Early neurodevelopmental and hormonal treatment has been shown to have a minimizing effect on the physical and neurodevelopmental manifestations in individuals with 47,XXY. With innovative and current research studies, the features common to the neurodevelopmental profile of 47,XXY have been further expanded and defined. Further research is necessary to elucidate and understand the relationship between the brain, behavior, and the phenotypic profile of 47,XXY.
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Affiliation(s)
- Carole A Samango-Sprouse
- Department of Pediatrics, George Washington University, Washington, DC, USA
- Department of Human and Molecular Genetics, Florida International University, Miami, FL, USA
- The Focus Foundation, Davidsonville, MD, USA
| | - Debra R Counts
- Pediatric Endocrinology, Sinai Hospital, Baltimore, MD, USA
| | | | | | | | - Andrea L Gropman
- Department of Neurology, George Washington University, Washington, DC, USA
- Division of Neurogenetics and Developmental Pediatrics, Children’s National Medical Center, Washington, DC, USA
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38
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Clinical utility of noninvasive prenatal screening for expanded chromosome disease syndromes. Genet Med 2019; 21:1998-2006. [PMID: 30828085 DOI: 10.1038/s41436-019-0467-4] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/12/2019] [Indexed: 12/11/2022] Open
Abstract
PURPOSE To assess the clinical performance of an expanded noninvasive prenatal screening (NIPS) test ("NIPS-Plus") for detection of both aneuploidy and genome-wide microdeletion/microduplication syndromes (MMS). METHODS A total of 94,085 women with a singleton pregnancy were prospectively enrolled in the study. The cell-free plasma DNA was directly sequenced without intermediate amplification and fetal abnormalities identified using an improved copy-number variation (CNV) calling algorithm. RESULTS A total of 1128 pregnancies (1.2%) were scored positive for clinically significant fetal chromosome abnormalities. This comprised 965 aneuploidies (1.026%) and 163 (0.174%) MMS. From follow-up tests, the positive predictive values (PPVs) for T21, T18, T13, rare trisomies, and sex chromosome aneuploidies were calculated as 95%, 82%, 46%, 29%, and 47%, respectively. For known MMS (n = 32), PPVs were 93% (DiGeorge), 68% (22q11.22 microduplication), 75% (Prader-Willi/Angleman), and 50% (Cri du Chat). For the remaining genome-wide MMS (n = 88), combined PPVs were 32% (CNVs ≥10 Mb) and 19% (CNVs <10 Mb). CONCLUSION NIPS-Plus yielded high PPVs for common aneuploidies and DiGeorge syndrome, and moderate PPVs for other MMS. Our results present compelling evidence that NIPS-Plus can be used as a first-tier pregnancy screening method to improve detection rates of clinically significant fetal chromosome abnormalities.
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Bianchi DW. Turner syndrome: New insights from prenatal genomics and transcriptomics. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2019; 181:10.1002/ajmg.c.31675. [PMID: 30706680 PMCID: PMC10110351 DOI: 10.1002/ajmg.c.31675] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 12/30/2018] [Indexed: 01/08/2023]
Abstract
In some parts of the world, prenatal screening using analysis of circulating cell-free (cf) DNA in the plasma of pregnant women has become part of routine prenatal care with limited professional guidelines and without significant input from the Turner syndrome community. In contrast to the very high positive predictive values (PPVs) achieved with cfDNA analysis for trisomy 21 (91% for high-risk and 82% for low-risk cases), the PPVs for monosomy X are much lower (~26%). This is because the maternal plasma sample contains both maternal cfDNA and placental DNA, which is a proxy for the fetal genome. Underlying biological mechanisms for false positive monosomy X screening results include confined placental mosaicism, co-twin demise, and maternal mosaicism. Somatic loss of a single X chromosome in the mother is a natural phenomenon that occurs with aging; this could explain many of the false positive cfDNA results. There is also increased awareness of women who have constitutional mosaicism for 45, X who are fertile. It is important to recognize that a positive cfDNA screen for 45, X does not mean that the fetus has Turner syndrome. A follow-up diagnostic test, either amniocentesis or neonatal karyotype/chromosome microarray, is recommended. Research studies on cell-free mRNA in second trimester amniotic fluid, which is almost exclusively fetal, demonstrate consistent dysregulation of genes involved in the hematologic, immune, and neurologic systems. This suggests that some of the pathophysiology of Turner syndrome occurs early in fetal life and presents novel opportunities for consideration of antenatal treatments.
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Affiliation(s)
- Diana W Bianchi
- Section on Prenatal Genomics and Fetal Therapy, Medical Genetics Branch, National Human Genome Research Institute, and Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
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40
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Zhang J, Li J, Saucier JB, Feng Y, Jiang Y, Sinson J, McCombs AK, Schmitt ES, Peacock S, Chen S, Dai H, Ge X, Wang G, Shaw CA, Mei H, Breman A, Xia F, Yang Y, Purgason A, Pourpak A, Chen Z, Wang X, Wang Y, Kulkarni S, Choy KW, Wapner RJ, Van den Veyver IB, Beaudet A, Parmar S, Wong LJ, Eng CM. Non-invasive prenatal sequencing for multiple Mendelian monogenic disorders using circulating cell-free fetal DNA. Nat Med 2019; 25:439-447. [PMID: 30692697 DOI: 10.1038/s41591-018-0334-x] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 12/17/2018] [Indexed: 02/02/2023]
Abstract
Current non-invasive prenatal screening is targeted toward the detection of chromosomal abnormalities in the fetus1,2. However, screening for many dominant monogenic disorders associated with de novo mutations is not available, despite their relatively high incidence3. Here we report on the development and validation of, and early clinical experience with, a new approach for non-invasive prenatal sequencing for a panel of causative genes for frequent dominant monogenic diseases. Cell-free DNA (cfDNA) extracted from maternal plasma was barcoded, enriched, and then analyzed by next-generation sequencing (NGS) for targeted regions. Low-level fetal variants were identified by a statistical analysis adjusted for NGS read count and fetal fraction. Pathogenic or likely pathogenic variants were confirmed by a secondary amplicon-based test on cfDNA. Clinical tests were performed on 422 pregnancies with or without abnormal ultrasound findings or family history. Follow-up studies on cases with available outcome results confirmed 20 true-positive, 127 true-negative, zero false-positive, and zero-false negative results. The initial clinical study demonstrated that this non-invasive test can provide valuable molecular information for the detection of a wide spectrum of dominant monogenic diseases, complementing current screening for aneuploidies or carrier screening for recessive disorders.
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Affiliation(s)
- Jinglan Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | | | | | | | | | | | - Anne K McCombs
- Office of Clinical Research, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xiaoyan Ge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Statistics, Rice University, Houston, TX, USA
| | - Hui Mei
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Amy Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Zhao Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yue Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shashikant Kulkarni
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China
| | - Ronald J Wapner
- Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Arthur Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Abstract
The field of prenatal screening and diagnosis has undergone enormous progress over the past four decades. Most of this period has been characterized by gradual improvements in the technical and public health aspects of prenatal screening for Down syndrome. Compared to the direct analysis of fetal cells from amniocentesis or chorionic villus sampling, noninvasive approaches using maternal blood or ultrasound have the great advantage of posing no risk of miscarriage to the pregnancy. Recent advances in molecular genetics and DNA sequencing have revolutionized both the accuracy and the range of noninvasive testing for genetic abnormalities using cell-free DNA in maternal plasma. Many of these advances have already been incorporated into clinical care, including diagnosis of fetal blood group and aneuploidy screening. The accelerated pace of these recent developments is creating not just technical and logistical challenges, but is also magnifying the ethical and public policy issues traditionally associated with this field.
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Affiliation(s)
- Lisa Hui
- Department of Perinatal Medicine, Mercy Hospital for Women, Heidelberg, VIC, Australia.
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia.
- Reproductive Epidemiology, Murdoch Children's Research Institute, Parkville, VIC, Australia.
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42
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Abstract
Noninvasive prenatal genetic tests analyzing the cell-free fetal DNA in the circulation of expectant mothers are now performed routinely in clinical diagnostic laboratories. Leveraging the power of next generation sequencing (NGS), these tests can detect variation in chromosomal copy number or microdeletions early in gestation. All methods begin with blood collection followed by transport to the diagnostic lab, plasma separation, and purification of ccfDNA from the plasma to prepare it for molecular analysis. Preservation of ccfDNA in blood samples and highly efficient purification from plasma are paramount since the quality and quantity of target nucleic acids determine the sensitivity and therefore success of these assays. Maximizing quality and quantity and minimizing variation in extraction yield pose significant challenges for diagnostic labs, many of which use manual isolation methods for plasma volumes greater than 5 mL. One way to reduce variability is to automate the extraction processes and, to the extent possible, minimize hand-on operations. This chapter details two procedures for isolating ccfDNA from 10 mL plasma by manual and automated means using the QIAamp Circulating Nucleic Acid Kit and the QIAsymphony Circulating DNA Kit. The ccfDNA recovered is suitable for downstream processing in noninvasive prenatal tests for aneuploidy detection.
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43
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Verma IC, Puri R, Venkataswamy E, Tayal T, Nampoorthiri S, Andrew C, Kabra M, Bagga R, Gowda M, Batra M, Hegde S, Kaul A, Gupta N, Mishra P, Subramanian JG, Lingaiah S, Akhtar R, Kidangan F, Chandran R, Kiran C, Ravi Kumar GR, Ramprasad VL, Kadam P. Single Nucleotide Polymorphism-Based Noninvasive Prenatal Testing: Experience in India. J Obstet Gynaecol India 2018; 68:462-470. [PMID: 30416273 PMCID: PMC6207553 DOI: 10.1007/s13224-017-1061-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/26/2017] [Indexed: 11/24/2022] Open
Abstract
INTRODUCTION Noninvasive prenatal testing (NIPT) has revolutionized prenatal screening for chromosomal aneuploidies in some countries. Its implementation has been sporadic in developing countries. Given the genetic variation of the people in different countries, we evaluated the performance of the SNP-based NIPT in India . MATERIALS AND METHODS The Panorama™ NIPT was performed in 516 pregnancies, which had tested intermediate-to-high risk on conventional first and second trimester screening. Results were confirmed either by invasive diagnostic testing or by clinical evaluation after birth. RESULTS Of 511 samples analyzed, results were obtained in 499 (97.7%). Of these, 480 (98.2%) were low risk and 19 were high risk. A sensitivity of 100% was obtained for detection of trisomies 21, 18, 13 and sex chromosomal abnormalities. The specificity ranged from 99.3 to 100% for abnormalities tested. Taken together, the positive predictive value for trisomies 21, 18, 13 and monosomy X was 85.7%. The average fetal fraction was 8.2%, which is lower than the average observed elsewhere. CONCLUSION This is the first report of detailed experience with NIPT in India and demonstrates comparable performance in all aspects of testing to the results elsewhere.
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Affiliation(s)
| | - Ratna Puri
- Sir Ganga Ram Hospital, New Delhi, India
| | - Eswarachary Venkataswamy
- Medgenome Laboratory Private Limited, 3rd Floor, 258/A, Narayana Nethralaya, Narayana Health City, Hosur Road, Bommasandra, Bengaluru, 560099 India
| | | | | | | | | | - Rashmi Bagga
- Postgraduate Institute and Medical Research Center, Chandigarh, India
| | - Mamatha Gowda
- Jawaharlal Nehru Institute of Postgraduate Medical Education and Research, Pondicherry, India
| | | | | | - Anita Kaul
- Indraprastha Apollo Hospital, New Delhi, India
| | - Neerja Gupta
- All India Institute of Medical Sciences, New Delhi, India
| | - Pallavi Mishra
- All India Institute of Medical Sciences, New Delhi, India
| | | | - Shruti Lingaiah
- Medgenome Laboratory Private Limited, 3rd Floor, 258/A, Narayana Nethralaya, Narayana Health City, Hosur Road, Bommasandra, Bengaluru, 560099 India
| | - Riyaz Akhtar
- Medgenome Laboratory Private Limited, 3rd Floor, 258/A, Narayana Nethralaya, Narayana Health City, Hosur Road, Bommasandra, Bengaluru, 560099 India
| | - Francis Kidangan
- Medgenome Laboratory Private Limited, 3rd Floor, 258/A, Narayana Nethralaya, Narayana Health City, Hosur Road, Bommasandra, Bengaluru, 560099 India
| | - R. Chandran
- Medgenome Laboratory Private Limited, 3rd Floor, 258/A, Narayana Nethralaya, Narayana Health City, Hosur Road, Bommasandra, Bengaluru, 560099 India
| | - C. Kiran
- Medgenome Laboratory Private Limited, 3rd Floor, 258/A, Narayana Nethralaya, Narayana Health City, Hosur Road, Bommasandra, Bengaluru, 560099 India
| | - G. R. Ravi Kumar
- Medgenome Laboratory Private Limited, 3rd Floor, 258/A, Narayana Nethralaya, Narayana Health City, Hosur Road, Bommasandra, Bengaluru, 560099 India
| | - V. L. Ramprasad
- Medgenome Laboratory Private Limited, 3rd Floor, 258/A, Narayana Nethralaya, Narayana Health City, Hosur Road, Bommasandra, Bengaluru, 560099 India
| | - Priya Kadam
- Medgenome Laboratory Private Limited, 3rd Floor, 258/A, Narayana Nethralaya, Narayana Health City, Hosur Road, Bommasandra, Bengaluru, 560099 India
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Ramdaney A, Hoskovec J, Harkenrider J, Soto E, Murphy L. Clinical experience with sex chromosome aneuploidies detected by noninvasive prenatal testing (NIPT): Accuracy and patient decision-making. Prenat Diagn 2018; 38:841-848. [PMID: 30068017 DOI: 10.1002/pd.5339] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/21/2018] [Accepted: 07/21/2018] [Indexed: 12/14/2022]
Abstract
OBJECTIVE The objectives of the study are to assess the accuracy of noninvasive prenatal testing (NIPT) for sex chromosome aneuploidies (SCAs) and to investigate patient decision-making in clinical practice. STUDY DESIGN This is a retrospective cohort study review of positive NIPT results for SCAs from January 2013 to September 2017. RESULTS Of the 136 positive NIPT results for SCAs, 73 (53.7%) were positive for 45,X, 62 (45.6%) were a sex chromosome trisomy, and 1 was a sex chromosome tetrasomy. Of the 134 viable pregnancies, 46 (34.3%) elected to pursue prenatal diagnosis. Fewer women underwent invasive prenatal testing when counseled regarding a positive NIPT for monosomy X in the presence of suggestive ultrasound findings (4/23; 17.4%) compared with those who had a positive NIPT result without ultrasound findings (24/46, 52.2%). Abnormal karyotypes consistent with the NIPT result were confirmed in 30/64 (46.9%). Even in the context of ultrasound abnormalities, there was not 100% concordance. CONCLUSIONS The majority (88/134; 65.7%) of patients in our cohort declined prenatal diagnosis even in the presence of associated ultrasound findings. Comprehensive pretest and posttest counseling is recommended and should address the importance of confirmatory testing and benefits of early diagnosis. Practice guidelines are needed to address provider responsibilities about postnatal testing.
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Affiliation(s)
- Aarti Ramdaney
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jennifer Hoskovec
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jacqueline Harkenrider
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eleazar Soto
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Lauren Murphy
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, USA
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Liang D, Lin Y, Qiao F, Li H, Wang Y, Zhang J, Liu A, Ji X, Ma D, Jiang T, Hu P, Xu Z. Perinatal outcomes following cell-free DNA screening in >32 000 women: Clinical follow-up data from a single tertiary center. Prenat Diagn 2018; 38:755-764. [PMID: 29966040 DOI: 10.1002/pd.5328] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/24/2018] [Accepted: 06/25/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Dong Liang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Ying Lin
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Fengchang Qiao
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Hang Li
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Yan Wang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Jingjing Zhang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - An Liu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Xiuqing Ji
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Dingyuan Ma
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Tao Jiang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Ping Hu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Zhengfeng Xu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
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Eswarachari V, Kadam P, Movva S, Lingaiah S, Akther RM, Kidangan FX, Gowda KC, Golakoti RRK, Lall M, Mahajan S, Saviour P, Puri R, Verma IC, Vedam RL. Noninvasive prenatal testing (NIPT) detects variant of Turner syndrome not detectable by fluorescent in situ hybridization. J Matern Fetal Neonatal Med 2018; 32:4177-4180. [PMID: 29793366 DOI: 10.1080/14767058.2018.1481383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Introduction: Noninvasive prenatal testing (NIPT) is a reliable screening method for fetal aneuploidy detection of trisomy 18, 13, 21 along with few sex chromosome abnormalities monosomy X, XXX, XXY (Klinefelter), XYY (Jacob) syndromes and certain microdeletions which include cri-du-chat, DiGeorge, 1p36, Angelman, and Prader-Willi syndromes in comparison to the available screening methods. Prenatal screening of Turners syndrome is possible by ultrasound in certain conditions only. Recently benefits of early detection and treatment of Turners syndrome has been emphasized, enforcing on accurate and early screening prenatally.Case details: The current case emphasizes on the reliability of NIPT testing which comes with an advantage of early screening. A 24-year-old primi gravida was referred for NIPT as she tested for high risk on biochemical screening. The Panorama™ NIPT results showed low risk for trisomies, 21, 18, and 13 but high risk of monosomy X and was advised confirmatory amniocentesis. The fluorescence in situ hybridization (FISH) report revealed no numerical abnormality detected for any of the five chromosomes tested. On receiving this discordant report, the sample was rerun for NIPT, to rule out any laboratory-related issues. The result obtained on a rerun was consistent with the first report and showed monosomy X again. The karyotype report was available three weeks later and a rare variant of Turners syndrome was identified.Discussion: Panorama™ NIPT considers single nucleotide polymorphisms spread across the chromosomes for analysis, different variants of aneuploidy can be picked up in comparison to FISH, similar to the current case wherein it could not as it was a centromeric probe. Reported first case of X chromosome variant detected by NIPT confirmed by karyotyping, missed by FISH.
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Affiliation(s)
| | - Priya Kadam
- Medgenome Labs Ltd., Narayana Nethralaya, Bangalore, India
| | - Sireesha Movva
- Medgenome Labs Ltd., Narayana Nethralaya, Bangalore, India
| | | | - Riyaz M Akther
- Medgenome Labs Ltd., Narayana Nethralaya, Bangalore, India
| | | | - Kiran C Gowda
- Medgenome Labs Ltd., Narayana Nethralaya, Bangalore, India
| | | | - Meena Lall
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Surbhi Mahajan
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Pushpa Saviour
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ratna Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ishwar C Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
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Gray KJ, Wilkins-Haug LE. Have we done our last amniocentesis? Updates on cell-free DNA for Down syndrome screening. Pediatr Radiol 2018; 48:461-470. [PMID: 29550862 PMCID: PMC7088458 DOI: 10.1007/s00247-017-3958-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 06/11/2017] [Accepted: 07/26/2017] [Indexed: 12/19/2022]
Abstract
Prenatal aneuploidy screening changed significantly in 2012 when cell-free fetal deoxyribonucleic acid (DNA) was introduced as a noninvasive prenatal test. A noninvasive prenatal test detects cell free fragments of fetal DNA from the placenta circulating in maternal blood that coexist with cell-free DNA (cfDNA) of maternal origin. Using next-generation sequencing, the noninvasive prenatal test compares maternal and fetal cfDNA ratios for chromosomes of interest (i.e., 21, 18, 13, X, and Y) to assess chromosomal aneuploidy. Compared to traditional screening using ultrasound and serum markers, the noninvasive prenatal test has superior test characteristics, including a higher detection rate and positive predictive value, and a lower false-positive rate. The noninvasive prenatal test is already used for primary screening in high-risk women and is rapidly expanding to all women. Given its increasing use, understanding the noninvasive prenatal test's limitations is critical. Discordant results (i.e. noninvasive prenatal test is positive for aneuploidy with a normal fetal karyotype) can occur because of biological processes such as aneuploidy confined to the placenta, a vanished twin, maternal aneuploidy or maternal cancer. Use of the noninvasive prenatal test for screening beyond the most common aneuploidies is not recommended. The noninvasive prenatal test is a major advance in prenatal aneuploidy screening but it is not diagnostic and does not replace invasive testing (i.e. chorionic villous sampling or amniocentesis) for confirmation of fetal chromosomal disorders.
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Affiliation(s)
- Kathryn J Gray
- Division of Maternal-Fetal Medicine, Brigham & Women's Hospital, 75 Francis St., Boston, MA, 02115, USA
| | - Louise E Wilkins-Haug
- Division of Maternal-Fetal Medicine, Brigham & Women's Hospital, 75 Francis St., Boston, MA, 02115, USA.
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Reiss RE, Discenza M, Foster J, Dobson L, Wilkins-Haug L. Sex chromosome aneuploidy detection by noninvasive prenatal testing: helpful or hazardous? Prenat Diagn 2018; 37:515-520. [PMID: 28326560 DOI: 10.1002/pd.5039] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 02/21/2017] [Accepted: 03/17/2017] [Indexed: 12/22/2022]
Abstract
OBJECTIVES To assess the incidence of sex chromosome aneuploidy (SCA) predicted by noninvasive prenatal testing (NIPT), assess test performance, and compare it with nuchal translucency (NT) screening among patients seen in our prenatal diagnosis center. METHODS We identified suspected cases of SCA by reviewing results from all NIPT samples sent from our center to commercial laboratories offering analysis by cell-free DNA between 1 December 2012 and 31 July 2015. Records of pregnancies positive for SCA were reviewed for ultrasound findings, NIPT indications, and karyotype results on maternal, fetal, and postnatal samples. Other SCA cases presenting during this period regardless of NIPT status were identified from genetic counseling and cytogenetics laboratory logbooks. RESULTS Noninvasive prenatal testing predicted SCA in 18/2851 patients (0.63%). All had diagnostic testing of fetal or newborn samples. No patients terminated pregnancies on the basis of NIPT. NIPT suggested triple X in five cases, two with elevated NT: all were confirmed on karyotype. Two Klinefelter syndrome cases were also accurately predicted by NIPT. NIPT indicated monosomy X in 11 cases. Only one was a true positive. Ten were false positives, with 46, XX found on fetal or newborn karyotype. Maternal karyotype was mosaic (45, X[4], 46, XX[26]) in one case. Over the same time period, four additional cases of 45, X were confirmed on fetal samples, all with cystic hygromas. One of these had had a false negative NIPT result. The remaining patients pursued only direct testing via CVS or amniocentesis. CONCLUSIONS Sex chromosome aneuploidy was frequently suspected on NIPT. False positive rate for monosomy X was surprisingly high (91%). Prediction of other SCA was more accurate. Diagnostic fetal chromosome analysis should be offered after abnormal NIPT or in the presence of cystic hygromas despite normal NIPT. NIPT limitations should be explained in pretest counseling. © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Rosemary E Reiss
- Center for Fetal Medicine and Prenatal Genetics, Brigham and Women's Hospital, Boston, MA, USA.,Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Marie Discenza
- Center for Fetal Medicine and Prenatal Genetics, Brigham and Women's Hospital, Boston, MA, USA.,Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Judith Foster
- Center for Fetal Medicine and Prenatal Genetics, Brigham and Women's Hospital, Boston, MA, USA.,Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Lori Dobson
- Center for Fetal Medicine and Prenatal Genetics, Brigham and Women's Hospital, Boston, MA, USA.,Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Louise Wilkins-Haug
- Center for Fetal Medicine and Prenatal Genetics, Brigham and Women's Hospital, Boston, MA, USA.,Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
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A National Referral Laboratory’s Experience with the Implementation of SNP-Based Non-invasive Prenatal Screening for Fetal Aneuploidy and Select Microdeletion Syndromes. JOURNAL OF FETAL MEDICINE 2018. [DOI: 10.1007/s40556-017-0143-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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50
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Putra M, Hicks MA, Abramowicz JS. False Low-Risk Single Nucleotide Polymorphism-Based Noninvasive Prenatal Screening in Pentasomy 49,XXXXY. AJP Rep 2018; 8:e4-e6. [PMID: 29362687 PMCID: PMC5775094 DOI: 10.1055/s-0037-1621722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 12/09/2017] [Indexed: 10/31/2022] Open
Abstract
Introduction Pentasomy 49,XXXXY is a sex chromosome anomaly difficult to be diagnosed prenatally. We describe a patient of pentasomy 49,XXXXY with false low-risk results using a noninvasive prenatal screening (NIPS). A 30-year-old G1P0 woman presented at 33 6/7 weeks, secondary to sonographic fetal anomalies. She had low-risk NIPS at 13 6/7 weeks. Anatomy survey showed bilateral clubfeet, clinodactyly of the left fifth digit, micropenis, and echogenic bowel. Cytogenetics analysis revealed pentasomy 49,XXXXY syndrome. We report third-trimester sonographic features of a fetus with pentasomy 49,XXXXY and the importance of thorough pre- and posttest counseling for NIPS.
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Affiliation(s)
- Manesha Putra
- Department of Obstetrics and Gynecology, Detroit Medical Center, Wayne State University, Detroit, Michigan
| | - Melissa A Hicks
- Detroit Medical Center University Laboratories, Detroit Medical Center, Detroit, Michigan
| | - Jacques S Abramowicz
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, Illinois
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