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Mitrakos A, Kosma K, Makrythanasis P, Tzetis M. Prenatal Chromosomal Microarray Analysis: Does Increased Resolution Equal Increased Yield? Genes (Basel) 2023; 14:1519. [PMID: 37628571 PMCID: PMC10454647 DOI: 10.3390/genes14081519] [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: 06/26/2023] [Revised: 07/16/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Chromosomal microarray analysis (CMA) is considered a first-tier test for patients with developmental disabilities and congenital anomalies and is also routinely applied in prenatal diagnosis. The current consensus size cut-off for reporting copy number variants (CNVs) in the prenatal setting ranges from 200 Kb to 400 Kb, with the intention of minimizing the impact of variants of uncertain significance (VUS). Very limited data are currently available on the application of higher resolution platforms prenatally. The aim of this study is to investigate the feasibility and impact of applying high-resolution CMA in the prenatal setting. To that end, we report on the outcomes of applying CMA with a size cut-off of 20 Kb in 250 prenatal samples and discuss the findings and diagnostic yield and also provide follow-up for cases with variants of uncertain significance. Overall, 19.6% (49) showed one or more chromosomal abnormalities, with the findings classified as Pathogenic (P) or Likely Pathogenic (LP) in 15.6% and as VUS in 4%. When excluding the cases with known familial aberrations, the diagnostic yield was 12%. The smallest aberration detected was a 32 Kb duplication of the 16p11.2 region. In conclusion, this study demonstrates that prenatal diagnosis with a high-resolution aCGH platform can reliably detect smaller CNVs that are often associated with neurodevelopmental phenotypes while providing an increased diagnostic yield, regardless of the indication for testing, with only a marginal increase in the VUS incidence. Thus, it can be an important tool in the prenatal setting.
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Affiliation(s)
- Anastasios Mitrakos
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, 11527 Athens, Greece; (K.K.); (P.M.)
| | | | | | - Maria Tzetis
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, 11527 Athens, Greece; (K.K.); (P.M.)
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2
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Sadeghi S, Rahaie M, Ostad-Hasanzadeh B. Nanostructures in non-invasive prenatal genetic screening. Biomed Eng Lett 2022; 12:3-18. [PMID: 35186357 PMCID: PMC8825889 DOI: 10.1007/s13534-021-00208-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/22/2021] [Accepted: 10/02/2021] [Indexed: 11/24/2022] Open
Abstract
Prenatal screening is an important issue during pregnancy to ensure fetal and maternal health, as well as preventing the birth of a defective fetus and further problems such as extra costs for the family and society. The methods for the screening have progressed to non-invasive approaches over the recent years. Limitations of common standard screening tests, including invasive sampling, high risk of abortion and a big delay in result preparation have led to the introduction of new rapid and non-invasive approaches for screening. Non-invasive prenatal screening includes a wide range of procedures, including fetal cell-free DNA analysis, proteome, RNAs and other fetal biomarkers in maternal serum. These biomarkers require less invasive sampling than usual methods such as chorionic villus sampling, amniocentesis or cordocentesis. Advanced strategies including the development of nanobiosensors and the use of special nanoparticles have provided optimization and development of NIPS tests, which leads to more accurate, specific and sensitive screening tests, rapid and more reliable results and low cost, as well. This review discusses the specifications and limitations of current non-invasive prenatal screening tests and introduces a novel collection of detection methods reported studies on nanoparticles' aided detection. It can open a new prospect for further studies and effective investigations in prenatal screening field.
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Affiliation(s)
- Samira Sadeghi
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14399-57131 Tehran, Iran
| | - Mahdi Rahaie
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14399-57131 Tehran, Iran
| | - Bita Ostad-Hasanzadeh
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14399-57131 Tehran, Iran
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3
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Atlas G, Sreenivasan R, Sinclair A. Targeting the Non-Coding Genome for the Diagnosis of Disorders of Sex Development. Sex Dev 2021; 15:392-410. [PMID: 34634785 DOI: 10.1159/000519238] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/12/2021] [Indexed: 11/19/2022] Open
Abstract
Disorders of sex development (DSD) are a complex group of conditions with highly variable clinical phenotypes, most often caused by failure of gonadal development. DSD are estimated to occur in around 1.7% of all live births. Whilst the understanding of genes involved in gonad development has increased exponentially, approximately 50% of patients with a DSD remain without a genetic diagnosis, possibly implicating non-coding genomic regions instead. Here, we review how variants in the non-coding genome of DSD patients can be identified using techniques such as array comparative genomic hybridization (CGH) to detect copy number variants (CNVs), and more recently, whole genome sequencing (WGS). Once a CNV in a patient's non-coding genome is identified, putative regulatory elements such as enhancers need to be determined within these vast genomic regions. We will review the available online tools and databases that can be used to refine regions with potential enhancer activity based on chromosomal accessibility, histone modifications, transcription factor binding site analysis, chromatin conformation, and disease association. We will also review the current in vitro and in vivo techniques available to demonstrate the functionality of the identified enhancers. The review concludes with a clinical update on the enhancers linked to DSD.
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Affiliation(s)
- Gabby Atlas
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia, .,Department of Endocrinology and Diabetes, Royal Children's Hospital, Melbourne, Victoria, Australia, .,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia,
| | - Rajini Sreenivasan
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew Sinclair
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
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4
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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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5
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Tanner LM, Alitalo T, Stefanovic V. Prenatal array comparative genomic hybridization in a well-defined cohort of high-risk pregnancies. A 3-year implementation results in a public tertiary academic referral hospital. Prenat Diagn 2020; 41:422-433. [PMID: 33340112 DOI: 10.1002/pd.5877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/17/2020] [Accepted: 12/02/2020] [Indexed: 11/11/2022]
Abstract
OBJECTIVE To find out whether the diagnostic yield of prenatal array comparative genomic hybridization (aCGH) can be improved by targeting preselected high-risk pregnancies. METHOD All the in-house arrays ordered by the Fetomaternal Medical Center from February 2016 until December 2018 were retrospectively analyzed. The indications for array analysis included fetal structural abnormalities, increased nuchal translucency ≥3.5 mm and a chromosomal abnormality in a parent or a sibling. Common aneuploidies were excluded. RESULTS Diagnostic yield was 15.1% in the entire patient cohort and as high as 20% in fetuses with multiple structural anomalies. The diagnostic yield was lowest in the group with isolated growth retardation. A total of 76 copy number variants (CNVs) were reported from a total of 65 samples, including 16 CNVs associated with a well-described microdeletion/microduplication syndrome, six autosomal trisomies in mosaic form, and three pathogenic single-gene deletions with dominant inheritance and 12 CNVs known to be risk factors for eg developmental delay. CONCLUSION The diagnostic yield of aCGH was higher than what has previously been reported in less defined patient cohorts. However, the number of CNVs with unclear correlation to the fetal ultrasound findings was still relatively high. The importance of adequate pre- and posttest counseling must therefore be emphasized.
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Affiliation(s)
- Laura M Tanner
- HUSLAB Department of Clinical Genetics, Helsinki University Hospital, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Department of Obstetrics and Gynecology, Fetomaternal Medical Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Tiina Alitalo
- HUSLAB Genetics Laboratory, Helsinki University Hospital, Helsinki, Finland
| | - Vedran Stefanovic
- Department of Obstetrics and Gynecology, Fetomaternal Medical Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
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6
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Huy Le B, Nguyen VT, Seo YJ. Site-specific incorporation of multiple units of functional nucleotides into DNA using a step-wise approach with polymerase and its application to monitoring DNA structural changes. Chem Commun (Camb) 2019; 55:2158-2161. [PMID: 30675606 DOI: 10.1039/c8cc09444f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have developed a new method, a step-wise approach with polymerase, for site-specific incorporation of multiple units of functional nucleotides into DNA to form hairpin secondary structures. The fluorescence of the resulting DNA incorporating the functional nucleotides varied upon transitioning from single-strand to hairpin and duplex structures.
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Affiliation(s)
- Binh Huy Le
- Department of Bioactive Material Sciences, Chonbuk National University, South Korea
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7
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8
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Vermeesch JR, Voet T, Devriendt K. Prenatal and pre-implantation genetic diagnosis. Nat Rev Genet 2017; 17:643-56. [PMID: 27629932 DOI: 10.1038/nrg.2016.97] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The past decade has seen the development of technologies that have revolutionized prenatal genetic testing; that is, genetic testing from conception until birth. Genome-wide single-cell arrays and high-throughput sequencing analyses are dramatically increasing our ability to detect embryonic and fetal genetic lesions, and have substantially improved embryo selection for in vitro fertilization (IVF). Moreover, both invasive and non-invasive mutation scanning of the genome are helping to identify the genetic causes of prenatal developmental disorders. These advances are changing clinical practice and pose novel challenges for genetic counselling and prenatal care.
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Affiliation(s)
- Joris Robert Vermeesch
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
| | - Thierry Voet
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
| | - Koenraad Devriendt
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
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9
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Pons L, Till M, Alix E, Abel C, Boggio D, Bordes A, Caloone J, Raskin FC, Chatron N, Cordier MP, Fichez A, Labalme A, Lajeunesse C, Liaras É, Massoud M, Miribel J, Ollagnon E, Schluth-Bolard C, Vichier-Cerf A, Edery P, Attia J, Huissoud C, Rudigoz RC, Massardier J, Gaucherand P, Sanlaville D. Prenatal microarray comparative genomic hybridization: Experience from the two first years of activity at the Lyon university-hospital. J Gynecol Obstet Hum Reprod 2017; 46:275-283. [PMID: 28403926 DOI: 10.1016/j.jogoh.2016.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 11/07/2016] [Accepted: 11/17/2016] [Indexed: 11/17/2022]
Abstract
OBJECTIVES This study aims to describe how microarray comparative genomic hybridization (aCGH) has shifted to become a prenatal diagnosis tool at the Lyon university-hospital. MATERIALS AND METHODS This retrospective study included all patients who were referred in the 3 pluridisciplinary centers for prenatal diagnosis of the Lyon university-hospital and who received a prenatal aCGH between June 2013 and June 2015. aCGH was systematically performed in parallel with a karyotype, using the PréCytoNEM array design. RESULTS A total of 260 microarrays were performed for the following indications: 249 abnormal ultrasounds (95.8%), 7 characterizations of chromosomal rearrangements (2.7%), and 4 twins with no abnormal ultrasounds (1.5%). With a resolution of 1 mega base, we found 235 normal results (90.4%), 23 abnormal results (8.8%) and 2 non-returns (0.8%). For the chromosomal rearrangements visible on the karyotype, aCGH identified all of the 12 unbalanced rearrangements and did not identify the 2 balanced rearrangements. Among the fetuses with normal karyotypes, 11 showed abnormal microarray results, corresponding to unbalanced cryptic chromosomal rearrangements (4.2%). CONCLUSION Transferring aCGH to a prenatal diagnosis at the Lyon university-hospital has increased the detection rate of chromosomal abnormalities by 4.2% compared to the single karyotype.
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Affiliation(s)
- L Pons
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France; Université Claude-Bernard Lyon 1, 69008 Lyon, France.
| | - M Till
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France
| | - E Alix
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France
| | - C Abel
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France
| | - D Boggio
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France
| | - A Bordes
- Département d'obstétrique et de gynécologie, groupement hospitalier Est, HCL, 69500 Bron, France
| | - J Caloone
- Département d'obstétrique et de gynécologie, centre hospitalier de la Croix-Rousse, HCL, 69004 Lyon, France
| | - F C Raskin
- Département d'obstétrique et de gynécologie, centre hospitalier Lyon Sud, HCL, 69310 Pierre-Bénite, France
| | - N Chatron
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France; Université Claude-Bernard Lyon 1, 69008 Lyon, France; Équipe Gendev, CNRS UMR 5292, Inserm U1028, centre de recherche en neuroscience de Lyon, 69500 Bron, France
| | - M-P Cordier
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France
| | - A Fichez
- Département d'obstétrique et de gynécologie, centre hospitalier de la Croix-Rousse, HCL, 69004 Lyon, France
| | - A Labalme
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France
| | - C Lajeunesse
- Département d'obstétrique et de gynécologie, groupement hospitalier Est, HCL, 69500 Bron, France
| | - É Liaras
- Département d'obstétrique et de gynécologie, centre hospitalier Lyon Sud, HCL, 69310 Pierre-Bénite, France
| | - M Massoud
- Département d'obstétrique et de gynécologie, groupement hospitalier Est, HCL, 69500 Bron, France
| | - J Miribel
- Département d'obstétrique et de gynécologie, groupement hospitalier Est, HCL, 69500 Bron, France
| | - E Ollagnon
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France
| | - C Schluth-Bolard
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France; Université Claude-Bernard Lyon 1, 69008 Lyon, France; Équipe Gendev, CNRS UMR 5292, Inserm U1028, centre de recherche en neuroscience de Lyon, 69500 Bron, France
| | - A Vichier-Cerf
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France
| | - P Edery
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France; Université Claude-Bernard Lyon 1, 69008 Lyon, France; Équipe Gendev, CNRS UMR 5292, Inserm U1028, centre de recherche en neuroscience de Lyon, 69500 Bron, France
| | - J Attia
- Université Claude-Bernard Lyon 1, 69008 Lyon, France; Département d'obstétrique et de gynécologie, centre hospitalier Lyon Sud, HCL, 69310 Pierre-Bénite, France
| | - C Huissoud
- Département d'obstétrique et de gynécologie, centre hospitalier de la Croix-Rousse, HCL, 69004 Lyon, France
| | - R C Rudigoz
- Université Claude-Bernard Lyon 1, 69008 Lyon, France; Département d'obstétrique et de gynécologie, centre hospitalier de la Croix-Rousse, HCL, 69004 Lyon, France
| | - J Massardier
- Département d'obstétrique et de gynécologie, groupement hospitalier Est, HCL, 69500 Bron, France
| | - P Gaucherand
- Université Claude-Bernard Lyon 1, 69008 Lyon, France; Département d'obstétrique et de gynécologie, groupement hospitalier Est, HCL, 69500 Bron, France
| | - D Sanlaville
- Service de génétique, groupement hospitalier Est, HCL, 59, boulevard Pinel, 69677 Bron, France; Université Claude-Bernard Lyon 1, 69008 Lyon, France; Équipe Gendev, CNRS UMR 5292, Inserm U1028, centre de recherche en neuroscience de Lyon, 69500 Bron, France
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Abstract
Copy number variations (CNVs) in the genomes have been suggested to play important roles in human evolution, genetic diversity, and disease susceptibility. A number of assays have been developed for the detection of CNVs, including fluorescent in situ hybridization (FISH), array-based comparative genomic hybridization (aCGH), PCR-based assays, and next-generation sequencing (NGS). In this chapter, we describe a microarray method that has been used for the detection of genome-wide CNVs, loss of heterozygosity (LOH), and uniparental disomy (UPD) associated with constitutional and neoplastic disorders.
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Affiliation(s)
- Chengsheng Zhang
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA.
| | - Eliza Cerveira
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Mallory Romanovitch
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Qihui Zhu
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
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11
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Evans MI, Vermeesch JR. Current controversies in prenatal diagnosis 3: industry drives innovation in research and clinical application of genetic prenatal diagnosis and screening. Prenat Diagn 2016; 36:1172-1177. [DOI: 10.1002/pd.4967] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/03/2016] [Accepted: 11/04/2016] [Indexed: 01/12/2023]
Affiliation(s)
- Mark I. Evans
- Department of Obstetrics and Gynecology, Fetal Medicine Foundation of America, Comprehensive Genetics, PLLC; Mt. Sinai School of Medicine; New York NY USA
| | - Joris Robert Vermeesch
- Department of Human Genetics, University Hospital Gasthuisberg; University of Leuven; Leuven Belgium
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12
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Leavitt K, Goldwaser T, Bhat G, Kalia I, Klugman SD, Dolan SM. Chromosomal microarray in prenatal diagnosis: case studies and clinical challenges. Per Med 2016; 13:249-255. [PMID: 29767605 DOI: 10.2217/pme-2015-0003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Chromosomal microarray analysis (CMA) is a diagnostic tool used in the evaluation of pediatric patients with congenital anomalies or developmental and intellectual disability. In both the pediatric and prenatal patient population, CMA has been shown to have a higher detection rate of chromosomal abnormalities than conventional karyotype alone. Currently, the diagnostic yield of prenatal CMA is highest when applied to the evaluation of a fetus with multiple ultrasound anomalies. Challenges arise when CMA yields isolated findings not associated with a phenotype on ultrasound or variants of uncertain significance, which warrants evaluation of the risks, benefits, limitations and optimal incorporation of CMA into prenatal care. The clinical cases presented here will be used to illustrate these issues.
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Affiliation(s)
- Karla Leavitt
- Division of Reproductive Genetics, Department of Obstetrics & Gynecology & Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine 1695 Eastchester Road Suite 301, Bronx, NY 10463, USA
| | - Tamar Goldwaser
- Division of Reproductive Genetics, Department of Obstetrics & Gynecology & Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine 1695 Eastchester Road Suite 301, Bronx, NY 10463, USA
| | - Gifty Bhat
- Genetics Division, Department of Pediatrics, Montefiore Medical Center/Albert Einstein College of Medicine, The Children's Hospital at Montefiore, 3415 Bainbridge Ave., Bronx, NY 10467, USA
| | - Isha Kalia
- Division of Reproductive Genetics, Department of Obstetrics & Gynecology & Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine 1695 Eastchester Road Suite 301, Bronx, NY 10463, USA
| | - Susan D Klugman
- Division of Reproductive Genetics, Department of Obstetrics & Gynecology & Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine 1695 Eastchester Road Suite 301, Bronx, NY 10463, USA
| | - Siobhan M Dolan
- Division of Reproductive Genetics, Department of Obstetrics & Gynecology & Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine 1695 Eastchester Road Suite 301, Bronx, NY 10463, USA
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13
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Malan V, Lapierre JM, Egloff M, Goidin D, Beaujard MP, Maurin ML, Attié-Bitach T, Bessières B, Bernard JP, Roth P, Stirnemann J, Salomon L, Romana S, Vekemans M, Ville Y, Turleau C. A French Approach to Test Fetuses with Ultrasound Abnormalities Using a Customized Microarray as First-Tier Genetic Test. Cytogenet Genome Res 2016; 147:103-10. [DOI: 10.1159/000442904] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2015] [Indexed: 11/19/2022] Open
Abstract
Cytogenetic microarray analysis is now the first-tier genetic test used in a postnatal clinical setting to explore genomic imbalances in individuals with developmental disability and/or birth defects. However, in a prenatal setting, this technique is not widely implemented, largely because the clinical impact of some copy number variants (CNVs) remains difficult to assess. This limitation is especially true in France where termination of pregnancy for medical reasons may be performed at any stage of gestation. During a period of 15 months, we investigated 382 fetuses presenting with ultrasound anomalies, using a customized microarray designed to avoid the detection of CNVs raising challenges for genetic counseling. After excluding common aneuploidies, 20/374 (5.3%) fetuses had a pathogenic CNV, among which 12/374 (3.2%) could have been detected by karyotyping, whereas 8/374 (2.1%) were cryptic. Within these 374 cases, 300 were ongoing pregnancies at the time of array comparative genomic hybridization (aCGH) testing. For these pregnancies, we detected 18/300 (6%) pathogenic CNVs, among which 6/300 (2%) were cryptic. Using this approach, only 2/300 (0.6%) of the detected CNVs raised difficulties for genetic counseling. This study confirms the added value of this strategy in a prenatal clinical setting to minimize ethical issues for genetic counseling while enhancing the detection of genomic imbalances.
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Ernst LM, Rand CM, Bao R, Andrade J, Linn RL, Minturn L, Zhang C, Kang W, Weese-Mayer DE. Stillbirth: Genome-wide copy number variation profiling in archived placental umbilical cord samples with pathologic and clinical correlation. Placenta 2015; 36:783-9. [PMID: 26094028 DOI: 10.1016/j.placenta.2015.04.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/30/2015] [Accepted: 04/25/2015] [Indexed: 02/01/2023]
Abstract
INTRODUCTION Stillbirth remains a devastating health issue with 26,000 stillbirths occurring annually in the United States. Formalin-fixed, paraffin-embedded (FFPE) umbilical cord samples are available for many stillbirths. Our aim was to validate the use of these samples in identifying genetic variations in stillbirth through microarray analysis. METHODS This is a retrospective case-control study from a single institution of stillbirths ≥ 23 weeks gestational age and control liveborn infants. Fetal genomic DNA was extracted from FFPE umbilical cord samples of stillborn and control placentas, and genotyping was performed using the Illumina HumanOmniExpresss-12v1 Beadchip. Array results were verified with qPCR. RESULTS 31 case-specific CNVs (17 deletions and 14 amplifications) with an average size of 294 kb for amplifications and 74 kb for deletions were identified among 94 FFPE samples (86 cases; 8 controls). In total 38 (44%) of the stillbirth samples had a CNV detected. Validation of a subset of microarray findings with qPCR confirmed deletions on 1p (2 cases), 11q (4 cases) and amplifications on 18 (1 case). Placental underperfusion changes were seen in stillborns with deletions on 1p, a region containing complement regulatory genes which have been shown to play a role in preeclampsia. DISCUSSION This study validated the use of archived FFPE umbilical cord samples for genome-wide copy number profiling in stillbirths, and demonstrates specific CNV deletions and amplifications. Microarray analysis in an expanded cohort of stillbirth FFPE samples has the potential to identify biomarkers involved in stillbirth pathogenesis.
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Affiliation(s)
- L M Ernst
- Northwestern University, Feinberg School of Medicine, Department of Pathology, USA.
| | - C M Rand
- Ann & Robert H. Lurie Children's Hospital of Chicago, Center for Autonomic Medicine in Pediatrics (CAMP) and Stanley Manne Children's Research Institute, USA
| | - R Bao
- University of Chicago, Center for Research Informatics, USA
| | - J Andrade
- University of Chicago, Center for Research Informatics, USA
| | - R L Linn
- Northwestern University, Feinberg School of Medicine, Department of Pathology, USA
| | - L Minturn
- Northwestern University, Feinberg School of Medicine, Department of Pathology, USA
| | - C Zhang
- University of Chicago, Center for Research Informatics, USA
| | - W Kang
- University of Chicago, Center for Research Informatics, USA
| | - D E Weese-Mayer
- Ann & Robert H. Lurie Children's Hospital of Chicago, Center for Autonomic Medicine in Pediatrics (CAMP) and Stanley Manne Children's Research Institute, USA; Northwestern University, Feinberg School of Medicine, Department of Pediatrics, USA
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Crolla JA, Wapner R, Van Lith JMM. Controversies in prenatal diagnosis 3: should everyone undergoing invasive testing have a microarray? Prenat Diagn 2014; 34:18-22. [PMID: 24302430 DOI: 10.1002/pd.4287] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 11/25/2013] [Indexed: 12/23/2022]
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Abstract
Determining a genetic diagnosis prenatally permits patients to make informed reproductive decisions and to be counseled about possible fetal outcomes. Therefore, it is important for the provider to be aware of the spectrum of genetic conditions and to use appropriate testing modality to obtain specific diagnosis. This article reviews genetic techniques available for prenatal diagnosis such as preimplantation genetic testing, chromosomal microarray, non-invasive prenatal screening, and next-generation sequencing. Chromosomal microarray has emerged as the first diagnostic test for evaluation of multiple congenital anomalies and developmental delay as most of the next-generation sequencing methods do not detect copy-number variants (CNVs). Exome sequencing and whole genome sequencing are time-consuming, so if this needs to be done to obtain an accurate genetic diagnosis, allow sufficient time.
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Yin A, Lu J, Liu C, Guo L, Wu J, Mai M, Zhong Y, Zhang X. A prenatal missed diagnosed case of submicroscopic chromosomal abnormalities by karyotyping: the clinical utility of array-based CGH in prenatal diagnostics. Mol Cytogenet 2014; 7:26. [PMID: 24735551 PMCID: PMC4005634 DOI: 10.1186/1755-8166-7-26] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/26/2014] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Array-based comparative genomic hybridization possesses a number of significant advantages over conventional cytogenetic and other molecular cytogenetic techniques, providing a sensitive and comprehensive detection platform for unexpected imbalances in the genome wide. CASE PRESENTATION The newborn proband, demonstrated with craniofacial dysmorphism and multiple malformations, was born to a family with spontaneous abortions. This pregnancy was uneventful, except the prenatal ultrasound examination showed an increased nuchal translucency at 12(+) weeks of gestation. Cytogenetics revealed an apparently normal karyotype, and the couple decided to continue the pregnancy. Array-based CGH analysis was applied to the affected infant, identified a combination of 18p deletion and 7q duplication. Further study indicates that the unbalanced translocation was inherited from a balanced translocation carrier parent. CONCLUSIONS In review of the case, several overlooked points leading to the missed diagnosis should be discussed and certain quality control strategies should be adopted to avoid similar problems in the future. Array-based CGH and karyotyping techniques are complemented by diverse detection spectrum and resolutions, and a combination of these methods could help providing optimal genetic diagnosis. Given that the array-CGH analysis will not introduce additional risk to patients, it is reasonable to recommend those already undergoing invasive testing should take array-based CGH as an adjunct to conventional cytogenetic tests and other molecular cytogenetic analysis.
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Affiliation(s)
- Aihua Yin
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Jian Lu
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Chang Liu
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Li Guo
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Jing Wu
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Mingqin Mai
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Yanfang Zhong
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Xiaozhuang Zhang
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
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18
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Chen M, Yang YS, Shih JC, Lin WH, Lee DJ, Lin YS, Chou CH, Cameron AD, Ginsberg NA, Chen CA, Lee ML, Ma GC. Microdeletions/duplications involving TBX1 gene in fetuses with conotruncal heart defects which are negative for 22q11.2 deletion on fluorescence in-situ hybridization. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2014; 43:396-403. [PMID: 23828768 DOI: 10.1002/uog.12550] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/21/2013] [Accepted: 06/19/2013] [Indexed: 05/26/2023]
Abstract
OBJECTIVES Conotruncal heart defects (CTD) are associated with del22q11.2 syndrome, which is often diagnosed by fluorescence in-situ hybridization (FISH). However, in those negative for del22q11.2 on FISH, the etiology is usually obscure. We aimed to use high-resolution array comparative genomic hybridization (array CGH) to clarify the underlying genetic causes in these cases. METHODS In this retrospective study, fetal samples of amniocytes or fibroblasts, taken either for prenatal diagnosis by amniocentesis or for postnatal survey after termination of pregnancy, were obtained from 45 fetuses with CTD and were investigated by cytogenetic analysis including karyotyping and FISH for del22q11.2 syndrome. Eight fetuses with no findings on karyotyping and FISH were investigated further by array CGH, real-time quantitative polymerase chain reaction (qPCR) and Sanger sequencing of TBX1. RESULTS Array CGH revealed that three of the eight fetuses carried submicroscopic genomic imbalances. Of these, two cases showed similar small microdeletions/duplications in 22q11.2 (one 0.85 kb microdeletion and one 8.51 kb microduplication). The minimal shared region spanned exon 2 of TBX1, a candidate gene responsible for cardiovascular defects in del22q11.2 syndrome. In all eight cases, the array CGH results were confirmed by qPCR, and Sanger sequencing did not detect other molecular pathologies. CONCLUSION Our findings indicate an association between TBX1 variations and fetal CTD. The results also demonstrate the power of array CGH to further scrutinize the critical gene(s) of del22q11.2 syndrome responsible for heart defects. Array CGH apparently has diagnostic sensitivity superior to that of FISH in fetuses with CTD associated with del22q11.2 (and dup22q11.2) syndrome.
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Affiliation(s)
- M Chen
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua, Taiwan; Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua, Taiwan; Department of Obstetrics and Gynecology, College of Medicine and Hospital, National Taiwan University, Taipei, Taiwan; Department of Life Sciences, Tunghai University, Taichung, Taiwan; Department of Obstetrics and Gynecology, Chung Shan Medical University, Taichung, Taiwan
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Harper LM, Sutton ALM, Longman RE, Odibo AO. An economic analysis of prenatal cytogenetic technologies for sonographically detected fetal anomalies. Am J Med Genet A 2014; 164A:1192-7. [PMID: 24664552 DOI: 10.1002/ajmg.a.36435] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 11/10/2013] [Indexed: 02/01/2023]
Abstract
When congenital anomalies are diagnosed on prenatal ultrasound, the current standard of care is to perform G-banded karyotyping on cultured amniotic cells. Chromosomal microarray (CMA) can detect smaller genomic deletions and duplications than traditional karyotype analysis. CMA is the first-tier test in the postnatal evaluation of children with multiple congenital anomalies. Recent studies have demonstrated the utility of CMA in the prenatal setting and have advocated for widespread implementation of this technology as the preferred test in prenatal diagnosis. However, CMA remains significantly more expensive than karyotype. In this study, we performed an economic analysis of cytogenetic technologies in the prenatal diagnosis of sonographically detected fetal anomalies comparing four strategies: (i) karyotype alone, (ii) CMA alone, (iii) karyotype and CMA, and (iv) karyotype followed by CMA if the karyotype was normal. In a theoretical cohort of 1,000 patients, CMA alone and karyotype followed by CMA if the karyotype was normal identified a similar number of chromosomal abnormalities. In this model, CMA alone was the most cost-effective strategy, although karyotype alone and CMA following a normal karyotype are both acceptable alternatives. This study supports the clinical utility of CMA in the prenatal diagnosis of sonographically detected fetal anomalies.
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Affiliation(s)
- Lorie M Harper
- Department of Obstetrics and Gynecology, The University of Alabama at Birmingham, Birmingham, Alabama
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20
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Haoud K, Mellali S, Gouas L, Tchirkov A, Vago P, Moulessehoul S. Prevalence of aneuploidies in products of spontaneous abortion: interest of FISH and MLPA. Morphologie 2014; 98:40-6. [PMID: 24646446 DOI: 10.1016/j.morpho.2014.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 02/12/2014] [Indexed: 12/14/2022]
Abstract
Spontaneous abortion (SA) is the loss of the conceptus before 22 weeks of gestation when fetal weight is less than 500 g. The genetic etiology accounts for more than two third of SA, and autosomal aneuploidies alone account for up to 70% fetal loss. The aim of this study was to highlight the most common chromosomal causes of fetal loss. In this study, 220 products of abortion and in utero fetal death were analyzed by using FISH (AneuVysion) on interphase nuclei from chorionic villus and by using MLPA (SALSA P036, P070 and P245 kits) on DNA extracted from fetal tissues. The gestational age ranged from the 7th to the 38th week of gestation. Of a total of 151 samples analyzed by using FISH, 10 chromosomal abnormalities were observed: four trisomies 21 (one of them was mosaic), a trisomy 18, a trisomy 13, three triploidies and one monosomy X (Turner). From the additional 69 samples analyzed by using MLPA, two anomalies were found: two monosomies X (Turner). FISH and MLPA are simple, rapid and sensitive tools for the detection of chromosomal aneuploidies. Avoiding the cell culture step necessary for karyotyping, they represent very interesting alternative methods to diagnose genomic disorders in products of abortion in which poor sample quality often leads to cell culture failure.
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Affiliation(s)
- K Haoud
- UFR médecine, cytologie, histologie, embryologie cytogénétique, université Clermont 1, 63001 Clermont-Ferrand, France; Service de cytogénétique médicale, CHU d'Estaing, 1, place Lucie-et-Raymond-Aubrac, 63003 Clermont-Ferrand cedex 1, France; ERTICA EA4677, UFR médecine, université Clermont 1, 63003 Clermont-Ferrand, France; Laboratoire de biotoxicologie, université Djillali Liabès, BP 89, Faubourg Larbi Ben M'Hidi, Sidi Bel Abbès, Algeria
| | - S Mellali
- Laboratoire de biotoxicologie, université Djillali Liabès, BP 89, Faubourg Larbi Ben M'Hidi, Sidi Bel Abbès, Algeria
| | - L Gouas
- UFR médecine, cytologie, histologie, embryologie cytogénétique, université Clermont 1, 63001 Clermont-Ferrand, France; Service de cytogénétique médicale, CHU d'Estaing, 1, place Lucie-et-Raymond-Aubrac, 63003 Clermont-Ferrand cedex 1, France; ERTICA EA4677, UFR médecine, université Clermont 1, 63003 Clermont-Ferrand, France
| | - A Tchirkov
- UFR médecine, cytologie, histologie, embryologie cytogénétique, université Clermont 1, 63001 Clermont-Ferrand, France; Service de cytogénétique médicale, CHU d'Estaing, 1, place Lucie-et-Raymond-Aubrac, 63003 Clermont-Ferrand cedex 1, France; ERTICA EA4677, UFR médecine, université Clermont 1, 63003 Clermont-Ferrand, France
| | - P Vago
- UFR médecine, cytologie, histologie, embryologie cytogénétique, université Clermont 1, 63001 Clermont-Ferrand, France; Service de cytogénétique médicale, CHU d'Estaing, 1, place Lucie-et-Raymond-Aubrac, 63003 Clermont-Ferrand cedex 1, France; ERTICA EA4677, UFR médecine, université Clermont 1, 63003 Clermont-Ferrand, France.
| | - S Moulessehoul
- Laboratoire de biotoxicologie, université Djillali Liabès, BP 89, Faubourg Larbi Ben M'Hidi, Sidi Bel Abbès, Algeria
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21
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Tzetis M, Kitsiou-Tzeli S, Frysira H, Xaidara A, Kanavakis E. The clinical utility of molecular karyotyping using high-resolution array-comparative genomic hybridization. Expert Rev Mol Diagn 2014; 12:449-57. [DOI: 10.1586/erm.12.40] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Maria Tzetis
- Department of Medical Genetics, Aghia Sophia Childrens Hospital, Thivon & Levadias, Medical School, University of Athens, 11527, Athens, Greece
- Department of Medical Genetics, Aghia Sophia Childrens Hospital, Thivon & Levadias, Medical School, University of Athens, 11527, Athens, Greece
| | - Sofia Kitsiou-Tzeli
- Department of Medical Genetics, Aghia Sophia Childrens Hospital, Thivon & Levadias, Medical School, University of Athens, 11527, Athens, Greece
| | - Helen Frysira
- Department of Medical Genetics, Aghia Sophia Childrens Hospital, Thivon & Levadias, Medical School, University of Athens, 11527, Athens, Greece
| | - Athena Xaidara
- First Department of Pediatrics, Aghia Sophia, Children’s Hospital, Medical School, University of Athens, Greece
| | - Emmanuel Kanavakis
- Department of Medical Genetics, Aghia Sophia Childrens Hospital, Thivon & Levadias, Medical School, University of Athens, 11527, Athens, Greece
- Research Institute for the Study of Genetic and Malignant Disorders in Childhood, Aghia Sophia, Children’s Hospital, Athens, Greece
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22
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Strassberg M, Fruhman G, Van den Veyver IB. Copy-number changes in prenatal diagnosis. Expert Rev Mol Diagn 2014; 11:579-92. [DOI: 10.1586/erm.11.43] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Shaffer LG, Rosenfeld JA. Microarray-based prenatal diagnosis for the identification of fetal chromosome abnormalities. Expert Rev Mol Diagn 2013; 13:601-11. [PMID: 23895129 DOI: 10.1586/14737159.2013.811912] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The goal of prenatal cytogenetic testing is to provide reassurance to the couple seeking testing for their pregnancy, identify chromosome abnormalities in the fetus, if present, and provide treatments and medical management for affected babies. Cytogenetic analysis of banded chromosomes has been the standard for identifying chromosome abnormalities in the fetus for over 40 years. With chromosome analysis, whole chromosome aneuploidies and large structural rearrangements can be identified. The sequencing of the human genome has provided the resources to develop molecular tools that allow higher resolution observations of human chromosomes. The future holds the promise of sequencing that may identify chromosomal imbalances and deleterious single nucleotide variants. This review will focus on the use of genomic microarrays for the testing and identification of chromosome anomalies in prenatal diagnosis and will discuss the future directions of fetal testing.
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Affiliation(s)
- Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., Spokane, WA, USA.
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Rapid and non invasive prenatal diagnosis. Balkan J Med Genet 2013; 15:39-43. [PMID: 24052742 PMCID: PMC3776684 DOI: 10.2478/v10034-012-0017-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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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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Hillman SC, McMullan DJ, Hall G, Togneri FS, James N, Maher EJ, Meller CH, Williams D, Wapner RJ, Maher ER, Kilby MD. Use of prenatal chromosomal microarray: prospective cohort study and systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2013; 41:610-620. [PMID: 23512800 DOI: 10.1002/uog.12464] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 02/25/2013] [Accepted: 03/01/2013] [Indexed: 06/01/2023]
Abstract
OBJECTIVES Chromosomal microarray analysis (CMA) is utilized in prenatal diagnosis to detect chromosomal abnormalities not visible by conventional karyotyping. A prospective cohort of women undergoing fetal CMA and karyotyping following abnormal prenatal ultrasound findings is presented in the context of a systematic review and meta-analysis of the literature describing detection rates by CMA and karyotyping. METHODS We performed a prospective cohort study of 243 women undergoing CMA alongside karyotyping when a structural abnormality was detected on prenatal ultrasound. A systematic review of the literature was also performed. MEDLINE (1970-Dec 2012), EMBASE (1980-Dec 2012) and CINAHL (1982-June 2012) databases were searched electronically. Selected studies included > 10 cases and prenatal CMA in addition to karyotyping. The search yielded 560 citations. Full papers were retrieved for 86, and 25 primary studies were included in the systematic review. RESULTS Our cohort study found an excess detection rate of abnormalities by CMA of 4.1% over conventional karyotyping when the clinical indication for testing was an abnormal fetal ultrasound finding; this was lower than the detection rate of 10% (95% CI, 8-13%) by meta-analysis. The rate of detection for variants of unknown significance (VOUS) was 2.1% (95% CI, 1.3-3.3%) when the indication for CMA was an abnormal scan finding. The VOUS detection rate was lower (1.4%; 95% CI, 0.5-3.7%) when any indication for prenatal CMA was meta-analyzed. CONCLUSION We present evidence for a higher detection rate by CMA than by karyotyping not just in the case of abnormal ultrasound findings but also in cases of other indications for invasive testing. It is likely that CMA will replace karyotyping in high-risk pregnancies.
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Affiliation(s)
- S C Hillman
- School of Clinical and Experimental Medicine, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham, UK
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An improved method to extract DNA from 1 ml of uncultured amniotic fluid from patients at less than 16 weeks' gestation. PLoS One 2013; 8:e59956. [PMID: 23565177 PMCID: PMC3614959 DOI: 10.1371/journal.pone.0059956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 02/20/2013] [Indexed: 11/30/2022] Open
Abstract
The aim of this study was to develop an improved technique for DNA extraction from 1 ml of uncultured AF from patients with a gestational age less than 16 weeks and to allow the use of array-CGH without DNA amplification. The DNA extraction protocol was tested in a series of 90 samples including 41 of uncultured AF at less than 16 weeks of gestation. Statistical analyses were performed using linear regression. To evaluate the sensitivity and the specificity of array-CGH on 1 ml of uncultured AF, five samples with an abnormal karyotype (three with aneuploidy, two with structural abnormalities) and five with a normal karyotype were studied. This protocol was reproducible and we were able to show a great improvement with higher yield of DNA obtained from all patients, including those with a gestational age less than 16 weeks (p = 0.003). All chromosomal abnormalities were detected and characterized by array-CGH and normal samples showed normal profiles. This new DNA extraction protocol associated with array-CGH analysis could be used in prenatal testing even when gestational age is less than 16 weeks, especially in cases with abnormal ultrasound findings.
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Simsek S, Turkyilmaz A, Oral D, Yalinkaya A, Tekes S, Akbas H, Budak T. Genetic Analysis in Pregnancy with Fetal Pathologic Ultrasound Findings. BIOTECHNOL BIOTEC EQ 2013. [DOI: 10.5504/bbeq.2013.0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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29
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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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30
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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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Shaffer LG, Dabell MP, Rosenfeld JA, Neill NJ, Ballif BC, Coppinger J, Diwan NR, Chong K, Shohat M, Chitayat D. Referral patterns for microarray testing in prenatal diagnosis. Prenat Diagn 2012; 32:344-50. [PMID: 22467165 DOI: 10.1002/pd.3856] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVE To understand the prenatal referral patterns from the United States, Canada, and Israel for two whole-genome microarray platforms, each with a different resolution. METHOD Physicians selected one of the two array designs to be performed on 1483 prenatal specimens for a 1-year period. We retrospectively examined detection rates, indications for study, and physician array selection. RESULTS The lower resolution array (55 K) showed an ~32% decrease in the detection of results of unclear clinical significance while retaining the ability to detect all but one significant abnormality identified by the higher resolution array (135 K). A majority of samples were referred for abnormal ultrasound findings. Whereas the United States and Canada utilized the higher resolution array more often for this indication, Israel preferred the 55 K array. Referral patterns for parental anxiety were similar for the United States and Israel, with most cases being tested on the 55 K array. Few cases were referred for advanced maternal age or family history of a genetic condition from either Canada or Israel. CONCLUSION Referral patterns varied between the countries and between indications for study. Understanding these differences will provide laboratories the critical information needed to develop array designs to meet the medical needs and patient desires for prenatal testing.
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Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA.
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Abstract
The diagnostic benefits of array comparative genomic hybridisation (CGH) have been demonstrated, with this technique now being applied as the first-line test for patients with intellectual disabilities and/or multiple congenital anomalies in numerous laboratories. There are no technical barriers preventing the introduction of array CGH to prenatal diagnosis. The question is rather how this is best implemented, and for whom. The challenges lie in the interpretation of copy number variations, particularly those which exhibit reduced penetrance or variable expression, and how to deal with incidental findings, which are not related to the observed foetal anomalies, or unclassified variants which are currently of uncertain clinical significance. Recently, applications of array technologies to the field of pre-implantation genetic diagnosis have also been demonstrated. It is important to address the ethical questions raised concerning the genome-wide analysis of prenatal samples to ensure the maximum benefit for patients. We provide an overview of the recent developments on the use of array CGH in the prenatal setting, and address the challenges posed.
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Simmons AD, Carvalho CMB, Lupski JR. What have studies of genomic disorders taught us about our genome? Methods Mol Biol 2012; 838:1-27. [PMID: 22228005 DOI: 10.1007/978-1-61779-507-7_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The elucidation of genomic disorders began with molecular technologies that enabled detection of genomic changes which were (a) smaller than those resolved by traditional cytogenetics (less than 5 Mb) and (b) larger than what could be determined by conventional gel electrophoresis. Methods such as pulsed field gel electrophoresis (PFGE) and fluorescent in situ hybridization (FISH) could resolve such changes but were limited to locus-specific studies. The study of genomic disorders has rapidly advanced with the development of array-based techniques. These enabled examination of the entire human genome at a higher level of resolution, thus allowing elucidation of the basis of many new disorders, mechanisms that result in genomic changes that can result in copy number variation (CNV), and most importantly, a deeper understanding of the characteristics, features, and plasticity of our genome. In this chapter, we focus on the structural and architectural features of the genome, which can potentially result in genomic instability, delineate how mechanisms, such as NAHR, NHEJ, and FoSTeS/MMBIR lead to disease-causing rearrangements, and briefly describe the relationship between the leading methods presently used in studying genomic disorders. We end with a discussion on our new understanding about our genome including: the contribution of new mutation CNV to disease, the abundance of mosaicism, the extent of subtelomeric rearrangements, the frequency of de novo rearrangements associated with sporadic birth defects, the occurrence of balanced and unbalanced translocations, the increasing discovery of insertional translocations, the exploration of complex rearrangements and exonic CNVs. In the postgenomic era, our understanding of the genome has advanced very rapidly as the level of technical resolution has become higher. This leads to a greater understanding of the effects of rearrangements present both in healthy subjects and individuals with clinically relevant phenotypes.
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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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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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Kremer V, Girard F, Gasser B, Marcellin L, Christmann D, Nisand I, Schmitt E, Florent S, Flori E. Prenatal diagnosis of a 12q22q23.2 interstitial deletion by array CGH in a malformed fetus. Eur J Med Genet 2012; 55:269-73. [PMID: 22425634 DOI: 10.1016/j.ejmg.2012.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 02/06/2012] [Indexed: 11/13/2022]
Abstract
We report the prenatal diagnosis of a 12q22q23.2 de novo interstitial deletion performed by array based comparative genomic hybridization (array CGH) in a fetus with cystic hygroma colli, intrauterine growth retardation, microcephaly and micrognathism. Haploinsufficiency for insuline-like growth factor 1 gene (IGF1), which is mapped in the deleted region, is suggested because of its implication in prenatal and postnatal growth and in neuronal maturation. This case demonstrates the contribution of array CGH in prenatal diagnosis for detecting small unbalanced chromosomal abnormalities in malformed fetuses and, subsequently, for genetic counselling.
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Affiliation(s)
- Valérie Kremer
- Service de Cytogénétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
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Srebniak MI, Boter M, Oudesluijs GO, Cohen-Overbeek T, Govaerts LC, Diderich KE, Oegema R, Knapen MF, van de Laar IM, Joosten M, Van Opstal D, Galjaard RJH. Genomic SNP array as a gold standard for prenatal diagnosis of foetal ultrasound abnormalities. Mol Cytogenet 2012; 5:14. [PMID: 22413963 PMCID: PMC3328283 DOI: 10.1186/1755-8166-5-14] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 03/13/2012] [Indexed: 01/10/2023] Open
Abstract
Background We have investigated whether replacing conventional karyotyping by SNP array analysis in cases of foetal ultrasound abnormalities would increase the diagnostic yield and speed of prenatal diagnosis in clinical practice. Findings/results From May 2009 till June 2011 we performed HumanCytoSNP-12 array (HCS) (http://www.Illumina.com) analysis in 207 cases of foetal structural abnormalities. HCS allows detecting unbalanced genomic abnormalities with a resolution of about 150/200 kb. All cases were selected by a clinical geneticist after excluding the most common aneuploidies by RAD (rapid aneuploidy detection). Pre-test genetic counselling was offered in all cases. In 24/207 (11,6%) foetuses a clinically relevant genetic abnormality was detected. Only 8/24 abnormalities would have been detected if only routine karyotyping was performed. Submicroscopic abnormalities were found in 16/207 (7,7%) cases. The array results were achieved within 1-2 weeks after amniocentesis. Conclusions Prenatal SNP array testing is faster than karyotyping and allows detecting much smaller aberrations (~0.15 Mb) in addition to the microscopic unbalanced chromosome abnormalities detectable with karyotyping (~ > 5 Mb). Since karyotyping would have missed 66% (16/24) of genomic abnormalities in our cohort, we propose to perform genomic high resolution array testing assisted by pre-test counselling as a primary prenatal diagnostic test in cases of foetal ultrasound abnormalities.
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Wu JF, Xia L, Liu YX, Zhang X, Li C, Li ML. The high incidence of STR D21S1446 homozygosity in Han and She populations living in South Eastern China. J Assist Reprod Genet 2011; 29:337-41. [PMID: 22193752 DOI: 10.1007/s10815-011-9699-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 12/13/2011] [Indexed: 10/14/2022] Open
Abstract
PURPOSE This study investigated the allelic frequency of 4 short terminal repeats (STRs) in Han and She populations from eastern China. METHODS DNA samples from Han (N = 110) and She (N = 110) healthy subjects were amplified using PCR and primers specific for the STRs. D21S11 and D21S1446 (chromosome 21) and D18S865 and D18S535 (chromosome 18). The frequency and homozygocity of different STRs were evaluated. RESULTS For both populations, D21S11 and D18S535 were more polymorphic than D21S1446 and D18S865, and the D21S1446 1 allele was very common (48.6% and 55.0% for the Han and She groups, respectively).The Han and She groups significantly differed from one another in respect to the distribution of D21S11, D18S865, and D18S535 allelic frequency (all P -values ≤ 0.48) but had a similar allelic distribution for D21S1446 (P = 0.106). D21S1446 was found to be homozygous about 50% of the time which was significantly greater compared to the other STRs analyzed. CONCLUSION This study found that the Han and She differ genetically at 3 autosomal STRs located on chromosome 18 and 21. The STR D21S1146 was often homozygous within these groups, indicating it would be poor marker for analyzing trisomy within these populations.
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Affiliation(s)
- Jin-Fang Wu
- Department of Obstetrics and Gynecology, Xi'an Jiaotong University Medical School Second Affiliated Hospital, Xi Wu Road 157, Xi'an City, Xi'an, 710004, China.
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Fiorentino F, Caiazzo F, Napolitano S, Spizzichino L, Bono S, Sessa M, Nuccitelli A, Biricik A, Gordon A, Rizzo G, Baldi M. Introducing array comparative genomic hybridization into routine prenatal diagnosis practice: a prospective study on over 1000 consecutive clinical cases. Prenat Diagn 2011; 31:1270-82. [PMID: 22034057 DOI: 10.1002/pd.2884] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 08/28/2011] [Accepted: 09/06/2011] [Indexed: 02/05/2023]
Abstract
OBJECTIVE To assess the feasibility of offering array-based comparative genomic hybridization testing for prenatal diagnosis as a first-line test, a prospective study was performed, comparing the results achieved from array comparative genomic hybridization (aCGH) with those obtained from conventional karyotype. METHOD Women undergoing amniocentesis or chorionic villus sampling were offered aCGH analysis. A total of 1037 prenatal samples were processed in parallel using both aCGH and G-banding for standard karyotyping. Specimen types included amniotic fluid (89.0%), chorionic villus sampling (9.5%) and cultured amniocytes (1.5%). RESULTS Chromosomal abnormalities were identified in 34 (3.3%) samples; in 9 out of 34 cases (26.5%) aCGH detected pathogenic copy number variations that would not have been found if only a standard karyotype had been performed. aCGH was also able to detect chromosomal mosaicism at as low as a 10% level. There was complete concordance between the conventional karyotyping and aCGH results, except for 2 cases that were only correctly diagnosed by aCGH. CONCLUSIONS This study demonstrates that aCGH represents an improved diagnostic tool for prenatal detection of chromosomal abnormalities. Although larger studies are needed, our results provide further evidence on the feasibility of introducing aCGH as a first-line diagnostic test in routine prenatal diagnosis practice.
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Srebniak M, Boter M, Oudesluijs G, Joosten M, Govaerts L, Van Opstal D, Galjaard RJH. Application of SNP array for rapid prenatal diagnosis: implementation, genetic counselling and diagnostic flow. Eur J Hum Genet 2011; 19:1230-7. [PMID: 21694736 DOI: 10.1038/ejhg.2011.119] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We report on the validation and implementation of the HumanCytoSNP-12 array (Illumina) (HCS) in prenatal diagnosis. In total, 64 samples were used to validate the Illumina platform (20 with a known (sub) microscopic chromosome abnormality, 5 with known maternal cell contamination (MCC) and 39 normal control samples). There were no false-positive or false-negative results. In addition to the diagnostic possibilities of arrayCGH, the HCS allows detection of regions of homozygosity (ROH), triploidy and helps recognising MCC. Moreover, in two cases of MCC, a deletion was correctly detected. Furthermore we found out that only about 50 ng of DNA is required, which allows a reporting time of only 3 days. We also present a prospective pilot study of 61 fetuses with ultrasound abnormalities and a normal karyotype tested with HCS. In 4 out of 61 (6.5%) fetuses, a clinically relevant abnormality was detected. We designed and present pre-test genetic counselling information on categories of possible test outcomes. On the basis of this information, about 90% of the parents chose to be informed about adverse health outcomes of their future child at infancy and childhood, and 55% also about outcomes at an adult stage. The latter issue regarding the right of the future child itself to decide whether or not to know this information needs to be addressed.
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Affiliation(s)
- Malgorzata Srebniak
- Department of Clinical Genetics, Erasmus Medical Center, Dr Molewaterplein 50, Rotterdam, The Netherlands.
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Shaffer LG, Coppinger J, Morton SA, Alliman S, Burleson J, Traylor R, Walker C, Byerly S, Lamb AN, Schultz R, Ravnan JB, Kashork CD, Torchia BS, Sulpizio S, Sundin K, Schermer M, Adler K, Dallaire S, Ballif BC. The development of a rapid assay for prenatal testing of common aneuploidies and microdeletion syndromes. Prenat Diagn 2011; 31:778-87. [DOI: 10.1002/pd.2766] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 03/11/2011] [Accepted: 03/25/2011] [Indexed: 02/01/2023]
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D'Amours G, Kibar Z, Mathonnet G, Fetni R, Tihy F, Désilets V, Nizard S, Michaud JL, Lemyre E. Whole-genome array CGH identifies pathogenic copy number variations in fetuses with major malformations and a normal karyotype. Clin Genet 2011; 81:128-41. [PMID: 21496010 DOI: 10.1111/j.1399-0004.2011.01687.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Despite a wide range of clinical tools, the etiology of mental retardation and multiple congenital malformations remains unknown for many patients. Array-based comparative genomic hybridization (aCGH) has proven to be a valuable tool in these cases, as its pangenomic coverage allows the identification of chromosomal aberrations that are undetectable by other genetic methods targeting specific genomic regions. Therefore, aCGH is increasingly used in clinical genetics, both in the postnatal and the prenatal settings. While the diagnostic yield in the postnatal population has been established at 10-12%, studies investigating fetuses have reported variable results. We used whole-genome aCGH to investigate fetuses presenting at least one major malformation detected on ultrasound, but for whom standard genetic analyses (including karyotype) failed to provide a diagnosis. We identified a clinically significant chromosomal aberration in 8.2% of tested fetuses (4/49), and a result of unclear clinical significance in 12.2% of tested fetuses (6/49). Our results document the value of whole-genome aCGH as a prenatal diagnostic tool and highlight the interpretation difficulties associated with copy number variations of unclear significance.
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Affiliation(s)
- G D'Amours
- Service de Génétique Médicale, CHU Sainte-Justine, Montréal, QC, Canada
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43
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Park SJ, Jung EH, Ryu RS, Kang HW, Ko JM, Kim HJ, Cheon CK, Hwang SH, Kang HY. Clinical implementation of whole-genome array CGH as a first-tier test in 5080 pre and postnatal cases. Mol Cytogenet 2011; 4:12. [PMID: 21549014 PMCID: PMC3114015 DOI: 10.1186/1755-8166-4-12] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 05/09/2011] [Indexed: 01/08/2023] Open
Abstract
Background Array comparative genomic hybridization (CGH) is currently the most powerful method for detecting chromosomal alterations in pre and postnatal clinical cases. In this study, we developed a BAC based array CGH analysis platform for detecting whole genome DNA copy number changes including specific micro deletion and duplication chromosomal disorders. Additionally, we report our experience with the clinical implementation of our array CGH analysis platform. Array CGH was performed on 5080 pre and postnatal clinical samples from patients referred with a variety of clinical phenotypes. Results A total of 4073 prenatal cases (4033 amniotic fluid and 40 chorionic villi specimens) and 1007 postnatal cases (407 peripheral blood and 600 cord blood) were studied with complete concordance between array CGH, karyotype and fluorescence in situ hybridization results. Among 75 positive prenatal cases with DNA copy number variations, 60 had an aneuploidy, seven had a deletion, and eight had a duplication. Among 39 positive postnatal cases samples, five had an aneuploidy, 23 had a deletion, and 11 had a duplication. Conclusions This study demonstrates the utility of using our newly developed whole-genome array CGH as first-tier test in 5080 pre and postnatal cases. Array CGH has increased the ability to detect segmental deletion and duplication in patients with variable clinical features and is becoming a more powerful tool in pre and postnatal diagnostics.
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Affiliation(s)
| | | | | | | | - Jung-Min Ko
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, Korea
| | - Hyon J Kim
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, Korea
| | - Chong Kun Cheon
- Department of Pediatrics, School of Medicine, Pusan National University Children's Hospital, Yangsan, Korea
| | - Sang-Hyun Hwang
- Department of Laboratory Medicine, Center for Diagnostic Oncology, National Cancer Center, Gyeonggi-do, Korea
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Byeon SJ, Myung JK, Park SH. The Wolf-Hirschhorn Syndrome in Fetal Autopsy - A Case Report -. KOREAN JOURNAL OF PATHOLOGY 2011. [DOI: 10.4132/koreanjpathol.2011.45.s1.s15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Sun-ju Byeon
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jae Kyung Myung
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
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Lichtenbelt K, Knoers N, Schuring-Blom G. From Karyotyping to Array-CGH in Prenatal Diagnosis. Cytogenet Genome Res 2011; 135:241-50. [DOI: 10.1159/000334065] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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Hadjidekova S, Rukova B, Avdjieva-Tzavella D, Nesheva D, Tincheva R, Toncheva D. Comparison of Two Microarray CGH Platforms for Genome-Wide Copy Number Profilings: Oligo-Based Arrays Versus Bacterial Artificial Chromosome Arrays. BIOTECHNOL BIOTEC EQ 2011. [DOI: 10.5504/bbeq.2011.0064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Hillman SC, Pretlove S, Coomarasamy A, McMullan DJ, Davison EV, Maher ER, Kilby MD. Additional information from array comparative genomic hybridization technology over conventional karyotyping in prenatal diagnosis: a systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2011; 37:6-14. [PMID: 20658510 DOI: 10.1002/uog.7754] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
OBJECTIVE Array comparative genomic hybridization (CGH) is transforming clinical cytogenetics with its ability to interrogate the human genome at increasingly high resolution. The aim of this study was to determine whether array CGH testing in the prenatal population provides diagnostic information over conventional karyotyping. METHODS MEDLINE (1970 to December 2009), EMBASE (1980 to December 2009) and CINAHL (1982 to December 2009) databases were searched electronically. Studies were selected if array CGH was used on prenatal samples or if array CGH was used on postnatal samples following termination of pregnancy for structural abnormalities that were detected on an ultrasound scan. Of the 135 potential articles, 10 were included in this systematic review and eight were included in the meta-analysis. The pooled rate of extra information detected by array CGH when the prenatal karyotype was normal was meta-analyzed using a random-effects model. The pooled rate of receiving an array CGH result of unknown significance was also meta-analyzed. RESULTS Array CGH detected 3.6% (95% CI, 1.5-8.5) additional genomic imbalances when conventional karyo-typing was 'normal', regardless of referral indication. This increased to 5.2% (95% CI, 1.9-13.9) more than karyotyping when the referral indication was a structural malformation on ultrasound. CONCLUSIONS There appears to be an increased detection rate of chromosomal imbalances, compared with conventional karyotyping, when array CGH techniques are employed in the prenatal population. However, some are copy number imbalances that are not clinically significant. This carries implications for prenatal counseling and maternal anxiety.
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Affiliation(s)
- S C Hillman
- School of Clinical & Experimental Medicine, University of Birmingham, Birmingham, UK
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Lee C. The future of prenatal cytogenetic diagnostics: a personal perspective. Prenat Diagn 2010; 30:706-9. [PMID: 20572109 DOI: 10.1002/pd.2547] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Charles Lee
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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49
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Fruhman G, Van den Veyver IB. Applications of array comparative genomic hybridization in obstetrics. Obstet Gynecol Clin North Am 2010; 37:71-85, Table of Contents. [PMID: 20494259 DOI: 10.1016/j.ogc.2010.02.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Current prenatal cytogenetic diagnosis uses mostly G-banded karyotyping of fetal cells from chorionic villi or amniotic fluid cultures, which readily detects any aneuploidy and larger structural genomic rearrangements that are more than 4 to 5 megabases in size. Fluorescence in situ hybridization (FISH) is also used for rapid detection of the common aneuploidies seen in liveborns. If there is prior knowledge that increases risk for a specific deletion or duplication syndrome, FISH with a probe specific for the region in question is done. Over the past decade, array-based comparative genomic hybridization (aCGH) has been developed, which can survey the entire genome for submicroscopic microdeletions and microduplications, in addition to all unbalanced chromosomal abnormalities that are also detected by karyotype. aCGH in essence interrogates the genome with thousands of probes fixed on a slide in a single assay, and has already revolutionized cytogenetic diagnosis in the pediatric population. aCGH is being used increasingly for prenatal diagnosis where it is also beginning to make a significant impact. The authors review here principles of aCGH, its benefits for prenatal diagnosis and associated challenges, primarily the inability to detect balanced chromosomal abnormalities and a small risk for discovery of chromosomal abnormalities of uncertain clinical significance. The superior diagnostic power of aCGH far outweighs these concerns. Furthermore, such issues can be addressed during pre- and posttest counseling, and their impact will further diminish as the technology continues to develop and experience with its prenatal diagnostic use grows.
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Affiliation(s)
- Gary Fruhman
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6621 Fannin Street CC 1560, Houston, TX 77030, USA
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50
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Park JH, Woo JH, Shim SH, Yang SJ, Choi YM, Yang KS, Cha DH. Application of a target array comparative genomic hybridization to prenatal diagnosis. BMC MEDICAL GENETICS 2010; 11:102. [PMID: 20576126 PMCID: PMC2909938 DOI: 10.1186/1471-2350-11-102] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 06/24/2010] [Indexed: 11/30/2022]
Abstract
Background While conventional G-banded karyotyping still remains a gold standard in prenatal genetic diagnoses, the widespread adoption of array Comparative Genomic Hybridization (array CGH) technology for postnatal genetic diagnoses has led to increasing interest in the use of this same technology for prenatal diagnosis. We have investigated the value of our own designed DNA chip as a prenatal diagnostic tool for detecting submicroscopic deletions/duplications and chromosome aneuploidies. Methods We designed a target bacterial artificial chromosome (BAC)-based aCGH platform (MacArray™ M-chip), which specifically targets submicroscopic deletions/duplications for 26 known genetic syndromes of medical significance observed prenatally. To validate the DNA chip, we obtained genomic DNA from 132 reference materials generated from patients with 22 genetic diseases and 94 clinical amniocentesis samples obtained for karyotyping. Results In the 132 reference materials, all known genomic alterations were successfully identified. In the 94 clinical samples that were also subjected to conventional karyotyping, three cases of balanced chromosomal aberrations were not detected by aCGH. However, we identified eight cases of microdeletions in the Yq11.23 chromosomal region that were not found by conventional karyotyping. This region harbors the DAZ gene, and deletions may lead to non-obstructive spermatogenesis. Conclusions We have successfully designed and applied a BAC-based aCGH platform for prenatal diagnosis. This platform can be used in conjunction with conventional karyotyping and will provide rapid and accurate diagnoses for the targeted genomic regions while eliminating the need to interpret clinically-uncertain genomic regions.
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Affiliation(s)
- Ji Hyeon Park
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam-si, Korea
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