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Xie X, Su L, Li Y, Shen Q, Wang M, Wu X. Single nucleotide polymorphism array (SNP-array) analysis for fetuses with abnormal nasal bone. Arch Gynecol Obstet 2024; 309:2475-2482. [PMID: 37430178 DOI: 10.1007/s00404-023-07122-5] [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: 04/05/2023] [Accepted: 06/16/2023] [Indexed: 07/12/2023]
Abstract
PURPOSE This study aims to evaluate the prevalence of submicroscopic chromosomal abnormalities found on single nucleotide polymorphism array (SNP array) in pregnancies with either an absent or hypoplastic nasal bone. METHODS This retrospective study included 333 fetuses with either nasal bone hypoplasia or absence identified on prenatal ultrasound. SNP array analysis and conventional karyotyping were performed in all the subjects. The prevalence of chromosomal abnormalities was adjusted for maternal age and other ultrasound findings. Fetuses with either an isolated nasal bone absence or hypoplasia, those that had additional soft ultrasound markers, and those where structural defects were found on ultrasound were divided into three groups: A, B, and C, respectively. RESULTS Among the total cohort of 333 fetuses, 76 (22.8%) had chromosomal abnormalities, including 47 cases of trisomy 21, 4 cases of trisomy 18, 5 cases of sex chromosome aneuploidy, and 20 cases of copy number variations of which 12 were pathogenic or likely pathogenic. The prevalence of chromosomal abnormalities in group A (n = 164), B (n = 79), and C (n = 90) was 8.5%, 29.1% and 43.3%, respectively. The incremental yields by SNP-array compared with karyotyping in group A, B, and C were 3.0%, 2.5% and 10.7%, respectively (p > 0.05). Compared to karyotype analysis, SNP array detected an additional 2 (1.2%), 1 (1.3%), and 5 (5.6%) pathogenic or likely pathogenic CNVs in groups A, B, and C, respectively. In the 333 fetuses, the prevalence of chromosomal abnormalities in women with advanced maternal age (AMA) was significantly higher than that in non-AMA women, (47.8% vs. 16.5%, p < 0.05). CONCLUSION In addition to Down's syndrome, many other chromosomal abnormalities are present in fetuses with abnormal nasal bone. SNP array can improve the prevalence of chromosomal abnormalities associated with nasal bone abnormalities, especially in pregnancies with non-isolated nasal bone abnormalities and advanced maternal age.
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Affiliation(s)
- Xiaorui Xie
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou, 350001, China
| | - Linjuan Su
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou, 350001, China
| | - Ying Li
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou, 350001, China
| | - Qingmei Shen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou, 350001, China
| | - Meiying Wang
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou, 350001, China
| | - Xiaoqing Wu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou, 350001, China.
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Daum H, Segel R, Meiner V, Goldberg Y, Zeligson S, Weiss O, Stern S, Frumkin A, Zenvirt S, Ganz G, Shkedi-Rafid S. Detection of copy number variants associated with late-onset conditions in ~16 200 pregnancies: parameters for disclosure and pregnancy outcome. J Med Genet 2023; 60:99-105. [PMID: 35264407 DOI: 10.1136/jmedgenet-2021-107890] [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: 04/06/2021] [Accepted: 12/26/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUND Copy number variants (CNVs) associated with late-onset medical conditions are rare but important secondary findings in chromosomal microarray analysis (CMA) performed during pregnancy. Here, we critically review the cases at two tertiary centres to assess the criteria which guide the disclosure of such findings and develop a disclosure decision tool (DDT) aimed at facilitating disclosure decision. Parental decisions on receiving CNVs associated with risks for late-onset conditions were also recorded. METHODS Prenatal CMAs in Hadassah and Shaare Zedek Medical Centers from November 2013 to October 2021 were reviewed for CNVs associated with late-onset conditions. The DDT proposed uses a five-parameter scoring system, which considers the severity, median age of onset, penetrance, understanding of genotype-phenotype correlation and actionability of the finding. RESULTS Out of 16 238 prenatal CMAs, 16 (0.1%) harboured CNVs associated with late-onset conditions, 15 of which were disclosed. Outcome information was available on 13 of the 16 pregnancies, all of which continued to delivery. CONCLUSIONS Our suggested DDT will help clinicians to quantitatively weigh the variables associated with CNVs of this type and arrive at a well thought out clinical decision regarding disclosure. Although the prevalence of late-onset conditions as a major finding in the prenatal setup is low, it is expected to rise with the increasing use of non-invasive CMA testing and whole exome and genome sequencing.
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Affiliation(s)
- Hagit Daum
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Reeval Segel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Vardiella Meiner
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yael Goldberg
- Rabin Medical Center, Recanati Genetics Institute, Beilinson Hospital, Petach Tikva, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Sharon Zeligson
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Omri Weiss
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Shira Stern
- Obstetrics and Gynaecology, Hadassah Medical Center, Jerusalem, Israel
| | - Ayala Frumkin
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
| | - Shamir Zenvirt
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
| | - Gael Ganz
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
| | - Shiri Shkedi-Rafid
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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Lee JM, Shin SY, Kim GW, Kim WJ, Wie JH, Hong S, Kang D, Choi H, Yim J, Kim Y, Kim M, Park IY. Optimizing the Diagnostic Strategy to Identify Genetic Abnormalities in Miscarriage. Mol Diagn Ther 2021; 25:351-359. [PMID: 33792848 PMCID: PMC8139896 DOI: 10.1007/s40291-021-00523-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2021] [Indexed: 12/25/2022]
Abstract
INTRODUCTION The single most common cause of miscarriage is genetic abnormality. OBJECTIVE We conducted a prospective cohort study to compare the performance of conventional karyotyping and chromosomal microarray analysis (CMA) using array comparative genomic hybridization (array-CGH) and single nucleotide polymorphism array (SNP-array) to identify genetic abnormalities in miscarriage specimens. METHODS A total of 63 miscarriage specimens were included. Conventional karyotyping, array-CGH, and SNP-array were performed and the results compared. RESULTS Genetic abnormalities were detected in 31 cases (49.2%) by at least one testing modality. Single autosomal trisomy was the most common defect (71.0%), followed by polyploidy (16.1%), multiple aneuploidy (9.7%), and monosomy X (3.2%). Mosaicisms were identified in four cases and confirmed by fluorescence in situ hybridization (FISH) using appropriate probes. SNP-array had a higher detection rate of genetic abnormalities than array-CGH (93.5 vs. 77.4%), and conventional karyotyping had the lowest detection rate (76.0%). SNP-array enabled the detection of all types of genetic abnormalities, including polyploidy. CONCLUSIONS Although conventional karyotyping and FISH are still needed, SNP-array represents the first choice for miscarriage because the technique showed excellent performance in the detection of genetic abnormalities and minimized the probability of testing failure as well as time, costs, and labor.
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Affiliation(s)
- Jong-Mi Lee
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, 222 Banpodaero, Seocho-gu, Seoul, 06591, South Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpodaero, Seocho-gu, Seoul, 06591, South Korea
| | - So Young Shin
- Department of Obstetrics and Gynecology, College of Medicine, Kyung Hee University Hospital, Kyung Hee University, 23, Kyung Hee Dae-ro, Dongdaemun-gu, Seoul, 02447, South Korea
| | - Guk Won Kim
- Department of Obstetrics and Gynecology, College of Medicine, The Catholic University of Korea, 222 Banpodaero, Seocho-gu, Seoul, 06591, South Korea
| | - Woo Jeng Kim
- Department of Obstetrics and Gynecology, College of Medicine, The Catholic University of Korea, 222 Banpodaero, Seocho-gu, Seoul, 06591, South Korea
| | - Jeong Ha Wie
- Department of Obstetrics and Gynecology, College of Medicine, The Catholic University of Korea, 222 Banpodaero, Seocho-gu, Seoul, 06591, South Korea
| | - Subeen Hong
- Department of Obstetrics and Gynecology, College of Medicine, The Catholic University of Korea, 222 Banpodaero, Seocho-gu, Seoul, 06591, South Korea
| | - Dain Kang
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpodaero, Seocho-gu, Seoul, 06591, South Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpodaero, Seocho-gu, Seoul, 06591, South Korea
| | - Jisook Yim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, 222 Banpodaero, Seocho-gu, Seoul, 06591, South Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpodaero, Seocho-gu, Seoul, 06591, South Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, 222 Banpodaero, Seocho-gu, Seoul, 06591, South Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpodaero, Seocho-gu, Seoul, 06591, South Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, 222 Banpodaero, Seocho-gu, Seoul, 06591, South Korea.
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpodaero, Seocho-gu, Seoul, 06591, South Korea.
| | - In Yang Park
- Department of Obstetrics and Gynecology, College of Medicine, The Catholic University of Korea, 222 Banpodaero, Seocho-gu, Seoul, 06591, South Korea.
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Popescu F, Jaslow CR, Kutteh WH. Recurrent pregnancy loss evaluation combined with 24-chromosome microarray of miscarriage tissue provides a probable or definite cause of pregnancy loss in over 90% of patients. Hum Reprod 2018. [DOI: 10.1093/humrep/dey021] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- F Popescu
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | - C R Jaslow
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | - W H Kutteh
- Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Memphis, TN 38120, USA
- Director of Fertility Preservation, Department of Gynecology, St. Jude Children’s Research Center, Memphis, TN 38105, USA
- Director of Recurrent Pregnancy Loss Center, Fertility Associates of Memphis, Memphis, TN 38120, USA
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Srebniak MI, Knapen MF, Polak M, Joosten M, Diderich KE, Govaerts LC, Boter M, Kromosoeto JN, van Hassel DAC, Huijbregts G, van IJcken WF, Heydanus R, Dijkman A, Toolenaar T, de Vries FA, Knijnenburg J, Go AT, Galjaard RJH, Van Opstal D. The influence of SNP-based chromosomal microarray and NIPT on the diagnostic yield in 10,000 fetuses with and without fetal ultrasound anomalies. Hum Mutat 2017; 38:880-888. [DOI: 10.1002/humu.23232] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/24/2017] [Accepted: 04/09/2017] [Indexed: 12/11/2022]
Affiliation(s)
| | - Maarten F.C.M. Knapen
- Department of Obstetrics and Gynecology; Erasmus Medical Centre; Rotterdam The Netherlands
- Foundation Prenatal Screening Southwest region of the Netherlands; Rotterdam The Netherlands
| | - Marike Polak
- Institute of Psychology; Erasmus University Rotterdam; Rotterdam The Netherlands
| | - Marieke Joosten
- Department of Clinical Genetics; Erasmus Medical Centre; Rotterdam The Netherlands
| | - Karin E.M. Diderich
- Department of Clinical Genetics; Erasmus Medical Centre; Rotterdam The Netherlands
| | | | - Marjan Boter
- Department of Clinical Genetics; Erasmus Medical Centre; Rotterdam The Netherlands
| | - Joan N.R. Kromosoeto
- Department of Clinical Genetics; Erasmus Medical Centre; Rotterdam The Netherlands
| | | | - Gido Huijbregts
- Department of Clinical Genetics; Erasmus Medical Centre; Rotterdam The Netherlands
| | | | - Roger Heydanus
- Department of Obstetrics and Gynecology; Amphia Hospital; Breda The Netherlands
| | - Anneke Dijkman
- Department of Obstetrics and Gynecology; Reinier de Graaf Gasthuis; Delft The Netherlands
| | - Toon Toolenaar
- Department of Gynecology; Albert Schweitzer Hospital Dordrecht; Dordrecht The Netherlands
| | - Femke A.T. de Vries
- Department of Clinical Genetics; Erasmus Medical Centre; Rotterdam The Netherlands
| | - Jeroen Knijnenburg
- Department of Clinical Genetics; Erasmus Medical Centre; Rotterdam The Netherlands
| | - Attie T.J.I. Go
- Department of Obstetrics and Gynecology; Erasmus Medical Centre; Rotterdam The Netherlands
| | | | - Diane Van Opstal
- Department of Clinical Genetics; Erasmus Medical Centre; Rotterdam The Netherlands
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Oneda B, Rauch A. Microarrays in prenatal diagnosis. Best Pract Res Clin Obstet Gynaecol 2017; 42:53-63. [PMID: 28215395 DOI: 10.1016/j.bpobgyn.2017.01.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 12/13/2016] [Accepted: 01/04/2017] [Indexed: 01/09/2023]
Abstract
In prenatal diagnosis, chromosomal microarray (CMA) has not yet fully replaced conventional karyotyping but has rapidly become the recommended test in pregnancies with ultrasound abnormalities. In this review, we provide an overview of the published data concerning this technology and the controversies concerning its use in the prenatal setting. There is abundant evidence indicating the added detection of pathogenic abnormalities with CMA in comparison to the traditional karyotyping, especially in fetuses with multiple or isolated ultrasound abnormalities such as congenital heart disease, increased nuchal translucency, or oral cleft. On the other hand, there is also a risk to detect variants of unknown significance, late-onset disorders, and variants in susceptibility loci. However, it has been shown that pregnant couples tend to prefer a maximum of information about the health of their unborn child. Taken together, CMA has considerable diagnostic and prognostic values during pregnancy and should therefore be the test of choice.
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Affiliation(s)
- Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland.
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
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7
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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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8
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Fiorentino F, Napoletano S, Caiazzo F, Sessa M, Bono S, Spizzichino L, Gordon A, Nuccitelli A, Rizzo G, Baldi M. Chromosomal microarray analysis as a first-line test in pregnancies with a priori low risk for the detection of submicroscopic chromosomal abnormalities. Eur J Hum Genet 2013; 21:725-30. [PMID: 23211699 PMCID: PMC3722951 DOI: 10.1038/ejhg.2012.253] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In this study, we aimed to explore the utility of chromosomal microarray analysis (CMA) in groups of pregnancies with a priori low risk for detection of submicroscopic chromosome abnormalities, usually not considered an indication for testing, in order to assess whether CMA improves the detection rate of prenatal chromosomal aberrations. A total of 3000 prenatal samples were processed in parallel using both whole-genome CMA and conventional karyotyping. The indications for prenatal testing included: advanced maternal age, maternal serum screening test abnormality, abnormal ultrasound findings, known abnormal fetal karyotype, parental anxiety, family history of a genetic condition and cell culture failure. The use of CMA resulted in an increased detection rate regardless of the indication for analysis. This was evident in high risk groups (abnormal ultrasound findings and abnormal fetal karyotype), in which the percentage of detection was 5.8% (7/120), and also in low risk groups, such as advanced maternal age (6/1118, 0.5%), and parental anxiety (11/1674, 0.7%). A total of 24 (0.8%) fetal conditions would have remained undiagnosed if only a standard karyotype had been performed. Importantly, 17 (0.6%) of such findings would have otherwise been overlooked if CMA was offered only to high risk pregnancies.The results of this study suggest that more widespread CMA testing of fetuses would result in a higher detection of clinically relevant chromosome abnormalities, even in low risk pregnancies. Our findings provide substantial evidence for the introduction of CMA as a first-line diagnostic test for all pregnant women undergoing invasive prenatal testing, regardless of risk factors.
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Srebniak MI, Mout L, Van Opstal D, Galjaard RJH. 0.5 Mb array as a first-line prenatal cytogenetic test in cases without ultrasound abnormalities and its implementation in clinical practice. Hum Mutat 2013; 34:1298-303. [PMID: 23674485 DOI: 10.1002/humu.22355] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 05/02/2013] [Indexed: 01/08/2023]
Abstract
Using whole-genome array testing instead of karyotyping in prenatal diagnosis for all indications may be desirable because of the higher diagnostic yield and shorter reporting time. The goal of this research was finding the optimal array resolution that could replace routine prenatal karyotyping in cases without ultrasound abnormalities, for example, referred for advanced maternal age or abnormal first trimester screening. As variants of unknown clinical significance (VOUS), if reported, might complicate decision-making about continuation of pregnancy, such an optimal array resolution should have a high abnormality detection rate and reveal a minimal amount of VOUS. The array data of 465 fetuses were retrospectively evaluated with several resolution levels, and the Decipher microdeletion/microduplication syndrome list was reviewed to assess what could be theoretically missed with a lower resolution. A 0.5-Mb resolution showed a high diagnostic yield potential and significantly minimized the number of VOUS. Based on our experience, we recommend genomic SNP array as a first-tier test in prenatal diagnosis. The resolution should be chosen based on the indication. In cases of fetal ultrasound abnormalities or intrauterine fetal death (IUFD), high-resolution analysis should be done. In other cases, we advise replacing karyotyping by SNP array analysis with 0.5 Mb resolution.
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Schmid M, Stary S, Springer S, Bettelheim D, Husslein P, Streubel B. Prenatal microarray analysis as second-tier diagnostic test: single-center prospective study. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2013; 41:267-273. [PMID: 23292918 DOI: 10.1002/uog.12389] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/06/2012] [Indexed: 06/01/2023]
Abstract
OBJECTIVE To evaluate the usefulness of chromosome microarrays as a second-tier test in prenatal genetic testing. METHODS We prospectively analyzed 75 high-risk pregnancies undergoing invasive prenatal genetic testing in which the karyotype either was normal or had findings other than a common non-mosaic autosomal aneuploidy. RESULTS Chromosomal microarray analysis (CMA) was performed successfully in all cases. Pathological copy-number variations (CNVs) explaining the phenotypes were found in 11 cases (14.7%). Four cases were detected with an unbalanced translocation. In three of these cases, subsequent genetic analysis demonstrated that a parent was an unknown carrier of a balanced translocation. Among the 67 cases with normal karyo-types, submicroscopic rearrangements with pathological significance were detected in five (7.5%) and CNVs of unclear significance were detected in one (1.5%). CMA was able to discriminate correctly between true mosaicism and confined or pseudomosaicism in all six mosaic cases. CONCLUSION CMA is a valuable second-tier test in high-risk pregnancies for which identification or further delineation of genetic aberrations is important. Its higher resolution results in a higher detection rate of aberrant cases, with a clear clinical benefit for estimation of risk of recurrence.
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Affiliation(s)
- M Schmid
- Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
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11
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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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Prockop DJ, Keating A. Relearning the lessons of genomic stability of human cells during expansion in culture: implications for clinical research. Stem Cells 2012; 30:1051-2. [PMID: 22495826 DOI: 10.1002/stem.1103] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Abstract
Genomic microarrays are now widely used diagnostically for the molecular karyotyping of patients with intellectual disability, congenital anomalies and autistic spectrum disorder and have more recently been applied for the detection of genomic imbalances in prenatal genetic diagnosis. We present an overview of the different arrays, protocols used and discuss methods of genomic array data analysis.
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Affiliation(s)
- Paul D Brady
- Laboratory for Cytogenetics and Genome Research, Centre for Human Genetics, University Hospital Leuven, K.U. Leuven, Leuven, Belgium
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14
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Breman A, Pursley AN, Hixson P, Bi W, Ward P, Bacino CA, Shaw C, Lupski JR, Beaudet A, Patel A, Cheung SW, Van den Veyver I. Prenatal chromosomal microarray analysis in a diagnostic laboratory; experience with >1000 cases and review of the literature. Prenat Diagn 2012; 32:351-61. [PMID: 22467166 DOI: 10.1002/pd.3861] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
OBJECTIVE To evaluate the results of prenatal chromosomal microarray analysis (CMA) on >1000 fetal samples referred for testing at our institution and to compare these data to published reports. METHODS High resolution CMA was offered to women undergoing amniocentesis or chorionic villus sampling. Parental samples were obtained concurrently to exclude maternal cell contamination and assist interpretation of copy number variations. RESULTS Clinically significant copy number variations were observed in 85/1115 cases (7.6%) overall, and in 45/1075 cases (4.2 %) if 40 abnormal cases with known chromosome abnormalities or familial genomic imbalances were excluded. Eighteen of the 1115 cases had variants of unclear clinical significance (1.6%). Indications yielding the most clinically significant findings were abnormal karyotype/fluorescence in situ hybridization (26/61, 42.6%), family history of chromosomal abnormality (13/137, 9.5%), abnormal ultrasound (38/410, 9.3%), abnormal serum screening (2/37, 5.4%) and advanced maternal age (5/394, 1.3%). Of 1075 cases having no previously known cytogenetic abnormality or family history, 18 (1.7%) had clinically significant genomic changes undetectable by conventional prenatal chromosome analysis. CONCLUSION Current experience confirms that the detection rate of CMA for prenatal chromosomal abnormalities surpasses that of conventional karyotype analysis and continues to improve with higher resolution arrays, while maintaining a low frequency of results of unclear clinical significance.
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Affiliation(s)
- Amy Breman
- Medical Genetics Laboratories, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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15
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Current World Literature. Curr Opin Obstet Gynecol 2012; 24:265-72. [DOI: 10.1097/gco.0b013e3283564f02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Vetro A, Bouman K, Hastings R, McMullan DJ, Vermeesch JR, Miller K, Sikkema-Raddatz B, Ledbetter DH, Zuffardi O, van Ravenswaaij-Arts CMA. The introduction of arrays in prenatal diagnosis: a special challenge. Hum Mutat 2012; 33:923-9. [PMID: 22508381 DOI: 10.1002/humu.22050] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 02/03/2012] [Indexed: 01/14/2023]
Abstract
Genome-wide arrays are rapidly replacing conventional karyotyping in postnatal cytogenetic diagnostics and there is a growing request for arrays in the prenatal setting. Several studies have documented 1-3% additional abnormal findings in prenatal diagnosis with arrays compared to conventional karyotyping. A recent meta-analysis demonstrated that 5.2% extra diagnoses can be expected in fetuses with ultrasound abnormalities. However, no consensus exists as to whether the use of genome-wide arrays should be restricted to pregnancies with ultrasound abnormalities, performed in all women undergoing invasive prenatal testing or offered to all pregnant women. Moreover, the interpretation of array results in the prenatal situation is challenging due to the large numbers of copy number variants with no major phenotypic effect. This also raises the question of what, or what not to report, for example, how to deal with unsolicited findings. These issues were discussed at a working group meeting that preceded the European Society of Human Genetics 2011 Conference in Amsterdam. This article is the result of this meeting and explores the introduction of genome-wide arrays into routine prenatal diagnosis. We aim to give some general recommendations on how to develop practical guidelines that can be implemented in the local setting and that are consistent with the emerging international consensus.
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17
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Querejeta ME, Nieva B, Navajas J, Cigudosa JC, Suela J. Diagnóstico prenatal y array-CGH II: gestaciones de bajo riesgo. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.diapre.2012.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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18
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Mori MDLÁ, Mansilla E, García-Santiago F, Vallespín E, Palomares M, Martín R, Rodríguez R, Martínez-Payo C, Gil-Fournier B, Ramiro S, Lapunzina P, Nevado J. Diagnóstico prenatal y array-hibridación genómica comparada (CGH) (I). Gestaciones de elevado riesgo. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.diapre.2012.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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19
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Faas BHW, Feenstra I, Eggink AJ, Kooper AJA, Pfundt R, van Vugt JMG, de Leeuw N. Non-targeted whole genome 250K SNP array analysis as replacement for karyotyping in fetuses with structural ultrasound anomalies: evaluation of a one-year experience. Prenat Diagn 2012; 32:362-70. [DOI: 10.1002/pd.2948] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Brigitte HW Faas
- Department of Human Genetics; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - Ilse Feenstra
- Department of Human Genetics; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - Alex J. Eggink
- Department of Obstetrics and Gynecology; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
- Department of Obstetrics and Gynecology, Erasmus MC; University Medical Centre Rotterdam; Rotterdam The Netherlands
| | - Angelique JA Kooper
- Department of Human Genetics; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - John MG van Vugt
- Department of Obstetrics and Gynecology; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
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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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