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Olayiwola JO, Marhabaie M, Koboldt D, Matthews T, Siemon A, Mouhlas D, Porter T, Kyle G, Myers C, Mei H, Hou YC, Babcock M, Hunter J, Schieffer KM, Akkari Y, Reshmi S, Cottrell C, Mathew MT, Leung ML. Clinically significant findings in a decade-long retrospective study of prenatal chromosomal microarray testing. Mol Genet Genomic Med 2024; 12:e2349. [PMID: 38263869 PMCID: PMC10958178 DOI: 10.1002/mgg3.2349] [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: 07/04/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Chromosomal microarray (CMA) is commonly utilized in the obstetrics setting. CMA is recommended when one or more fetal structural abnormalities is identified. CMA is also commonly used to determine genetic etiologies for miscarriages, fetal demise, and confirming positive prenatal cell-free DNA screening results. METHODS In this study, we retrospectively examined 523 prenatal and 319 products-of-conception (POC) CMA cases tested at Nationwide Children's Hospital from 2011 to 2020. We reviewed the referral indications, the diagnostic yield, and the reported copy number variants (CNV) findings. RESULTS In our cohort, the diagnostic yield of clinically significant CNV findings for prenatal testing was 7.8% (n = 41/523) compared to POC testing (16.3%, n = 52/319). Abnormal ultrasound findings were the most common indication present in 81% of prenatal samples. Intrauterine fetal demise was the common indication identified in POC samples. The most common pathogenic finding observed in all samples was isolated trisomy 21, detected in seven samples. CONCLUSION Our CMA study supports the clinical utility of prenatal CMA for clinical management and identifying genetic etiology in POC arrays. In addition, it provides insight to the spectrum of prenatal and POC CMA results as detected in an academic hospital clinical laboratory setting that serves as a reference laboratory.
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Dolanc Merc M, Peterlin B, Lovrecic L. The genetic approach to stillbirth: A »systematic review«. Prenat Diagn 2023; 43:1220-1228. [PMID: 37072878 DOI: 10.1002/pd.6354] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/27/2023] [Accepted: 04/09/2023] [Indexed: 04/20/2023]
Abstract
Unexplained stillbirth is defined as a stillbirth with no known cause after the exclusion of common causes, including obstetric complications, infections, placental insufficiency or abruption, umbilical cord complications, and congenital abnormalities with or without known genetic cause. More than 60% of stillbirth cases remain unexplained. The aim of this systematic review was to investigate the known genetic causes of unexplained stillbirth cases and to evaluate the current position and future directions for the use of genetic and genomic testing in expanding the knowledge in this field. A systematic search through several databases was performed using the keywords genetics and stillbirths in humans. Different methods to detect various types of causal genetic aberrations have been used in the past decades, from standard karyotyping to novel methods such as chromosomal microarray analysis and next generation sequencing technologies. Apart from common chromosomal aneuploidies, a promising hypothesis about genetic causes included genes related to cardiomyopathies and channelopathies. However, these were tested in the research settings, since molecular karyotyping is currently the standard approach in the routine evaluation of genetic causes of stillbirth. Hereby, we provide evidence that expanding knowledge using novel genetic and genomic testing might uncover new genetic causes of unexplained stillbirth.
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Affiliation(s)
- Maja Dolanc Merc
- Department of Perinatology, Division of Obstetrics and Gynecology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute for Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Luca Lovrecic
- Clinical Institute for Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
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3
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The genomic basis of sporadic and recurrent pregnancy loss: a comprehensive in-depth analysis of 24,900 miscarriages. Reprod Biomed Online 2022; 45:125-134. [DOI: 10.1016/j.rbmo.2022.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/07/2022] [Accepted: 03/17/2022] [Indexed: 12/16/2022]
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Cai M, Lin N, Xu L, Huang H. Comparative clinical genetic testing in spontaneous miscarriage: Insights from a study in Southern Chinese women. J Cell Mol Med 2021; 25:5721-5728. [PMID: 33973351 PMCID: PMC8184667 DOI: 10.1111/jcmm.16588] [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: 02/03/2021] [Revised: 03/23/2021] [Accepted: 04/19/2021] [Indexed: 12/15/2022] Open
Abstract
Single nucleotide polymorphism (SNP) array and karyotype analyses were conducted on 441 spontaneous miscarriage placental villous tissues collected from women from southern China. Subsequently, the results from these two analyses were compared to evaluate the best diagnostic strategy for subsequent pre‐pregnancy planning. Here, the success rate of genetic testing using karyotyping and SNP array analysis was 78.46% (346/441) and 100.0% (441/441), respectively. The abnormality rate estimated by both methods was 54.9% (242/441). Three hundred and forty‐six cases were successfully detected via both SNP array and karyotype analyses; the rate of consistent detection was 96.24% (333/346), whereas 13 cases were not consistent. There was no substantial positive correlation between age and genetic abnormalities such as Turner syndrome, structural variation or euploidy state in the different age groups studied. However, the aneuploidy rate was significantly different in each age group. Thus, although SNP array has higher success rate and resolution in genetic abnormality detection, supplementary karyotype analysis is needed for a more accurate revelation of the genetic aetiology of miscarriages. Therefore, this study indicates that simultaneous karyotype and SNP array analyses should be performed for spontaneous miscarriages. Furthermore, miscarriages irrespective of maternal age must be genetically analysed.
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Affiliation(s)
- Meiying Cai
- Department of the Prenatal Diagnosis Center, Fujian Maternity and Child Health Hospital, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Na Lin
- Department of the Prenatal Diagnosis Center, Fujian Maternity and Child Health Hospital, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Liangpu Xu
- Department of the Prenatal Diagnosis Center, Fujian Maternity and Child Health Hospital, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Hailong Huang
- Department of the Prenatal Diagnosis Center, Fujian Maternity and Child Health Hospital, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Affiliated Hospital of Fujian Medical University, Fuzhou, China
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5
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McPherson EW. 3137 fetuses in 33 years: What we have learned from the Wisconsin stillbirth service program. Am J Med Genet A 2021; 185:2683-2689. [PMID: 33634578 DOI: 10.1002/ajmg.a.62143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/31/2020] [Accepted: 02/13/2021] [Indexed: 11/09/2022]
Abstract
The Wisconsin Stillbirth Service Program (WiSSP) provided expert review by a dysmorphologist for community-acquired data on 3137 fetal deaths between 1983 and 2017. Intrinsic fetal causes were consistently identified in about 25% while placental and maternal causes were recognized with increasing frequency as attention was shifted from a primarily fetal to a multifocal approach. Identification of causes increased from 40% to 78% and in about half of cases results of the review altered recurrence risk and/or future pregnancy management. Banked data from WiSSP formed the basis of 24 publications, more than half of which have a genetic counselor and/or summer premedical student intern as an author. The earlier publications emphasized validation of the concept of community-based evaluation with central review, the utility of various parts of the WiSSP protocol, the similarity of second-trimester miscarriages <20 weeks to later stillbirths with respect to causes identified and recurrence risks, and the potential for results of etiologic evaluation to influence future prenatal care. The most important recurrent theme, however, was the interaction of intrinsic fetal, placental, and maternal factors in contributing to fetal demise. This implies that, at least in developed nations with available obstetric care, reduction in stillbirth will require careful attention to the myriad of factors contributing to fetal, placental, and maternal well-being.
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Affiliation(s)
- Elizabeth W McPherson
- Departments of Obstetrics and Gynecology and Pediatrics, University of Wisconsin, Madison, Wisconsin, USA
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6
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Marquès B, Benitez L, Peguero A, Madrigal I, Gómez O, Figueras F, Borrell A. Cytogenetic Investigation in 136 Consecutive Stillbirths: Does the Tissue Type Affect the Success Rate of Chromosomal Microarray Analysis and Karyotype? Fetal Diagn Ther 2020; 47:315-320. [PMID: 31955157 DOI: 10.1159/000505399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 12/11/2019] [Indexed: 11/19/2022]
Abstract
BACKGROUND Chromosomal anomalies are a recognized cause of stillbirth, accounting for 6-17% of the cases. As a diagnostic laboratory method in this setting, conventional karyotyping has two main drawbacks: the need for viable fetal cells in a dead fetus and its limited resolution as compared to alternative techniques. OBJECTIVE To assess the effectiveness of cytogenetic analysis in stillbirths between different testing methods and different sampled tissues. METHODS From 2011 to 2017, 145 stillborn fetuses (defined as fetal losses after 22 weeks) were delivered in our center. The stillbirth protocol includes genetic testing by means of a karyotype, QF-PCR, or chromosomal microarray analysis (CMA), depending on the presence of fetal structural anomalies and the study time period. The success rates were compared between tests and between different sampled tissues. RESULTS Consent was granted for cytogenetic analysis in 136 stillbirths. Test success rate was 100% (38/38) for CMA independent of the sampled tissue, 99% (65/66) for QF-PCR, and 66% (65/98) for karyotyping. The success rate for karyotyping was 48% (69/145) of the total tissues samples, showing great variation according to the tissue sampled: 83% (40/48) in amniotic fluid, 78% (21/27) in the placenta, 13% (7/54) in fetal skin, and 6.3% (1/16) in fetal blood. Four full or partial aneuploidies (trisomy 9, trisomy 22, tetrasomy 18p, and monosomy X) and 2 microdeletions (del2p16.3 and del1q13.2q13.4) were found, resulting in a 3.9% (4/103) prevalence for full or partial aneuploidy and a 5.3% prevalence (2/38) for submicroscopic abnormalities. CONCLUSIONS Amniotic fluid should be the preferred tissue source in the cytogenetic analysis of stillbirth due to its high success rate. Between tests, CMA is a preferable method because of its higher test success rate, independent of the sampled tissue, and higher diagnostic yield including chromosomal and submicroscopic anomalies.
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Affiliation(s)
- Borja Marquès
- Barcelona Center for Fetal and Neonatal Medicine (BCNatal), Hospital Clínic Barcelona, Barcelona, Spain
| | - Leticia Benitez
- Barcelona Center for Fetal and Neonatal Medicine (BCNatal), Hospital Clínic Barcelona, Barcelona, Spain
| | - Anna Peguero
- Barcelona Center for Fetal and Neonatal Medicine (BCNatal), Hospital Clínic Barcelona, Barcelona, Spain
| | - Irene Madrigal
- Biomedical Diagnostic Center, Hospital Clínic Barcelona, Barcelona, Spain
| | - Olga Gómez
- Barcelona Center for Fetal and Neonatal Medicine (BCNatal), Hospital Clínic Barcelona, Barcelona, Spain
| | - Francesc Figueras
- Barcelona Center for Fetal and Neonatal Medicine (BCNatal), Hospital Clínic Barcelona, Barcelona, Spain
| | - Antoni Borrell
- Barcelona Center for Fetal and Neonatal Medicine (BCNatal), Hospital Clínic Barcelona, Barcelona, Spain,
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Martinez-Portilla RJ, Pauta M, Hawkins-Villarreal A, Rial-Crestelo M, Paz Y Miño F, Madrigal I, Figueras F, Borrell A. Added value of chromosomal microarray analysis over conventional karyotyping in stillbirth work-up: systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2019; 53:590-597. [PMID: 30549343 DOI: 10.1002/uog.20198] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 11/14/2018] [Accepted: 11/22/2018] [Indexed: 06/09/2023]
Abstract
OBJECTIVE To assess the added value of chromosomal microarray analysis (CMA) over conventional karyotyping to assess the genetic causes in stillbirth. METHODS To identify relevant studies, published in English or Spanish and without publication time restrictions, we performed a systematic search of PubMed, SCOPUS and ISI Web of Science databases, The Cochrane Library and the PROSPERO register of systematic reviews, for case series of fetal loss ≥ 20 weeks of gestation, with normal or suspected normal karyotype, undergoing CMA and with at least five subjects analyzed. To investigate quality, two reviewers evaluated independently the risk of bias using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. For the meta-analysis, the incremental yield of CMA over karyotyping was assessed by single-proportion analysis using a random-effects model (weighting by inverse variance). We assessed heterogeneity between studies and performed a sensitivity analysis and a subgroup analysis of structurally abnormal (malformed or growth-restricted) and normal fetuses. RESULTS Included in the meta-analysis were seven studies involving 903 stillborn fetuses which had normal karyotype. The test success rate achieved by conventional cytogenetic analysis was 75%, while that for CMA was 90%. The incremental yield of CMA over conventional karyotyping based on the random-effects model was 4% (95% CI, 3-5%) for pathogenic copy-number variants (pCNVs) and 8% (95% CI, 4-17%) for variants of unknown significance. Subgroup analysis showed a 6% (95% CI, 4-10%) incremental yield of CMA for pCNVs in structurally abnormal fetuses and 3% (95% CI, 1-5%) incremental yield for those in structurally normal fetuses. The pCNV found most commonly was del22q11.21. CONCLUSIONS CMA, incorporated into the stillbirth work-up, improves both the test success rate and the detection of genetic anomalies compared with conventional karyotyping. To achieve a genetic diagnosis in stillbirth is particularly relevant for the purpose of counseling regarding future pregnancies. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- R J Martinez-Portilla
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecologia, Obstetricia i Neonatologia Fetal i+D Fetal Medicine Research Center, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Fetal Medicine and Therapy Research Center Mexico, on behalf of the Iberoamerican Research Network in Translational, Molecular and Maternal-Fetal Medicine, Mexico
- IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Center of Biomedical Diagnosis, Hospital Clinic Barcelona, Barcelona, Catalonia, Spain
| | - M Pauta
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecologia, Obstetricia i Neonatologia Fetal i+D Fetal Medicine Research Center, Universitat de Barcelona, Barcelona, Catalonia, Spain
- IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Center of Biomedical Diagnosis, Hospital Clinic Barcelona, Barcelona, Catalonia, Spain
| | - A Hawkins-Villarreal
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecologia, Obstetricia i Neonatologia Fetal i+D Fetal Medicine Research Center, Universitat de Barcelona, Barcelona, Catalonia, Spain
- IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Center of Biomedical Diagnosis, Hospital Clinic Barcelona, Barcelona, Catalonia, Spain
| | - M Rial-Crestelo
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecologia, Obstetricia i Neonatologia Fetal i+D Fetal Medicine Research Center, Universitat de Barcelona, Barcelona, Catalonia, Spain
- IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Center of Biomedical Diagnosis, Hospital Clinic Barcelona, Barcelona, Catalonia, Spain
| | - F Paz Y Miño
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecologia, Obstetricia i Neonatologia Fetal i+D Fetal Medicine Research Center, Universitat de Barcelona, Barcelona, Catalonia, Spain
- IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Center of Biomedical Diagnosis, Hospital Clinic Barcelona, Barcelona, Catalonia, Spain
| | - I Madrigal
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecologia, Obstetricia i Neonatologia Fetal i+D Fetal Medicine Research Center, Universitat de Barcelona, Barcelona, Catalonia, Spain
- IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Center of Biomedical Diagnosis, Hospital Clinic Barcelona, Barcelona, Catalonia, Spain
| | - F Figueras
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecologia, Obstetricia i Neonatologia Fetal i+D Fetal Medicine Research Center, Universitat de Barcelona, Barcelona, Catalonia, Spain
- IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Center of Biomedical Diagnosis, Hospital Clinic Barcelona, Barcelona, Catalonia, Spain
- Center for Biomedical Research on Rare Diseases (CIBER-ER), Madrid, Spain
| | - A Borrell
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecologia, Obstetricia i Neonatologia Fetal i+D Fetal Medicine Research Center, Universitat de Barcelona, Barcelona, Catalonia, Spain
- IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Center of Biomedical Diagnosis, Hospital Clinic Barcelona, Barcelona, Catalonia, Spain
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8
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Holmes LB, Nasri H, Beroukhim R, Hunt AT, Roberts DJ, Toufaily MH, Westgate MN. Stillborn Infants: Associated Malformations. Birth Defects Res 2018; 110:114-121. [PMID: 29377646 DOI: 10.1002/bdr2.1097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 07/06/2017] [Indexed: 01/24/2023]
Abstract
BACKGROUND Stillbirth, defined as death of a fetus in utero after 20 weeks of gestation, occurs in 1 to 2% of pregnancies in the United States. Many of these stillborn infants have associated malformations, including chromosome abnormalities, neural tube defects, and malformation syndromes. Other causes are abnormalities of the placenta and maternal conditions, such as pre-eclampsia and obesity. A consecutive sample of malformed stillborn infants can establish the relative frequency and severity of the associated malformations. METHODS Stillbirths were identified in the Active Malformations Surveillance Program at Brigham and Women's Hospital (1972-2012). The findings at autopsy, including the findings in the placenta and the results of diagnostic studies, were compiled. RESULTS One hundred twenty-seven stillborn infants with malformations were identified at autopsy among 289,365 pregnancies, including trisomies 21, 18, and 13; 45,X; triploidy; anencephaly; lower urinary tract obstruction; holoprosencephaly and severe heart defects, such as hypoplastic left heart syndrome and tetralogy of Fallot with pulmonary atresia. The severity of the abnormalities in stillborn infants was more severe than the spectrum of abnormalities identified in live-born infants. CONCLUSION An autopsy of the stillborn fetus, including chromosome microarray and an examination of the placenta, can identify the underlying causes of the stillbirth. This review of stillborn fetuses with malformations showed that several different lethal malformations and heart defects are more common than among live-born infants. These postmortem examinations can improve the counseling of the parents about risks in future pregnancies. Birth Defects Research 110:114-121, 2018.© 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Lewis B Holmes
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Medical Genetics Unit, MassGeneral Hospital for Children, Boston, Massachusetts.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Hanah Nasri
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Medical Genetics Unit, MassGeneral Hospital for Children, Boston, Massachusetts
| | - Rebecca Beroukhim
- Division of Pediatric Congenital Cardiology, MassGeneral Hospital for Children, Boston, Massachusetts
| | | | - Drucilla J Roberts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.,Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - M Hassan Toufaily
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Medical Genetics Unit, MassGeneral Hospital for Children, Boston, Massachusetts
| | - Marie-Noel Westgate
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Medical Genetics Unit, MassGeneral Hospital for Children, Boston, Massachusetts
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9
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Li H, Liu M, Xie M, Zhang Q, Xiang J, Duan C, Ding Y, Liu Y, Mao J, Wang T, Li H. Submicroscopic chromosomal imbalances contribute to early abortion. Mol Cytogenet 2018; 11:41. [PMID: 30038665 PMCID: PMC6054741 DOI: 10.1186/s13039-018-0386-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/24/2018] [Indexed: 12/13/2022] Open
Abstract
Background Chromosomal abnormalities are one of the genetic mechanisms associated with abortion. However, the roles of submicroscopic chromosomal imbalances in early abortion are still unclear. This study aims to find out whether submicroscopic chromosomal imbalances contribute to early abortion. Methods A total of 78 chorionic villus specimens from early spontaneous abortion patients with no obvious abnormality are collected after miccroassay analysis (the case group). At the same time, 60 chorionic villus specimens from induced abortion patients with no obvious abnormality are selected as the control group. The submicroscopic structures of chromosomes from two groups are analyzed using an array-based comparative genomic hybridization (aCGH). Results In the case group, 15 specimens show submicroscopic chromosomal abnormalities including 14 micro-deletion/micro-duplication in chromosomes 2, 4, 5, 6, 7, 8, 9, 12, 15, 16, 18, and 22, and 1 uniparental disomy (UPD) in chromosome 19. Moreover, no pathogenic copy number variations are found in the control group. The results between these two groups exhibit significantly statistical difference. Conclusion Submicroscopic chromosomal imbalances may be one of the main reasons for early abortion.
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Affiliation(s)
- Haibo Li
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Minjuan Liu
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Min Xie
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Qin Zhang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Jingjing Xiang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Chengying Duan
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Yang Ding
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Yinghua Liu
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Jun Mao
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Ting Wang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
| | - Hong Li
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, NO. 26 Daoqian Street, Suzhou, 215002 Jiangsu Province China
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10
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Armour CM, Dougan SD, Brock JA, Chari R, Chodirker BN, DeBie I, Evans JA, Gibson WT, Kolomietz E, Nelson TN, Tihy F, Thomas MA, Stavropoulos DJ. Practice guideline: joint CCMG-SOGC recommendations for the use of chromosomal microarray analysis for prenatal diagnosis and assessment of fetal loss in Canada. J Med Genet 2018; 55:215-221. [PMID: 29496978 PMCID: PMC5869456 DOI: 10.1136/jmedgenet-2017-105013] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/23/2017] [Accepted: 12/29/2017] [Indexed: 01/01/2023]
Abstract
Background The aim of this guideline is to provide updated recommendations for Canadian genetic counsellors, medical geneticists, maternal fetal medicine specialists, clinical laboratory geneticists and other practitioners regarding the use of chromosomal microarray analysis (CMA) for prenatal diagnosis. This guideline replaces the 2011 Society of Obstetricians and Gynaecologists of Canada (SOGC)-Canadian College of Medical Geneticists (CCMG) Joint Technical Update. Methods A multidisciplinary group consisting of medical geneticists, genetic counsellors, maternal fetal medicine specialists and clinical laboratory geneticists was assembled to review existing literature and guidelines for use of CMA in prenatal care and to make recommendations relevant to the Canadian context. The statement was circulated for comment to the CCMG membership-at-large for feedback and, following incorporation of feedback, was approved by the CCMG Board of Directors on 5 June 2017 and the SOGC Board of Directors on 19 June 2017. Results and conclusions Recommendations include but are not limited to: (1) CMA should be offered following a normal rapid aneuploidy screen when multiple fetal malformations are detected (II-1A) or for nuchal translucency (NT) ≥3.5 mm (II-2B) (recommendation 1); (2) a professional with expertise in prenatal chromosomal microarray analysis should provide genetic counselling to obtain informed consent, discuss the limitations of the methodology, obtain the parental decisions for return of incidental findings (II-2A) (recommendation 4) and provide post-test counselling for reporting of test results (III-A) (recommendation 9); (3) the resolution of chromosomal microarray analysis should be similar to postnatal microarray platforms to ensure small pathogenic variants are detected. To minimise the reporting of uncertain findings, it is recommended that variants of unknown significance (VOUS) smaller than 500 Kb deletion or 1 Mb duplication not be routinely reported in the prenatal context. Additionally, VOUS above these cut-offs should only be reported if there is significant supporting evidence that deletion or duplication of the region may be pathogenic (III-B) (recommendation 5); (4) secondary findings associated with a medically actionable disorder with childhood onset should be reported, whereas variants associated with adult-onset conditions should not be reported unless requested by the parents or disclosure can prevent serious harm to family members (III-A) (recommendation 8). The working group recognises that there is variability across Canada in delivery of prenatal testing, and these recommendations were developed to promote consistency and provide a minimum standard for all provinces and territories across the country (recommendation 9).
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Affiliation(s)
- Christine M Armour
- Department of Genetics, Children's Hospital of Eastern and Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | | | - Jo-Ann Brock
- Departments of Obstetrics and Gynecology, Dalhousie University Medical School, Halifax, Nova Scotia, Canada.,Department of Laboratory Medicine, Dalhousie University Medical School, Halifax, Nova Scotia, Canada
| | - Radha Chari
- Department of Obstetrics and Gynecology, University of Alberta, Edmonton, Alberta, Canada
| | - Bernie N Chodirker
- Department of Pediatrics and Child Health, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Isabelle DeBie
- Department of Medical Genetics and Core Molecular Diagnostic Laboratory, McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | - Jane A Evans
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - William T Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elena Kolomietz
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Tanya N Nelson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, BC Children's and BC Women's Hospitals, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Frédérique Tihy
- Service de Génétique Médicale, CHU Sainte-Justine, Université de Montréal, Montreal, Quebec, Canada
| | - Mary Ann Thomas
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Alberta, Canada
| | - Dimitri J Stavropoulos
- Genome Diagnostics, Department of Pediatric Laboratory Medicine, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
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11
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Sahoo T, Dzidic N, Strecker MN, Commander S, Travis MK, Doherty C, Tyson RW, Mendoza AE, Stephenson M, Dise CA, Benito CW, Ziadie MS, Hovanes K. Comprehensive genetic analysis of pregnancy loss by chromosomal microarrays: outcomes, benefits, and challenges. Genet Med 2016; 19:83-89. [PMID: 27337029 DOI: 10.1038/gim.2016.69] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/19/2016] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Chromosomal microarray analysis (CMA) is currently considered first-tier testing in pediatric care and prenatal diagnosis owing to its high diagnostic sensitivity for chromosomal imbalances. The aim of this study was to determine the efficacy and diagnostic power of CMA in both fresh and formalin-fixed paraffin-embedded (FFPE) samples of products of conception (POCs). METHODS Over a 44-month period, 8,118 consecutive samples were received by our laboratory for CMA analysis. This included both fresh (76.4%) and FFPE samples (22.4%), most of which were ascertained for recurrent pregnancy loss and/or spontaneous abortion (83%). The majority of samples were evaluated by a whole-genome single-nucleotide polymorphism (SNP)-based array (81.6%); the remaining samples were evaluated by array-comparative genomic hybridization (CGH). RESULTS A successful result was obtained in 7,396 of 8,118 (91.1%), with 92.4% of fresh tissue samples and 86.4% of FFPE samples successfully analyzed. Clinically significant abnormalities were identified in 53.7% of specimens (3,975 of 7,396), 94% of which were considered causative. CONCLUSION Analysis of POC specimens by karyotyping fails in 20-40% of cases. SNP-based CMA is a robust platform, with successful results obtained in >90% of cases. SNP-based CMA can identify aneuploidy, polyploidy, whole-genome homozygosity, segmental genomic imbalances, and maternal cell contamination, thus maximizing sensitivity and decreasing false-negative results. Understanding the etiology of fetal loss enables clarification of recurrence risk and assists in determining appropriate management for future family planning.Genet Med 19 1, 83-89.
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Affiliation(s)
| | | | | | | | | | | | - R Weslie Tyson
- Department of Pathology, SCL Health System, Denver, Colorado, USA
| | - Arturo E Mendoza
- Department of Pathology, Sharp Memorial Hospital, San Diego, California, USA
| | - Mary Stephenson
- Department of Obstetrics and Gynecology, University of Illinois Hospital, Chicago, Illinois, USA
| | - Craig A Dise
- Morristown Medical Center, Morristown, New Jersey, USA
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12
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Rosenfeld JA, Tucker ME, Escobar LF, Neill NJ, Torchia BS, McDaniel LD, Schultz RA, Chong K, Chitayat D. Diagnostic utility of microarray testing in pregnancy loss. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2015; 46:478-486. [PMID: 25846569 DOI: 10.1002/uog.14866] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 03/25/2015] [Accepted: 03/29/2015] [Indexed: 06/04/2023]
Abstract
OBJECTIVES To determine the frequency of clinically significant chromosomal abnormalities identified by chromosomal microarray in pregnancy losses at any gestational age and to compare microarray performance with that of traditional cytogenetic analysis when testing pregnancy losses. METHODS Among 535 fetal demise specimens of any gestational age, clinical microarray-based comparative genomic hybridization (aCGH) was performed successfully on 515, and a subset of 107 specimens underwent additional single nucleotide polymorphism (SNP) analysis. RESULTS Overall, clinically significant abnormalities were identified in 12.8% (64/499) of specimens referred with normal or unknown karyotypes. Detection rates were significantly higher with earlier gestational age. In the subset with normal karyotype, clinically significant abnormalities were identified in 6.9% (20/288). This detection rate did not vary significantly with gestational age, suggesting that, unlike aneuploidy, the contribution of submicroscopic chromosomal abnormalities to fetal demise does not vary with gestational age. In the 107 specimens that underwent aCGH and SNP analysis, seven cases (6.5%) had abnormalities of potential clinical significance detected by the SNP component, including female triploidy. aCGH failed to yield fetal results in 8.3%, which is an improvement over traditional cytogenetic analysis of fetal demise specimens. CONCLUSIONS Both the provision of results in cases in which karyotype fails and the detection of abnormalities in the presence of a normal karyotype demonstrate the increased diagnostic utility of microarray in pregnancy loss. Thus, chromosomal microarray testing is a preferable, robust method of analyzing cases of pregnancy loss to better delineate possible genetic etiologies, regardless of gestational age.
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Affiliation(s)
- J A Rosenfeld
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - M E Tucker
- St. Vincent Hospital, Indianapolis, IN, USA
| | | | - N J Neill
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - B S Torchia
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA
| | - L D McDaniel
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA
| | - R A Schultz
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA
| | - K Chong
- The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, University of Toronto, Ontario, Canada
| | - D Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, University of Toronto, Ontario, Canada
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13
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Srebniak MI, Van Opstal D, Joosten M, Diderich KEM, de Vries FAT, Riedijk S, Knapen MFCM, Go ATJI, Govaerts LCP, Galjaard RJH. Whole-genome array as a first-line cytogenetic test in prenatal diagnosis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2015; 45:363-372. [PMID: 25488734 DOI: 10.1002/uog.14745] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 11/17/2014] [Accepted: 11/21/2014] [Indexed: 06/04/2023]
Affiliation(s)
- M I Srebniak
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
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14
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Abstract
Rapid progress in genomic medicine in recent years has made it possible to diagnose subtle genetic abnormalities in a clinical setting on routine basis. This has allowed for detailed genotype-phenotype correlations and the identification of the genetic basis of many congenital anomalies. In addition to the availability of chromosomal microarray analysis, exome and whole-genome sequencing on pre- and postnatal samples of cell-free DNA has revolutionized the field of prenatal diagnosis. Incorporation of these technologies in perinatal pathology is bound to play a major role in coming years. In this communication, we briefly present the current experience with use of classical chromosome analysis, fluorescence in situ hybridization, and microarray testing, development of whole-genome analysis by next-generation sequencing technology, offer a detailed review of the history and current status of non-invasive prenatal testing using cell-free DNA, and discuss the advents of these new genomic technologies in perinatal medicine.
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Affiliation(s)
- David G. Peters
- Department of Obstetrics, Gynecology, and Reproductive Sciences,
University of Pittsburgh, Pittsburgh, PA 15213,Magee-Womens Research Institute, University of Pittsburgh,
Pittsburgh, PA 15213
| | - Svetlana A. Yatsenko
- Department of Obstetrics, Gynecology, and Reproductive Sciences,
University of Pittsburgh, Pittsburgh, PA 15213,Department of Pathology, University of Pittsburgh, Pittsburgh, PA
15213
| | - Urvashi Surti
- Department of Obstetrics, Gynecology, and Reproductive Sciences,
University of Pittsburgh, Pittsburgh, PA 15213,Department of Pathology, University of Pittsburgh, Pittsburgh, PA
15213,Magee-Womens Research Institute, University of Pittsburgh,
Pittsburgh, PA 15213,Department of Human Genetics, University of Pittsburgh, Pittsburgh,
PA 15213
| | - Aleksandar Rajkovic
- Department of Obstetrics, Gynecology, and Reproductive Sciences,
University of Pittsburgh, Pittsburgh, PA 15213,Department of Pathology, University of Pittsburgh, Pittsburgh, PA
15213,Magee-Womens Research Institute, University of Pittsburgh,
Pittsburgh, PA 15213,Department of Human Genetics, University of Pittsburgh, Pittsburgh,
PA 15213
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15
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Kudesia R, Li M, Smith J, Patel A, Williams Z. Rescue karyotyping: a case series of array-based comparative genomic hybridization evaluation of archival conceptual tissue. Reprod Biol Endocrinol 2014; 12:19. [PMID: 24589081 PMCID: PMC3996014 DOI: 10.1186/1477-7827-12-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 02/27/2014] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Determination of fetal aneuploidy is central to evaluation of recurrent pregnancy loss (RPL). However, obtaining this information at the time of a miscarriage is not always possible or may not have been ordered. Here we report on "rescue karyotyping", wherein DNA extracted from archived paraffin-embedded pregnancy loss tissue from a prior dilation and curettage (D&C) is evaluated by array-based comparative genomic hybridization (aCGH). METHODS A retrospective case series was conducted at an academic medical center. Patients included had unexplained RPL and a prior pregnancy loss for which karyotype information would be clinically informative but was unavailable. After extracting DNA from slides of archived tissue, aCGH with a reduced stringency approach was performed, allowing for analysis of partially degraded DNA. Statistics were computed using STATA v12.1 (College Station, TX). RESULTS Rescue karyotyping was attempted on 20 specimens from 17 women. DNA was successfully extracted in 16 samples (80.0%), enabling analysis at either high or low resolution. The longest interval from tissue collection to DNA extraction was 4.2 years. There was no significant difference in specimen sufficiency for analysis in the collection-to-extraction interval (p=0.14) or gestational age at pregnancy loss (p=0.32). Eight specimens showed copy number variants: 3 trisomies, 2 partial chromosomal deletions, 1 mosaic abnormality and 2 unclassified variants. CONCLUSIONS Rescue karyotyping using aCGH on DNA extracted from paraffin-embedded tissue provides the opportunity to obtain critical fetal cytogenetic information from a prior loss, even if it occurred years earlier. Given the ubiquitous archiving of paraffin embedded tissue obtained during a D&C and the ease of obtaining results despite long loss-to-testing intervals or early gestational age at time of fetal demise, this may provide a useful technique in the evaluation of couples with recurrent pregnancy loss.
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Affiliation(s)
- Rashmi Kudesia
- Program for Early and Recurrent Pregnancy Loss (PEARL), Department of Obstetrics, Gynecology & Women’s Health, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Price Building, Room 474, Bronx, NY 10461, USA
| | - Marilyn Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop NAB 2015, Houston, TX 77030, USA
| | - Janice Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop NAB 2015, Houston, TX 77030, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop NAB 2015, Houston, TX 77030, USA
| | - Zev Williams
- Program for Early and Recurrent Pregnancy Loss (PEARL), Department of Obstetrics, Gynecology & Women’s Health, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Price Building, Room 474, Bronx, NY 10461, USA
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16
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Kooper AJA, Faas BHW, Feenstra I, de Leeuw N, Smeets DFCM. Best diagnostic approach for the genetic evaluation of fetuses after intrauterine death in first, second or third trimester: QF-PCR, karyotyping and/or genome wide SNP array analysis. Mol Cytogenet 2014; 7:6. [PMID: 24428858 PMCID: PMC3906897 DOI: 10.1186/1755-8166-7-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 12/17/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The aim of this study was to evaluate the best diagnostic approach for the genetic analysis of samples from first, second and third trimester intrauterine fetal deaths (IUFDs). We examined a total of 417 IUFD samples from fetuses with and without congenital anomalies. On 414 samples, karyotyping (N = 46) and/or rapid aneuploidy testing by QF-PCR (N = 371) was performed). One hundred sixty eight samples with a normal test result were subsequently tested by genome wide Single Nucleotide Polymorphism (SNP) array analysis. Three samples were only analyzed by array. RESULTS In 50 (12.0%) samples an aneuploidy was detected by QF-PCR and/or karyotyping, representing 47.1% of first, 13.2% of second and 3.4% of third trimester pregnancies. Karyotyping and QF-PCR failed in 4 (8.7%) and 7 (1.9%) samples, respectively, concerning mostly contaminated amniotic fluid samples from third trimester pregnancies.Clinically relevant aberrations were identified in 4.2% (all fetuses with malformations) of the 168 samples tested by SNP array. Inherited copy number variants (CNVs) were detected in 5.4% and 8.9% showed CNVs of unknown clinical relevance as parental inheritance could not be studied yet. In a sample from a fetus suspect for Meckel-Grüber syndrome, the genotype information from the SNP array revealed various stretches of homozygosity, including one stretch encompassing the CEP290 gene. Subsequent CEP290 mutation analysis revealed a homozygous, pathogenic mutation in this gene. CONCLUSIONS Based on our experience we recommend QF-PCR as the first-line test in IUFD samples of first and second trimester pregnancies to exclude aneuploidy before performing array analysis. The chance to detect aneuploidy in third trimester pregnancies is relatively low and therefore array analysis can be performed as a first-tier test. A tissue sample, instead of amniotic fluid, is preferred because of a higher success rate in testing.We emphasize the need for analysis of parental samples whenever a rare, unique CNV is detected to allow for better interpretation of such findings and to improve future pregnancy management. Furthermore, we illustrate the strength of SNP arrays for genotype analysis, even though we realize it is crucial to have detailed phenotypic information to make optimal use of the genotype data in finding candidate recessive genes that may be related to the fetal phenotype.
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Affiliation(s)
- Angelique JA Kooper
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Brigitte HW Faas
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Ilse Feenstra
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Dominique FCM Smeets
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
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17
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Rowe LR, Thaker HM, Opitz JM, Schiffman JD, Haddadin ZM, Erickson LK, South ST. Molecular Inversion Probe Array for the Genetic Evaluation of Stillbirth Using Formalin-Fixed, Paraffin-Embedded Tissue. J Mol Diagn 2013; 15:466-72. [DOI: 10.1016/j.jmoldx.2013.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/28/2013] [Accepted: 03/15/2013] [Indexed: 11/25/2022] Open
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18
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Reddy UM, Page GP, Saade GR, Silver RM, Thorsten VR, Parker CB, Pinar H, Willinger M, Stoll BJ, Heim-Hall J, Varner MW, Goldenberg RL, Bukowski R, Wapner RJ, Drews-Botsch CD, O'Brien BM, Dudley DJ, Levy B. Karyotype versus microarray testing for genetic abnormalities after stillbirth. N Engl J Med 2012; 367:2185-93. [PMID: 23215556 PMCID: PMC4295117 DOI: 10.1056/nejmoa1201569] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Genetic abnormalities have been associated with 6 to 13% of stillbirths, but the true prevalence may be higher. Unlike karyotype analysis, microarray analysis does not require live cells, and it detects small deletions and duplications called copy-number variants. METHODS The Stillbirth Collaborative Research Network conducted a population-based study of stillbirth in five geographic catchment areas. Standardized postmortem examinations and karyotype analyses were performed. A single-nucleotide polymorphism array was used to detect copy-number variants of at least 500 kb in placental or fetal tissue. Variants that were not identified in any of three databases of apparently unaffected persons were then classified into three groups: probably benign, clinical significance unknown, or pathogenic. We compared the results of karyotype and microarray analyses of samples obtained after delivery. RESULTS In our analysis of samples from 532 stillbirths, microarray analysis yielded results more often than did karyotype analysis (87.4% vs. 70.5%, P<0.001) and provided better detection of genetic abnormalities (aneuploidy or pathogenic copy-number variants, 8.3% vs. 5.8%; P=0.007). Microarray analysis also identified more genetic abnormalities among 443 antepartum stillbirths (8.8% vs. 6.5%, P=0.02) and 67 stillbirths with congenital anomalies (29.9% vs. 19.4%, P=0.008). As compared with karyotype analysis, microarray analysis provided a relative increase in the diagnosis of genetic abnormalities of 41.9% in all stillbirths, 34.5% in antepartum stillbirths, and 53.8% in stillbirths with anomalies. CONCLUSIONS Microarray analysis is more likely than karyotype analysis to provide a genetic diagnosis, primarily because of its success with nonviable tissue, and is especially valuable in analyses of stillbirths with congenital anomalies or in cases in which karyotype results cannot be obtained. (Funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development.).
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Affiliation(s)
- Uma M Reddy
- Pregnancy and Perinatology Branch, the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, MD 20892-7510, USA
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19
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Bianchi DW. From prenatal genomic diagnosis to fetal personalized medicine: progress and challenges. Nat Med 2012; 18:1041-51. [PMID: 22772565 DOI: 10.1038/nm.2829] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Thus far, the focus of personalized medicine has been the prevention and treatment of conditions that affect adults. Although advances in genetic technology have been applied more frequently to prenatal diagnosis than to fetal treatment, genetic and genomic information is beginning to influence pregnancy management. Recent developments in sequencing the fetal genome combined with progress in understanding fetal physiology using gene expression arrays indicate that we could have the technical capabilities to apply an individualized medicine approach to the fetus. Here I review recent advances in prenatal genetic diagnostics, the challenges associated with these new technologies and how the information derived from them can be used to advance fetal care. Historically, the goal of prenatal diagnosis has been to provide an informed choice to prospective parents. We are now at a point where that goal can and should be expanded to incorporate genetic, genomic and transcriptomic data to develop new approaches to fetal treatment.
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Affiliation(s)
- Diana W Bianchi
- The Mother Infant Research Institute at Tufts Medical Center and the Division of Genetics, Department of Pediatrics, Floating Hospital for Children, Boston, Massachusetts, USA.
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20
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Reddy UM, Page GP, Saade GR. The role of DNA microarrays in the evaluation of fetal death. Prenat Diagn 2012; 32:371-5. [DOI: 10.1002/pd.3825] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Uma M. Reddy
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health; Bethesda MD USA
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21
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Abstract
PURPOSE OF REVIEW Evaluation of copy number variation by microarray analysis has significant advantages over standard metaphase karyotyping and is quickly becoming the primary means of postnatal genetic evaluation for neonates and infants with dysmorphic features or cognitive difficulties. Before this technology is routinely used for prenatal diagnosis, further evaluation of its value and the clinical dilemmas it may introduce requires further study. This article reviews the recent literature on array technology use in prenatal diagnosis. RECENT FINDINGS The use of microarray analysis for routine prenatal diagnosis is still being investigated. Use in certain prenatal situations such as the fetus with structural anomalies or those who are stillborn appears to add important, clinically relevant information. There are a broad range of array designs available and recent research has focused on the appropriate design for prenatal testing. Patient counseling may occasionally be difficult because of the uncertain phenotype associated with some array findings. SUMMARY We present a brief overview of microarray technology including benefits and limitations. Previous research regarding use of microarray in prenatal diagnosis including specific scenarios of anomalous fetuses and abnormal karyotype is reviewed. Current guidelines and the authors' recommendations are presented.
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22
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Harris RA, Ferrari F, Ben-Shachar S, Wang X, Saade G, Van Den Veyver I, Facchinetti F, Aagaard-Tillery K. Genome-wide array-based copy number profiling in human placentas from unexplained stillbirths. Prenat Diagn 2011; 31:932-44. [PMID: 21732394 DOI: 10.1002/pd.2817] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 05/29/2011] [Accepted: 06/01/2011] [Indexed: 01/12/2023]
Abstract
OBJECTIVE Accumulating evidence suggests that genomic structural variations, particularly copy number variations (CNV), are a common occurrence in humans that may bear phenotypic consequences for living individuals possessing the variant. While precise estimates vary, large-scale karyotypic abnormalities are present in 6-12% of stillbirths (SB). However, due to inherent limitations of conventional cytogenetics, the contribution of genomic aberrations to stillbirth is likely underrepresented. High-resolution copy number variant analysis by genomic array-based profiling may overcome such limitations. METHODS Prospectively acquired SB cases > 22 weeks underwent classification of 'unexplained' stillbirth by Wigglesworth and Aberdeen criteria after extensive testing and rigorous multidisciplinary audit. Genome-wide analysis was conducted using high-resolution Illumina single nucleotide polymorphism (SNP) arrays (Human CNV370-Duo) on placental and fetal samples. Potential alternate detection methods were completed by one or more of three independent means (quantitative PCR, Illumina1M, or Agilent105K comparative genomic hybridization arrays). RESULTS In our cohort of 54 stillbirths, 29 met strict unexplained criteria. Among these, we identified 24 putative novel CNVs. Subsequent interrogation detected 18 of 24 CNVs (75%) in placental samples, 8 of which were also confirmed in available fetal samples; none were present in maternal blood. CONCLUSION We describe the potential of whole-genome placental profiling to identify small genomic imbalances, which might contribute to a small proportion of well-characterized, unexplained stillbirths.
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Affiliation(s)
- R Alan Harris
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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23
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Abstract
Fetal disorders (including congenital malformations) are among the most frequent of causes of intrauterine death. Assessment to detect fetal processes is straightforward: history (prenatal, perinatal, and family); external clinical examination; photographs; whole body radiographs; cytogenetic investigation; and internal necropsy. Unfortunately such investigations are profoundly underused. When appropriately and nonselectively assessed, about one-fifth of all stillborn infants will be found to have a fetal cause of their death. Fetal diagnoses are markedly heterogeneous, with no single process accounting for more than 1.5% of all fetal deaths. Identifying a fetal cause has marked implications for the family and changes some elements of counseling and care in more than half of those whose stillborn infants were adequately evaluated. Currently unmet needs include research needs including efforts to understand the variability of intrauterine effects of fetal disorders and their causes, and clinical needs, particularly related to funding for evaluation of stillborns and development of geographically dispersed multidisciplinary commitment and expertise devoted to stillbirth evaluation.
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