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Qin Y, Touch K, Sha M, Sun Y, Zhang S, Wu J, Wu Y, Feng L, Chen S, Xiao J. The chromosomal characteristics of spontaneous abortion and its potential associated copy number variants and genes. J Assist Reprod Genet 2024; 41:1285-1296. [PMID: 38668959 PMCID: PMC11143157 DOI: 10.1007/s10815-024-03119-4] [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: 09/27/2023] [Accepted: 04/02/2024] [Indexed: 06/01/2024] Open
Abstract
PURPOSE This study aimed to investigate the correlation between chromosomal abnormalities in spontaneous abortion with clinical features and seek copy number variations (CNVs) and genes that might be connected to spontaneous abortion. METHODS Over 7 years, we used CNV-seq and STR analysis to study POCs, comparing chromosomal abnormalities with clinical features and identifying critical CNVs and genes associated with spontaneous abortion. RESULTS Total chromosomal variants in the POCs were identified in 66.8% (2169/3247) of all cases, which included 45.2% (1467/3247) numerical abnormalities and 21.6% (702/3247) copy number variants (CNVs). Chromosome number abnormalities, especially aneuploidy abnormalities, were more pronounced in the group of mothers aged ≥ 35 years, the early miscarriage group, and the chorionic villi group. We further analyzed 212 pathogenic and likely pathogenic CNVs in 146 POCs as well as identified 8 statistically significant SORs through comparison with both a healthy population and a group of non-spontaneously aborted fetuses. Our analysis suggests that these CNVs may play a crucial role in spontaneous abortion. Furthermore, by utilizing the RVIS score and MGI database, we identified 86 genes associated with spontaneous abortion, with particular emphasis on PARP6, ISLR, ULK3, FGFRL1, TBC1D14, SCRIB, and PLEC. CONCLUSION We found variability in chromosomal abnormalities across clinical features, identifying eight crucial copy number variations (CNVs) and multiple key genes that may be linked to spontaneous abortion. This research enhances the comprehension of genetic factors contributing to spontaneous abortion.
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Affiliation(s)
- Yu Qin
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Koksear Touch
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Menghan Sha
- Department of Obstetrics, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanan Sun
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Shunran Zhang
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Jianli Wu
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Yuanyuan Wu
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Ling Feng
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China
| | - Suhua Chen
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China.
| | - Juan Xiao
- Department of Obstetrics & Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, Hubei, China.
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Xia Z, Zhou R, Li Y, Meng L, Huang M, Tan J, Qiao F, Zhu H, Hu P, Zhu Q, Xu Z, Wang Y. Reproductive outcomes in couples with sporadic miscarriage after embryonic chromosomal microarray analysis. Ann Med 2023; 55:837-848. [PMID: 36869707 PMCID: PMC9987763 DOI: 10.1080/07853890.2023.2183986] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
Abstract
OBJECTIVES Chromosomal microarray analysis (CMA) has been widely applied to genetic diagnosis in miscarriages in clinical practice. However, the prognostic value of CMA testing of products of conception (POCs) after the first clinical miscarriage remains unknown. The aim of this study was to evaluate the reproductive outcomes after embryonic genetic testing by CMA in SM couples. METHODS In this retrospective study, a total of 1142 SM couples referred for embryonic genetic testing by CMA, and 1022 couples were successfully followed up after CMA. RESULTS Among 1130 cases without significant maternal cell contamination, pathogenic chromosomal abnormalities were detected in 680 cases (60.2%). The subsequent live birth rate did not differ significantly between couples with chromosomally abnormal and normal miscarriage (88.6% vs. 91.1%, p = .240), as well as the cumulative live birth rate (94.5% vs. 96.7%, p = .131). Couples with partial aneuploid miscarriage had a higher likelihood of spontaneous abortion both in the subsequent pregnancy (19.0% vs. 6.5%, p = .037) and cumulative pregnancies (19.0% vs. 6.8%, p = .044) when compared with couples with chromosomally normal miscarriage. CONCLUSIONS SM couples with chromosomally abnormal miscarriage manifested with a similar reproductive prognosis to couples with chromosomally normal miscarriage. Key messagesCMA testing of POCs could provide an accurate genetic diagnosis for couples with SM.The live birth rate of couples with partial aneuploid miscarriage was as high as couples with chromosomally normal miscarriage, despite a higher risk of adverse pregnancy event.Among couples with the most common single aneuploid miscarriage, the cumulative live birth rates of couples with trisomy 16, sex chromosomal abnormalities and trisomy 22 were 94.1%, 95.8% and 84.0%, respectively.
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Affiliation(s)
- Zhengyi Xia
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Ran Zhou
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Yiming Li
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Lulu Meng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Mingtao Huang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Jianxin Tan
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Fengchang Qiao
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Hui Zhu
- Department of Premarital Care, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Ping Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Qiaoying Zhu
- Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Yan Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
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Kowalczyk K, Smyk M, Bartnik-Głaska M, Plaskota I, Wiśniowiecka-Kowalnik B, Bernaciak J, Chojnacka M, Paczkowska M, Niemiec M, Dutkiewicz D, Kozar A, Magdziak R, Krawczyk W, Pietras G, Michalak E, Klepacka T, Obersztyn E, Bal J, Nowakowska BA. Application of array comparative genomic hybridization (aCGH) for identification of chromosomal aberrations in the recurrent pregnancy loss. J Assist Reprod Genet 2022; 39:357-367. [PMID: 35079943 PMCID: PMC8956756 DOI: 10.1007/s10815-022-02400-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/13/2022] [Indexed: 12/03/2022] Open
Abstract
Spontaneous abortion occurs in 8–20% of recognized pregnancies and usually takes place in the first trimester (7–11 weeks). There are many causes of pregnancy loss, but the most important (about 75%) is the presence of chromosomal aberrations. We present the results of oligonucleotide array application in a cohort of 62 miscarriage cases. The inclusion criteria for the study were the loss after 8th week of pregnancy and the appearance of recurrent miscarriages. DNA was extracted from trophoblast or fetal skin fibroblasts. In the 62 tested materials from recurrent miscarriages, the detection rate was 56.5% (35/62). The most commonly found were aneuploidies (65%) (chromosomal trisomy 14, 16, 18, 21, and 22), Turner syndrome, and triploidy (17.1%). Other chromosomal abnormalities included pathogenic and likely pathogenic structural aberrations: 1) pathogenic: deletion 7p22.3p12.3 and duplication 9p24.3p13.2 inherited from the normal father, deletion 3q13.31q22.2 and deletion 3q22.3q23 of unknown inheritance and duplication of 17p12 inherited from father with foot malformation; 2) likely pathogenic variants: deletion 17p13.1 inherited from normal mother, deletion 5q14.3 of unknown inheritance and de novo deletion 1q21.1q21.2. Among these aberrations, six CNVs (copy number variants) were responsible for the miscarriage: deletion 7p22.3p12.3 and duplication 9p24.3p13.2, deletion 3q13.31q22.2 and deletion 3q22.3q23, and deletion 17p13.1 and deletion 1q21.1q21.2. Other two findings were classified as incidental findings (deletion 5q14.3 and 17p12 duplication). Our research shows that 17% of the aberrations (6/35 abnormal results) that cannot be identified by the routine kariotype analysis are structural aberrations containing genes important for fetal development, the mutations of which may cause spontaneous abortion.
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Affiliation(s)
- Katarzyna Kowalczyk
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland.
| | - Marta Smyk
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | | | - Izabela Plaskota
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | | | - Joanna Bernaciak
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Marta Chojnacka
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | | | - Magdalena Niemiec
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Daria Dutkiewicz
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Agata Kozar
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Róża Magdziak
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Wojciech Krawczyk
- Department of Obstetrics and Perinatology, Medical University of Lublin, Lublin, Poland
| | - Grzegorz Pietras
- Department of Obstetrics and Perinatology, Medical University of Lublin, Lublin, Poland
| | - Elżbieta Michalak
- Deparment of Pathomorphology, Institute of Mother and Child, Warsaw, Poland
| | - Teresa Klepacka
- Deparment of Pathomorphology, Institute of Mother and Child, Warsaw, Poland
| | - Ewa Obersztyn
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Jerzy Bal
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
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Characterization of Copy-Number Variations and Possible Candidate Genes in Recurrent Pregnancy Losses. Genes (Basel) 2021; 12:genes12020141. [PMID: 33499090 PMCID: PMC7911754 DOI: 10.3390/genes12020141] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/09/2021] [Accepted: 01/19/2021] [Indexed: 12/12/2022] Open
Abstract
It is well established that embryonic chromosomal abnormalities (both in the number of chromosomes and the structure) account for 50% of early pregnancy losses. However, little is known regarding the potential differences in the incidence and distribution of chromosomal abnormalities between patients with sporadic abortion (SA) and recurrent pregnancy loss (RPL), let alone the role of submicroscopic copy-number variations (CNVs) in these cases. The aim of the present study was to systematically evaluate the role of embryonic chromosomal abnormalities and CNVs in the etiology of RPL compared with SA. Over a 3-year period, 1556 fresh products of conception (POCs) from miscarriage specimens were investigated using single nucleotide polymorphism array (SNP-array) and CNV sequencing (CNV-seq) in this study, along with further functional enrichment analysis. Chromosomal abnormalities were identified in 57.52% (895/1556) of all cases. Comparisons of the incidence and distributions of chromosomal abnormalities within the SA group and RPL group and within the different age groups were performed. Moreover, 346 CNVs in 173 cases were identified, including 272 duplications, 2 deletions and 72 duplications along with deletions. Duplications in 16q24.3 and 16p13.3 were significantly more frequent in RPL cases, and thereby considered to be associated with RPL. There were 213 genes and 131 signaling pathways identified as potential RPL candidate genes and signaling pathways, respectively, which were centered primarily on six functional categories. The results of the present study may improve our understanding of the etiologies of RPL and assist in the establishment of a population-based diagnostic panel of genetic markers for screening RPL amongst Chinese women.
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Wang Y, Zhou R, Jiang L, Meng L, Tan J, Qiao F, Wang Y, Zhang C, Cheng Q, Jiang Z, Hu P, Xu Z. Identification of Chromosomal Abnormalities in Early Pregnancy Loss Using a High-Throughput Ligation-Dependent Probe Amplification-Based Assay. J Mol Diagn 2020; 23:38-45. [PMID: 33069876 DOI: 10.1016/j.jmoldx.2020.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/08/2020] [Accepted: 10/05/2020] [Indexed: 11/16/2022] Open
Abstract
Embryonic chromosomal abnormalities are the major cause of miscarriage. An accurate, rapid, and cheap method of chromosome analysis in miscarriage is warranted in clinical practice. Thus, a high-throughput ligation-dependent probe amplification (HLPA)-based method of detecting aneuploidies and copy number variations in miscarriage was developed. A total of 1060 cases of miscarriage were assessed. Each specimen was subjected to quantitative fluorescence (QF)-PCR/HLPA and chromosomal microarray analysis (CMA) in parallel. All 1060 samples were successfully analyzed using both methods; of these samples, 1.7% (18/1060) were identified as having significant maternal cell contamination. Among the remaining 1042 cases without significant maternal cell contamination, QF-PCR/HLPA reached a diagnostic yield of 59.6% (621/1042), which is comparable to the yield of 60.3% (628/1042) with CMA. Compared with CMA results, the sensitivity and specificity of QF-PCR/HLPA in the identification of total pathogenic chromosomal abnormalities were 98.9% and 100%, respectively. Furthermore, the overall prevalence of chromosomal abnormalities in cases of spontaneous abortion was not significantly different from that in cases of recurrent miscarriage (61.3% versus 58.5%). In summary, QF-PCR/HLPA rapidly and accurately identified chromosomal abnormalities at a comparable performance and lower cost as compared with CMA. Combining simplicity and accuracy with cost-effectiveness, QF-PCR/HLPA may serve as a promising approach to routine genetic testing in miscarriage in clinical practice.
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Affiliation(s)
- Yan Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Ran Zhou
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Lili Jiang
- Genesky Diagnostics (Suzhou) Inc., Suzhou, China
| | - Lulu Meng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Jianxin Tan
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Fengchang Qiao
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yuguo Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Cuiping Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Qing Cheng
- Department of Obstetrics, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | | | - Ping Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China.
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China.
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Smits MA, van Maarle M, Hamer G, Mastenbroek S, Goddijn M, van Wely M. Cytogenetic testing of pregnancy loss tissue: a meta-analysis. Reprod Biomed Online 2020; 40:867-879. [DOI: 10.1016/j.rbmo.2020.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 01/12/2023]
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7
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Wang Y, Li Y, Chen Y, Zhou R, Sang Z, Meng L, Tan J, Qiao F, Bao Q, Luo D, Peng C, Wang YS, Luo C, Hu P, Xu Z. Systematic analysis of copy-number variations associated with early pregnancy loss. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2020; 55:96-104. [PMID: 31364215 DOI: 10.1002/uog.20412] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
OBJECTIVES Embryonic numerical and structural chromosomal abnormalities are the most common cause of early pregnancy loss. However, the role of submicroscopic copy-number variations (CNVs) in early pregnancy loss is unclear, and little is known about the critical regions and candidate genes for miscarriage, because of the large size of structural chromosomal abnormalities. The aim of this study was to identify potential miscarriage-associated submicroscopic CNVs and critical regions of large CNVs as well as candidate genes for miscarriage. METHODS Over a 5-year period, 5180 fresh miscarriage specimens were investigated using quantitative fluorescent polymerase chain reaction/CNV sequencing or chromosomal microarray analysis. Statistically significant submicroscopic CNVs were identified by comparing the frequency of recurrent submicroscopic CNVs between cases and a published control cohort. Furthermore, genes within critical regions of miscarriage-associated CNVs were prioritized by integrating the Residual Variation Intolerance Score and the human gene expression dataset for identification of potential miscarriage candidate genes. RESULTS Results without significant maternal-cell contamination were obtained in 5003 of the 5180 (96.6%) cases. Clinically significant chromosomal abnormalities were identified in 59.1% (2955/5003) of these cases. Three recurrent submicroscopic CNVs (microdeletions in 22q11.21, 2q37.3 and 9p24.3p24.2) were significantly more frequent in miscarriage cases, and were considered to be associated with miscarriage. Moreover, 44 critical regions of large CNVs were observed, including 14 deletions and 30 duplications. There were 309 genes identified as potential miscarriage candidate genes through gene-prioritization analysis. CONCLUSIONS We identified potential miscarriage candidate CNVs and genes. These data demonstrate the importance of CNVs in the etiology of miscarriage and highlight the importance of ongoing analysis of CNVs in the study of miscarriage. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- Y Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province, China
| | - Y Li
- Department of Rheumatology, Children's Hospital of Fudan University, Shanghai, China
| | - Y Chen
- CapitalBio Genomics Co., Ltd, Dongguan, Guangdong Province, China
- CapitalBio Technology Inc., Beijing, China
| | - R Zhou
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province, China
| | - Z Sang
- Biosan Biochemical Technologies Co., Ltd, Hangzhou, Zhejiang Province, China
| | - L Meng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province, China
| | - J Tan
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province, China
| | - F Qiao
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province, China
| | - Q Bao
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province, China
| | - D Luo
- CapitalBio Genomics Co., Ltd, Dongguan, Guangdong Province, China
- CapitalBio Technology Inc., Beijing, China
| | - C Peng
- CapitalBio Genomics Co., Ltd, Dongguan, Guangdong Province, China
- CapitalBio Technology Inc., Beijing, China
| | - Y S Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - C Luo
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province, China
| | - P Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province, China
| | - Z Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province, China
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Kashevarova AA, Skryabin NA, Nikitina TV, Lopatkina ME, Sazhenova EA, Zhigalina DI, Savchenko RR, Lebedev IN. Ontogenetic Pleiotropy of Genes Involved in CNVs in Human Spontaneous Abortions. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419100065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Mao J, Wang H, Li H, Song X, Wang T, Xiang J, Li H. Genetic analysis of products of conception using a HLPA/SNP-array strategy. Mol Cytogenet 2019; 12:40. [PMID: 31687045 PMCID: PMC6822274 DOI: 10.1186/s13039-019-0452-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 08/23/2019] [Indexed: 11/29/2022] Open
Abstract
Background Fetal chromosomal abnormalities was the most frequent cause of miscarriage, and the traditional testing method G-banded karyotyping has limitations. Then high-throughput ligation-dependent probe amplification (HLPA) and single nucleotide polymorphism array (SNP-array) were introduced for genetic analysis on products of conception (POC). Methods HLPA and SNP-array analysis were combined. POC samples were initially tested using HLPA, followed by SNP-array analysis on samples that were found to be normal by HLPA. Results Of the 326 POC samples tested, the overall abnormality rate was 54.6% (178/326), including 44.8% (146/326) chromosomal abnormalities identified by HLPA and 9.8% (32/326) additional chromosomal abnormalities further detected by SNP-array. Conclusions The combination of HLPA and SNP-array analysis is an efficient and cost-effective strategy for genetic analysis of POC.
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Affiliation(s)
- Jun Mao
- 1Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu China.,2Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, Jiangsu China
| | - Huiling Wang
- 3Department of Gynaecology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu China
| | - Haibo Li
- Ningbo Municipal Key Laboratory of Comprehensive Prevention and Treatment of Birth Defects, Ningbo Women & Children's Hospital, Ningbo, Zhejiang, China
| | - Xiaoyan Song
- 1Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu China.,2Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, Jiangsu China
| | - Ting Wang
- 1Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu China.,2Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, Jiangsu China
| | - Jingjing Xiang
- 1Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu China.,2Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, Jiangsu China
| | - Hong Li
- 1Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu China.,2Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, Jiangsu China
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10
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Pauta M, Grande M, Rodriguez-Revenga L, Kolomietz E, Borrell A. Added value of chromosomal microarray analysis over karyotyping in early pregnancy loss: systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2018; 51:453-462. [PMID: 29055063 DOI: 10.1002/uog.18929] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 09/29/2017] [Accepted: 10/06/2017] [Indexed: 06/07/2023]
Abstract
OBJECTIVE To estimate the increased test success rate and incremental yield of chromosomal microarray analysis (CMA) over conventional karyotyping in detection of pathogenic copy number variants (CNVs) and variants of unknown significance (VOUS) in early pregnancy loss. METHOD This was a systematic review conducted in accordance with PRISMA criteria. All articles identified in PubMed, Ovid MEDLINE and Web of Science, between January 2000 and April 2017, that described CNVs in early pregnancy losses (up to 20 weeks) were included. Risk differences were pooled to estimate the incremental yield of CMA over karyotyping overall, and after stratification. In addition, test success rate, defined as the proportion of informative results, was compared in series in which CMA and karyotyping were performed concurrently. RESULTS Twenty-three studies, reporting on 5507 pregnancy losses up to 20 weeks with full data available, met the inclusion criteria for analysis. In the series in which CMA and karyotyping were performed concurrently, CMA showed a significant improvement in success rate, providing informative results in 95% (95% CI, 94-96%) of cases compared with karyotyping in which informative results were provided in 68% (95% CI, 66-70%) of cases. Combined data from reviewed studies revealed that incremental yields of CMA over karyotyping were 2% (95% CI, 1-2%) for pathogenic CNVs and 4% (95% CI, 3-6%) for VOUS. The most common pathogenic CNVs reported were 22q11.21 and 1p36.33 deletion. CONCLUSION In comparison with conventional karyotyping, CMA provides a significant increase in test success rate and incremental diagnostic yield in early pregnancy loss. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- M Pauta
- BCNatal Hospital Clínic Barcelona and IDIBAPS, Barcelona, Spain
| | - M Grande
- BCNatal Hospital Clínic Barcelona and IDIBAPS, Barcelona, Spain
| | - L Rodriguez-Revenga
- Biochemistry and Molecular Genetics Department, Hospital Clínic Barcelona and IDIBAPS, Barcelona, Spain
| | - E Kolomietz
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, University of Toronto, Ontario, Canada
| | - A Borrell
- BCNatal Hospital Clínic Barcelona and IDIBAPS, Barcelona, Spain
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11
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Zhang T, Sun Y, Chen Z, Li T. Traditional and molecular chromosomal abnormality analysis of products of conception in spontaneous and recurrent miscarriage. BJOG 2018; 125:414-420. [PMID: 29220118 DOI: 10.1111/1471-0528.15052] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2017] [Indexed: 02/06/2023]
Abstract
Chromosome abnormalities account for half of the recorded miscarriages. Data from cytogenetic analysis of the products of conception (POC) in miscarriages are reviewed in the paper. Genetic analysis of POC allows patients to be given prognostic information. Molecular genetic techniques can overcome the pitfalls of conventional karyotyping, such as culture failure and trace submicroscopic abnormalities. We compare the pros and cons when these technologies are applied to the analysis of POC after miscarriage. Guidance is also provided for future clinical applications. The objective of the review is to help clinicians understand the limitations and to optimise the usefulness of genetic analysis of POC. TWEETABLE ABSTRACT Genetics and POC of miscarriage.
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Affiliation(s)
- T Zhang
- Centre for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - Y Sun
- Centre for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - Z Chen
- Centre for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - T Li
- Department of Obstetrics & Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
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12
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Qu S, Wang L, Cai A, Cui S, Bai N, Liu N, Kong X. Exploring the cause of early miscarriage with SNP-array analysis and karyotyping. J Matern Fetal Neonatal Med 2017; 32:1-10. [PMID: 29034762 DOI: 10.1080/14767058.2017.1367379] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE The aim of this study is to explore the cause of miscarriage, providing risk assessment to guide the next pregnancy. METHODS Four hundred eighty-four products-of-conception (POC) samples were analyzed by single nucleotide polymorphism (SNP) array, and peripheral blood samples of couples were collected for karyotyping or fluorescence in situ hybridization (FISH) analysis. RESULTS Four hundred sixty-eight of the 484 (96.7%) fresh POC samples were successfully analyzed using SNP-array. The rate of clinically significant chromosomal abnormalities were 58.3% (274/468), in which rates of aneuploidy, polyploidy, partial aneuploidy, uniparental isodisomy (isoUPD), and pathogenic microdeletion/microduplication were 43.4% (203/468), 8.8% (41/468), 3.6% (17/468), 1.9% (9/48), and 0.9% (4/468), respectively. The percentage of embryonic chromosomal abnormalities significantly increased with maternal age of patients older than 35 years old. Among 468 couples, 12 major chromosomal rearrangements were detected by G-banding, including nine reciprocal translocations, two Robertsonian translocations, and one superfemale. CONCLUSIONS Chromosome abnormality is the main causes of early miscarriage, and aneuploidies are the most common type of chromosomal abnormalities. Application of SNP array and karyotyping in early miscarriage can provide more genetic information about miscarriage, providing risk assessment to guide the next pregnancy.
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Affiliation(s)
- Suzhen Qu
- a Center for Genetics and Prenatal Diagnosis , the First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , China
| | - Li Wang
- a Center for Genetics and Prenatal Diagnosis , the First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , China
| | - Aojie Cai
- a Center for Genetics and Prenatal Diagnosis , the First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , China
| | - Siying Cui
- a Center for Genetics and Prenatal Diagnosis , the First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , China
| | - Nan Bai
- a Center for Genetics and Prenatal Diagnosis , the First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , China
| | - Ning Liu
- a Center for Genetics and Prenatal Diagnosis , the First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , China
| | - Xiangdong Kong
- a Center for Genetics and Prenatal Diagnosis , the First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , China
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13
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Wang Y, Cheng Q, Meng L, Luo C, Hu H, Zhang J, Cheng J, Xu T, Jiang T, Liang D, Hu P, Xu Z. Clinical application of SNP array analysis in first-trimester pregnancy loss: a prospective study. Clin Genet 2016; 91:849-858. [DOI: 10.1111/cge.12926] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/15/2016] [Accepted: 11/20/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Y. Wang
- State Key Laboratory of Reproductive Medicine; Department of Prenatal Diagnosis; Nanjing China
| | - Q. Cheng
- State Key Laboratory of Reproductive Medicine, Department of Obstetrics; Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University; Nanjing China
| | - L. Meng
- State Key Laboratory of Reproductive Medicine; Department of Prenatal Diagnosis; Nanjing China
| | - C. Luo
- State Key Laboratory of Reproductive Medicine; Department of Prenatal Diagnosis; Nanjing China
| | - H. Hu
- State Key Laboratory of Reproductive Medicine; Department of Prenatal Diagnosis; Nanjing China
| | - J. Zhang
- State Key Laboratory of Reproductive Medicine; Department of Prenatal Diagnosis; Nanjing China
| | - J. Cheng
- State Key Laboratory of Reproductive Medicine; Department of Prenatal Diagnosis; Nanjing China
| | - T. Xu
- State Key Laboratory of Reproductive Medicine; Department of Prenatal Diagnosis; Nanjing China
| | - T. Jiang
- State Key Laboratory of Reproductive Medicine; Department of Prenatal Diagnosis; Nanjing China
| | - D. Liang
- State Key Laboratory of Reproductive Medicine; Department of Prenatal Diagnosis; Nanjing China
| | - P. Hu
- State Key Laboratory of Reproductive Medicine; Department of Prenatal Diagnosis; Nanjing China
| | - Z. Xu
- State Key Laboratory of Reproductive Medicine; Department of Prenatal Diagnosis; Nanjing China
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14
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Massalska D, Zimowski JG, Bijok J, Pawelec M, Czubak-Barlik M, Jakiel G, Roszkowski T. First trimester pregnancy loss: Clinical implications of genetic testing. J Obstet Gynaecol Res 2016; 43:23-29. [DOI: 10.1111/jog.13179] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/21/2016] [Indexed: 01/26/2023]
Affiliation(s)
- Diana Massalska
- I Department of Obstetrics and Gynecology; Professor Witold Orlowski Clinical Hospital, Centre of Postgraduate Medical Education; Warsaw Poland
| | | | - Julia Bijok
- I Department of Obstetrics and Gynecology; Professor Witold Orlowski Clinical Hospital, Centre of Postgraduate Medical Education; Warsaw Poland
| | - Magdalena Pawelec
- Department of Genetics; Institute of Psychiatry and Neurology; Warsaw Poland
| | - Małgorzata Czubak-Barlik
- Department of Pathology; Professor Witold Orlowski Clinical Hospital, Centre of Postgraduate Medical Education; Warsaw Poland
| | - Grzegorz Jakiel
- I Department of Obstetrics and Gynecology; Professor Witold Orlowski Clinical Hospital, Centre of Postgraduate Medical Education; Warsaw Poland
| | - Tomasz Roszkowski
- I Department of Obstetrics and Gynecology; Professor Witold Orlowski Clinical Hospital, Centre of Postgraduate Medical Education; Warsaw Poland
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15
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Ozawa N, Sago H, Matsuoka K, Maruyama T, Migita O, Aizu Y, Inazawa J. Cytogenetic analysis of spontaneously discharged products of conception by array-based comparative genomic hybridization. SPRINGERPLUS 2016; 5:874. [PMID: 27386323 PMCID: PMC4920787 DOI: 10.1186/s40064-016-2594-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 06/15/2016] [Indexed: 12/12/2022]
Abstract
Background Cytogenetic analysis of products of conception (POC) is essential for the management of recurrent pregnancy loss (RPL), but the currently-performed G-banding method is not necessarily applicable to spontaneously discharged POC because of poor quality for culture. We analyzed the karyotypes of 15 spontaneously discharged POC by array-based comparative genomic hybridization (array-CGH). Results All specimens were successfully analyzed and 10 cases had abnormal results: gain in copy number (n = 7) and loss in copy number (n = 3). Most of them were estimated to be whole chromosome aneuploidy, whereas one case was compatible with microdeletion. Two cases were suspected to be male diploid contaminated by maternal DNA or triploid because of the unsatisfactory signal patterns on X/Y chromosomes. Two of three cases with normal female DNA pattern were identified to be contaminated with maternal DNA by the additional analysis of short tandem repeats. Conclusions Given the potential to analyze non-viable POC specimens, array-CGH is a feasible cytogenetic tool for women, in particular, with a history of RPL who desire non-surgical or expectant management of miscarriages and/or a thorough investigation on the cause for recurrent miscarriage, although it needs to take into account high incidence of maternal contamination in spontaneously discharged POC. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-2594-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nobuaki Ozawa
- Center of Maternal-Fetal, Neonatal and Reproductive Medicine, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535 Japan
| | - Haruhiko Sago
- Center of Maternal-Fetal, Neonatal and Reproductive Medicine, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535 Japan
| | - Kentaro Matsuoka
- Department of Pathology, National Center for Child Health and Development, Tokyo, Japan ; Department of Pathology, Kitasato Institute Hospital, Tokyo, Japan
| | - Tetsuo Maruyama
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Ohsuke Migita
- Department of Clinical Genetics and Molecular Medicine, National Center for Child Health and Development, Tokyo, Japan ; Department of Clinical Genetics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yoshinori Aizu
- Division of Advanced Technology and Development, BML, Inc., Kawagoe, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan ; Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
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16
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Sahoo T, Dzidic N, Strecker MN, Commander S, Travis MK, Doherty C, Tyson RW, Mendoza AE, Stephenson M, Dise CA, Benito CW, Ziadie MS, Hovanes K. Comprehensive genetic analysis of pregnancy loss by chromosomal microarrays: outcomes, benefits, and challenges. Genet Med 2016; 19:83-89. [PMID: 27337029 DOI: 10.1038/gim.2016.69] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/19/2016] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Chromosomal microarray analysis (CMA) is currently considered first-tier testing in pediatric care and prenatal diagnosis owing to its high diagnostic sensitivity for chromosomal imbalances. The aim of this study was to determine the efficacy and diagnostic power of CMA in both fresh and formalin-fixed paraffin-embedded (FFPE) samples of products of conception (POCs). METHODS Over a 44-month period, 8,118 consecutive samples were received by our laboratory for CMA analysis. This included both fresh (76.4%) and FFPE samples (22.4%), most of which were ascertained for recurrent pregnancy loss and/or spontaneous abortion (83%). The majority of samples were evaluated by a whole-genome single-nucleotide polymorphism (SNP)-based array (81.6%); the remaining samples were evaluated by array-comparative genomic hybridization (CGH). RESULTS A successful result was obtained in 7,396 of 8,118 (91.1%), with 92.4% of fresh tissue samples and 86.4% of FFPE samples successfully analyzed. Clinically significant abnormalities were identified in 53.7% of specimens (3,975 of 7,396), 94% of which were considered causative. CONCLUSION Analysis of POC specimens by karyotyping fails in 20-40% of cases. SNP-based CMA is a robust platform, with successful results obtained in >90% of cases. SNP-based CMA can identify aneuploidy, polyploidy, whole-genome homozygosity, segmental genomic imbalances, and maternal cell contamination, thus maximizing sensitivity and decreasing false-negative results. Understanding the etiology of fetal loss enables clarification of recurrence risk and assists in determining appropriate management for future family planning.Genet Med 19 1, 83-89.
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Affiliation(s)
| | | | | | | | | | | | - R Weslie Tyson
- Department of Pathology, SCL Health System, Denver, Colorado, USA
| | - Arturo E Mendoza
- Department of Pathology, Sharp Memorial Hospital, San Diego, California, USA
| | - Mary Stephenson
- Department of Obstetrics and Gynecology, University of Illinois Hospital, Chicago, Illinois, USA
| | - Craig A Dise
- Morristown Medical Center, Morristown, New Jersey, USA
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17
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Hardy K, Hardy PJ, Jacobs PA, Lewallen K, Hassold TJ. Temporal changes in chromosome abnormalities in human spontaneous abortions: Results of 40 years of analysis. Am J Med Genet A 2016; 170:2671-80. [PMID: 27287007 DOI: 10.1002/ajmg.a.37795] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 05/31/2016] [Indexed: 12/19/2022]
Abstract
Studies during the past 50 years demonstrate the importance of chromosome abnormalities to the occurrence of early pregnancy loss in humans. Intriguingly, there appears to be considerable variation in the rates of chromosome abnormality, with more recent studies typically reporting higher levels than those reported in early studies of spontaneous abortions. We were interested in examining the basis for these differences and accordingly, we reviewed studies of spontaneous abortions conducted in our laboratories over a 40-year-time span. Our analyses confirm a higher rate of abnormality in more recent series of spontaneous abortions, but indicate that the effect is largely, if not entirely, attributable to changes over time in the maternal age structures of the study populations. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | | | - Patricia A Jacobs
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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18
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Zhu J, Liu H, Tang J, Riaz Khan M, Wang B, Bukhari I. Identification of minor chromosomal defects causing abnormal foetus and spontaneous abortions. Br J Biomed Sci 2016; 73:67-73. [PMID: 27181173 DOI: 10.1080/09674845.2016.1157919] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
BACKGROUND Chromosomal abnormalities are the most common cause of recurrent abortions and miscarriages (RAM), but micro-variations on chromosomes causing RAM have never been previously studied. Single nucleotide polymorphisms (SNPs) are the single nucleotide variations frequently present at genome with the density of at least one common (>20% allele frequency) SNP per kilobase pair. It has already been reported that SNP array examination for chromosomal abnormalities has better performance than the conventional cytogenetic karyotyping. METHODS We applied SNP array to detect the chromosomal defects in 80 placental villi and foetal tissues of abnormal foetus and spontaneous abortions. RESULTS The analyses of data revealed that total 52.5% (42/80) cases were found to have chromosomal abnormalities. The trisomies were most commonly found 26/42 (61.9%) in current samples. Total 8/42 (19.1%) cases were found to have other structural aberrations including translocations in 2/8 (25%), duplications and deletions in 3/8 (37.5%) cases, respectively. SNP analysis also successfully detected triploidy 69,XXX and tetraploidy 92,XXXY. Total 12/80 cases were performed by cytogenetic karyotyping and results were compared with SNP data. Total 5/12 (41.7%) cases were found to have same findings with SNP data while results of 2/12 (16.7%) cases had partial similarity between both techniques. Four cases were declared as karyotypically normal (46,XY or 46,XX) by cytogenetic examination, but later on these four cases were found to have small chromosomal variation which could be the cause of RAM in women. CONCLUSION Therefore, we conclude that use of a high-density SNP platform in diagnosis can give better understanding of molecular causes of pregnancy loss and foetal abnormalities.
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Affiliation(s)
- Jiansheng Zhu
- a Maternity and Child Health Hospital of Anhui Province, The Maternal and Child Health Clinical College, Anhui Medical University , Hefei , China.,b Department of Laboratory Medicines , Anhui Provincial Hospital, Anhui Medical University , Hefei , China
| | - Hui Liu
- a Maternity and Child Health Hospital of Anhui Province, The Maternal and Child Health Clinical College, Anhui Medical University , Hefei , China
| | - Junxiang Tang
- a Maternity and Child Health Hospital of Anhui Province, The Maternal and Child Health Clinical College, Anhui Medical University , Hefei , China
| | - Muhammad Riaz Khan
- c School of life sciences , University of Science and Technology of China , Hefei , China
| | - Baolong Wang
- b Department of Laboratory Medicines , Anhui Provincial Hospital, Anhui Medical University , Hefei , China
| | - Ihtisham Bukhari
- c School of life sciences , University of Science and Technology of China , Hefei , China
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19
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Spectrum of Cytogenomic Abnormalities Revealed by Array Comparative Genomic Hybridization on Products of Conception Culture Failure and Normal Karyotype Samples. J Genet Genomics 2016; 43:121-31. [PMID: 27020032 DOI: 10.1016/j.jgg.2016.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 02/04/2016] [Accepted: 02/07/2016] [Indexed: 12/18/2022]
Abstract
Approximately 30% of pregnancies after implantation end up in spontaneous abortions, and 50% of them are caused by chromosomal abnormalities. However, the spectrum of genomic copy number variants (CNVs) in products of conception (POC) and the underlying gene-dosage-sensitive mechanisms causing spontaneous abortions remain largely unknown. In this study, array comparative genomic hybridization (aCGH) analysis was performed as a salvage procedure for 128 POC culture failure (POC-CF) samples and as a supplemental procedure for 106 POC normal karyotype (POC-NK) samples. Chromosomal abnormalities were detected in 10% of POC-CF and pathogenic CNVs were detected in 3.9% of POC-CF and 5.7% of POC-NK samples. Compiled results from this study and relevant case series through a literature review demonstrated an abnormality detection rate (ADR) of 35% for chromosomal abnormalities in POC-CF samples, 3.7% for pathogenic CNVs in POC-CF samples, and 4.6% for pathogenic CNVs in POC-NK samples. Ingenuity Pathway Analysis (IPA) was performed on the genes from pathogenic CNVs found in POC samples. The denoted primary gene networks suggested that apoptosis and cell proliferation pathways are involved in miscarriage. In summary, a similar spectrum of cytogenomic abnormalities was observed in POC culture success and POC-CF samples. A threshold effect correlating the number of dosage-sensitive genes in a chromosome with the observed frequency of autosomal trisomy is proposed. A rationalized approach using firstly fluorescence in situ hybridization (FISH) testing with probes of chromosomes X/Y/18, 13/21, and 15/16/22 for common aneuploidies and polyploidies and secondly aCGH for other cytogenomic abnormalities is recommended for POC-CF samples.
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20
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Duffy L, Zhang L, Sheath K, Love DR, George AM. The Diagnosis of Choriocarcinoma in Molar Pregnancies: A Revised Approach in Clinical Testing. J Clin Med Res 2015; 7:961-6. [PMID: 26566410 PMCID: PMC4625817 DOI: 10.14740/jocmr2236w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2015] [Indexed: 11/25/2022] Open
Abstract
Background Hydatidiform moles occur in approximately 1 in 1,500 pregnancies; however, early miscarriages or spontaneous abortions may not be correctly identified as molar pregnancies due to poor differentiation of chorionic villi. Methods The current clinical testing algorithm used for the detection of hydatidiform moles uses a combination of morphological analysis and p57 immunostaining followed by ploidy testing to establish a diagnosis of either a complete or partial molar pregnancy. We review here 198 referrals for fluorescence in situ hybridization (FISH) ploidy testing, where the initial diagnosis based on morphology is compared to the final diagnosis based on a combination of morphology, FISH and p57 immunohistochemical (IHC) staining. Results Approximately 40% of cases were determined to be genetically abnormal, but only 28.8% of cases were diagnosed as molar pregnancies. The underestimation of complete molar pregnancies and those with androgenetic inheritance was also found to be likely using conventional diagnostic methods, as atypical p57 staining was observed in approximately 10% of cases. Conclusions Our findings suggest that a revised approach to testing products of conception is necessary, with cases screened according to their clinical history in order to distinguish molar pregnancy referrals from hydropic pregnancies.
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Affiliation(s)
- Lisa Duffy
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Liangtao Zhang
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Karen Sheath
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Donald R Love
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Alice M George
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, Auckland, New Zealand
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21
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Liu S, Song L, Cram DS, Xiong L, Wang K, Wu R, Liu J, Deng K, Jia B, Zhong M, Yang F. Traditional karyotyping vs copy number variation sequencing for detection of chromosomal abnormalities associated with spontaneous miscarriage. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2015; 46:472-477. [PMID: 25767059 DOI: 10.1002/uog.14849] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 02/19/2015] [Accepted: 03/10/2015] [Indexed: 06/04/2023]
Abstract
OBJECTIVES To compare the performance of traditional G-banding karyotyping with that of copy number variation sequencing (CNV-Seq) for detection of chromosomal abnormalities associated with miscarriage. METHODS Products of conception (POC) were collected from spontaneous miscarriages. Chromosomal abnormalities were detected using high-resolution G-banding karyotyping and CNV sequencing. Quantitative fluorescent polymerase chain reaction analysis of maternal and POC DNA for short tandem repeat (STR) markers was used to both monitor maternal cell contamination and confirm the chromosomal status and sex of the miscarriage tissue. RESULTS A total of 64 samples of POC, comprising 16 with an abnormal and 48 with a normal karyotype, were selected and coded for analysis by CNV-Seq. CNV-Seq results were concordant for 14 (87.5%) of the 16 gross chromosomal abnormalities identified by karyotyping, including 11 autosomal trisomies and three sex chromosomal aneuploidies (45,X). Of the two discordant results, a 69,XXX polyploidy was missed by CNV-Seq, although supporting STR marker analysis confirmed the triploidy. In contrast, CNV-Seq identified a sample with 45,X karyotype as a 45,X/46,XY mosaic. In the remaining 48 samples of POC with a normal karyotype, CNV-Seq detected a 2.58-Mb 22q deletion associated with DiGeorge syndrome and nine different smaller CNVs of no apparent clinical significance. CONCLUSIONS CNV-Seq used in parallel with STR profiling is a reliable and accurate alternative to karyotyping for identifying chromosome copy number abnormalities associated with spontaneous miscarriage.
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Affiliation(s)
- S Liu
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - L Song
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - D S Cram
- Berry Genomics, Chaoyang District, Beijing, China
| | - L Xiong
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - K Wang
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - R Wu
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - J Liu
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Guangzhou, Guangdong, China
| | - K Deng
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - B Jia
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - M Zhong
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - F Yang
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
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22
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Rosenfeld JA, Tucker ME, Escobar LF, Neill NJ, Torchia BS, McDaniel LD, Schultz RA, Chong K, Chitayat D. Diagnostic utility of microarray testing in pregnancy loss. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2015; 46:478-486. [PMID: 25846569 DOI: 10.1002/uog.14866] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 03/25/2015] [Accepted: 03/29/2015] [Indexed: 06/04/2023]
Abstract
OBJECTIVES To determine the frequency of clinically significant chromosomal abnormalities identified by chromosomal microarray in pregnancy losses at any gestational age and to compare microarray performance with that of traditional cytogenetic analysis when testing pregnancy losses. METHODS Among 535 fetal demise specimens of any gestational age, clinical microarray-based comparative genomic hybridization (aCGH) was performed successfully on 515, and a subset of 107 specimens underwent additional single nucleotide polymorphism (SNP) analysis. RESULTS Overall, clinically significant abnormalities were identified in 12.8% (64/499) of specimens referred with normal or unknown karyotypes. Detection rates were significantly higher with earlier gestational age. In the subset with normal karyotype, clinically significant abnormalities were identified in 6.9% (20/288). This detection rate did not vary significantly with gestational age, suggesting that, unlike aneuploidy, the contribution of submicroscopic chromosomal abnormalities to fetal demise does not vary with gestational age. In the 107 specimens that underwent aCGH and SNP analysis, seven cases (6.5%) had abnormalities of potential clinical significance detected by the SNP component, including female triploidy. aCGH failed to yield fetal results in 8.3%, which is an improvement over traditional cytogenetic analysis of fetal demise specimens. CONCLUSIONS Both the provision of results in cases in which karyotype fails and the detection of abnormalities in the presence of a normal karyotype demonstrate the increased diagnostic utility of microarray in pregnancy loss. Thus, chromosomal microarray testing is a preferable, robust method of analyzing cases of pregnancy loss to better delineate possible genetic etiologies, regardless of gestational age.
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Affiliation(s)
- J A Rosenfeld
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - M E Tucker
- St. Vincent Hospital, Indianapolis, IN, USA
| | | | - N J Neill
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - B S Torchia
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA
| | - L D McDaniel
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA
| | - R A Schultz
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA
| | - K Chong
- The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, University of Toronto, Ontario, Canada
| | - D Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, University of Toronto, Ontario, Canada
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Bagheri H, Mercier E, Qiao Y, Stephenson MD, Rajcan-Separovic E. Genomic characteristics of miscarriage copy number variants. Mol Hum Reprod 2015; 21:655-61. [PMID: 26071097 DOI: 10.1093/molehr/gav030] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 06/09/2015] [Indexed: 01/08/2023] Open
Abstract
Studies of copy number variants (CNVs) in miscarriages are rare in comparison to post-natal cases with developmental abnormalities. The overall characteristics of miscarriage CNVs (size, gene content and function) are therefore largely unexplored. Our goal was to assess and compare the characteristics of CNVs identified in 101 euploid miscarriages from four high-resolution array studies that documented both common miscarriage CNVs (i.e. CNVs found in controls from the Database of Genomic Variants, DGV) and rare miscarriage CNVs (not reported in DGV). Our miscarriage analysis included 24 rare CNVs with 93 genes, and 372 common CNVs (merged into 119 common CNV regions; CNVRs) with 354 genes. The rare and common CNVs were comparable in size (median size of ∼ 0.16 and 0.14 Mb, respectively); however, rare CNVs showed a significantly higher gene density, with 56 genes/Mb in rare and 24 genes/Mb in common CNVs (P = 0.03). Rare CNVs also had two times more genes with mouse knock-out models which were reported for 42% of rare and 19% of common CNV genes. No specific pathway enrichment was noted for 24 rare CNV genes, but common CNV genes showed significant enrichment in genes from immune-response related pathways and pregnancy/reproduction-related biological processes. Our analysis of CNVs from euploid miscarriages suggests that both rare and common CNVs could have a role in miscarriage by impacting pregnancy-related genes or pathways. Cataloguing of all CNVs and detailed description of their characteristics (e.g. gene content, genomic breakpoints) is desirable in the future for better understanding of their relevance to pregnancy loss.
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Affiliation(s)
- Hani Bagheri
- Department of Pathology and Laboratory Medicine, BC Child and Family Research Institute, University of British Columbia (UBC), Vancouver, BC V5Z 4H4, Canada
| | | | - Ying Qiao
- Department of Pathology and Laboratory Medicine, BC Child and Family Research Institute, University of British Columbia (UBC), Vancouver, BC V5Z 4H4, Canada
| | - Mary D Stephenson
- Department of Obstetrics and Gynaecology, University of Illinois at Chicago, Chicago, IL, USA
| | - Evica Rajcan-Separovic
- Department of Pathology and Laboratory Medicine, BC Child and Family Research Institute, University of British Columbia (UBC), Vancouver, BC V5Z 4H4, Canada
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Abstract
Miscarriage is a very common occurrence in humans. This paper sets out to present published data on research that has provided increased understanding of pregnancy failure. Clarification of definitions, exploring the range of failures from preclinical to later pregnancy losses, and the scientific tools employed to find information on the losses have been documented. What is now understood, which tools work best, and the associated limitations are all discussed. Early studies used cytogenetic methods and tissue culture to obtain results. Improvements in laboratory tools such as better tissue culture incubators, inverted microscopes, laminar flow hoods, improvements in culture media, all contributed to obtaining more results for patients. These studies demonstrated the significant contribution of unbalanced chromosomal karyotypes to pregnancy failure. Maternal age as a contributing factor in trisomy was clearly demonstrated. First trimester miscarriage exhibits very high cytogenetic abnormality; in contrast to very low rates in later losses. Combining data across all time periods of pregnancy will affect the significance of chromosomal error in the early pregnancy failures. Cytogenetic methods investigate whole genomes, and are considered to represent the standard against which new methods must be validated. New molecular genetic methods provide the opportunity to examine samples without the necessity of tissue culture. Techniques may be site-specific or whole genome. Fluorescent in situ hybridisation (FISH), comparative genomic hybridisation (CGH), array-based CGH, single nucleotide polymorphism (SNP) detection, quantitative polymerase chain reaction (qPCR), and quantitative fluorescent PCR (QF-PCR), have all been utilised. In comparison studies with classical/conventional cytogenetics, each newer method offers advantages and limitations. At the present time, a combined approach using conventional and molecular methods will elucidate the cause of miscarriage for almost all samples. In a clinical setting this would be optimum.
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Affiliation(s)
- Kathy Hardy
- Cyto Labs Pty Ltd, Bentley, Western Australia
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25
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Abstract
PURPOSE This study was performed on miscarriage samples for chromosome analysis to detect copy number variations (CNVs) related to subtelomeric regions, and with these results we aimed to adapt multiplex ligation-dependent probe amplification (MLPA) method for prenatal diagnosis. MATERIALS AND METHODS The cell cultures and DNA isolations were performed on 60 miscarriage samples. For maternal contamination analysis, DNA isolations and quantitative fluorescent polymerase chain reactions were done using peripheric blood of mothers who had miscarriages. We compared short tandem repeat peak profiles of miscarriage samples and mothers. The subtelomeric regions of the chromosomes were assessed using the MLPA method. RESULTS Of 43 miscarriage samples, 19 had normal karyotype (44.2%), 10 had numerical abnormalities (23.3%), and 2 had structural abnormalities (4.7%). Subtelomeric 16q duplication was determined in 2 of the 30 miscarriage samples investigated with MLPA method (6.6%). CONCLUSION There is no statistically significant difference between two groups (p > 0.05). However, the fact that the 6.6% subtelomeric CNV found in miscarriage samples was not found in controls, showed that further studies are required. We recommend that the miscarriage samples of the couples with recurrent miscarriage should be analyzed in terms of subtelomeric CNV after the exclusion of other clinical reasons.
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Affiliation(s)
- Akin Tekcan
- a School of Health, Ahi Evran University , Kirsehir , Turkey
| | - Mehmet Elbistan
- b Section of Medical Genetic, Department of Medical Biology , and
| | - Sengul Tural
- b Section of Medical Genetic, Department of Medical Biology , and
| | - Mehmet Bilge Çetinkaya
- c Department of Gynecology and Obstetrics, Faculty of Medicine , Ondokuz Mayis University , Samsun , Turkey
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26
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Jia Y, Zhao H, Shi D, Peng W, Xie L, Wang W, Jiang F, Zhang H, Wang X. Genetic effects of a 13q31.1 microdeletion detected by noninvasive prenatal testing (NIPT). INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2014; 7:7003-7011. [PMID: 25400788 PMCID: PMC4230093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 09/13/2014] [Indexed: 06/04/2023]
Abstract
Microdeletions of chromosome 13q31.1 are relatively rare. These types of deletions may cause different genetic effects on genotypes and/or phenotypes. There are several ways to detect microdeletions; noninvasive prenatal testing (NIPT) is the newest detection method. In this study, we aimed to investigate the genetic effects of a 13q31.1 microdeletion detected by NIPT and to reconfirm the feasibility of this procedure in predicting sub-chromosomal copy number variations (CNVs). The 13q31.1 microdeletion, which has previously been described as a disease-associated fragment, was detected by NIPT in a pregnant woman. To validate the finding and to explain the origin of this sub-chromosomal CNV, we collected fetal amniotic fluid and parental blood samples and tested the samples using array-based comparative genomic hybridization (aCGH). Karyotype analysis was performed on all of the samples to rule out balanced or mosaic anomalies. The aCGH results confirmed the NIPT findings. We detected the same type of microdeletion in the fetus and the mother via aCGH. The mother had a normal phenotype; therefore, in a post-test genetic counseling session, we predicted a normal phenotype for the fetus. After delivery, the normal phenotype of the newborn confirmed our prediction. Based on the present study, this 13q31.1 microdeletion may be considered as a chromosomal polymorphism. This study also reconfirmed the feasibility of obtaining a molecular karyotype of a fetus via NIPT.
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Affiliation(s)
- Yifang Jia
- Shandong Provincial Hospital Affiliated to Shandong UniversityJinan, Shandong, China
| | - Heyong Zhao
- Shandong Provincial Hospital Affiliated to Shandong UniversityJinan, Shandong, China
- Zibo Maternal and Child Health Care HospitalZibo, Shandong, China
| | - Donghong Shi
- Shandong Provincial Hospital Affiliated to Shandong UniversityJinan, Shandong, China
| | - Wen Peng
- Shandong Provincial Hospital Affiliated to Shandong UniversityJinan, Shandong, China
| | - Luwen Xie
- Shandong Provincial Hospital Affiliated to Shandong UniversityJinan, Shandong, China
| | | | | | | | - Xietong Wang
- Shandong Provincial Hospital Affiliated to Shandong UniversityJinan, Shandong, China
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27
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Bug S, Solfrank B, Schmitz F, Pricelius J, Stecher M, Craig A, Botcherby M, Nevinny-Stickel-Hinzpeter C. Diagnostic utility of novel combined arrays for genome-wide simultaneous detection of aneuploidy and uniparental isodisomy in losses of pregnancy. Mol Cytogenet 2014; 7:43. [PMID: 25013457 PMCID: PMC4090657 DOI: 10.1186/1755-8166-7-43] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 05/27/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND This proof-of-principle study demonstrates the usefulness and robustness of a novel array based method for the elucidation of genetic causes underlying early pregnancy loss. A combined microarray utilizing comparative genomic hybridization and single nucleotide polymorphism detection (CGH + SNP) was used for parallel genome-wide identification of copy number and heterozygosity status of 70 products of conception. Results of samples with previously determined aneuploidies were juxtaposed to those of a second cohort appearing normal after routine genetic diagnostics. RESULTS All chromosomal imbalances were confirmed, in one sample of the aneuploid panel additional monosomy X was discovered. Genome-wide uniparental disomy causing a complete hydatidiform mole was identified in another sample. No specimen featured microaberrations of obvious clinical relevance. Among cases with presumable euploidy, one microdeletion and a single region of homozygosity were assigned unclear clinical significance. CONCLUSIONS The results prove the utility of combined imbalance and homozygosity mapping for routine workup of these challenging specimens. Moreover parallel screening at submicroscopic resolution facilitates the detection of novel genetic alterations underlying spontaneous abortion.
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Affiliation(s)
- Stefanie Bug
- synlab Medizinisches Versorgungszentrum Humane Genetik München, Lindwurmstraße 23, D-80337 Munich, Germany
| | - Beate Solfrank
- synlab Medizinisches Versorgungszentrum Humane Genetik München, Lindwurmstraße 23, D-80337 Munich, Germany
| | - Felizitas Schmitz
- synlab Medizinisches Versorgungszentrum Humane Genetik München, Lindwurmstraße 23, D-80337 Munich, Germany
| | - Jana Pricelius
- synlab Medizinisches Versorgungszentrum Humane Genetik München, Lindwurmstraße 23, D-80337 Munich, Germany
| | - Mona Stecher
- synlab Medizinisches Versorgungszentrum Humane Genetik München, Lindwurmstraße 23, D-80337 Munich, Germany
| | - Andrew Craig
- BlueGnome Ltd, An Illumina Company, Cambridge, UK
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28
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Jenderny J. Chromosome aberrations in a large series of spontaneous miscarriages in the German population and review of the literature. Mol Cytogenet 2014; 7:38. [PMID: 24976865 PMCID: PMC4073514 DOI: 10.1186/1755-8166-7-38] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 05/27/2014] [Indexed: 12/14/2022] Open
Abstract
Background In a review of the literature in 2000 the different cytogenetic aspects of spontaneous miscarriages were well documented. This review also included the spontaneous miscarriage results of one large German study published in 1990. However, to our knowledge there are no new data on spontaneous miscarriages in the German population. Therefore, the aim of the present retrospective large study was to find out the incidence and types of chromosome aberrations in an unselected series of spontaneous miscarriages in the German population, and whether our more recent results were different to data published previously. In case of culture failure we implemented a quantitative fluorescent polymerase chain reaction (QF-PCR) for chromosomes 13, 18, 21, X and Y. Results In the present German retrospective study cytogenetic analysis (CA) was attempted on 534 spontaneous miscarriages between weeks 7 and 34 of gestation, being successful in 73% (390/534) of them. Two hundred and thirty-seven of the cases (61%, 237/390) were chromosomally abnormal. Trisomy was the most common chromosome aberration and accounted for 53% (125/237) of the aberrant karyotypes. A multiple aneuploidy was observed in 7% (17/237) of the aberrant karyotypes. Chromosomes 16, 22, 15 and 21 were found most frequently involved in aneuploidies. Fifty-four cases (23%, 54/237) with a polyploidy were found in the present study. Single unbalanced structural chromosome aberrations accounted for 4% (10/237) of the aberrant karyotypes. Eleven samples (5%, 11/237) displayed a variety of numerical and/or structural chromosome aberrations. One hundred and forty-four spontaneous miscarriages (27%, 144/534) failed to grow in culture. A total of 27 cases were analysed by QF-PCR for chromosomes 13, 18, 21, X and Y, being informative in all cases. Conclusion In our German retrospective large study of spontaneous miscarriages, the incidence and types of chromosome aberrations by CA are within the reported range of other studies published previously before and after 2000. Therefore, we can conclude that cytogenetic aspects of spontaneous miscarriages have not changed over the years. Additionally 8 of 27 cases (30%) without cell growth showed a numerical chromosome aberration by QF-PCR. Therefore QF-PCR played an important role as a supplementary test when culture failure occurred.
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Affiliation(s)
- Jutta Jenderny
- Humangenetik, Labor Lademannbogen, Lademannbogen 61-63, DE-22339 Hamburg, Germany
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29
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Wang BT, Chong TP, Boyar FZ, Kopita KA, Ross LP, El-Naggar MM, Sahoo T, Wang JC, Hemmat M, Haddadin MH, Owen R, Anguiano AL. Abnormalities in spontaneous abortions detected by G-banding and chromosomal microarray analysis (CMA) at a national reference laboratory. Mol Cytogenet 2014; 7:33. [PMID: 24914406 PMCID: PMC4049495 DOI: 10.1186/1755-8166-7-33] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 04/22/2014] [Indexed: 11/12/2022] Open
Abstract
Background Cytogenetic evaluation of products of conception (POC) for chromosomal abnormalities is central to determining the cause of pregnancy loss. We compared the test success rates in various specimen types and the frequencies of chromosomal abnormalities detected by G-banding analysis with those found by Oligo-SNP chromosomal microarray analysis (CMA). We evaluated the benefit of CMA testing in cases of failed culture growth. Methods Conventional cytogenetic results of 5457 consecutive POC specimens were reviewed and categorized as placental villi, fetal parts, and unspecified POC tissue. The CMA was performed on 268 cases. Of those, 32 cases had concurrent G-banding results. The remaining 236 cases included 107 cases with culture failure and 129 cases evaluated by CMA alone. Results The overall POC culture success rate was 75%, with the lowest for fetal parts (37.4%) and the highest for placental villi (81%). The abnormality rate was 58% for placental villi, but only 25% for fetal parts. Of the abnormalities detected, the most common were aneuploidies, including trisomy 16, triploidy, monosomy X, trisomy 22, trisomy 21 and trisomy 15, while the least encountered aneuploidies were trisomy 1, trisomy 19 and monosomies (except monosomy 21). Overall, POC specimens studied by CMA were successful in 89.6% of cases and yielded a 44.6% abnormality rate. Conclusions Placental villi yielded higher rates of culture success and a higher percentage of abnormal karyotypes than did other specimen types. The Oligo-SNP CMA method has demonstrated a viable alternative to the G-banding method in view of its advantages in detection of submicroscopic genomic aberrations, shorter turnaround time due to elimination of time required for culture and a higher test success rate.
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Affiliation(s)
- Boris T Wang
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA 92690, California
| | - Thomas P Chong
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA 92690, California
| | - Fatih Z Boyar
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA 92690, California
| | - Kimberly A Kopita
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA 92690, California
| | - Leslie P Ross
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA 92690, California
| | - Mohamed M El-Naggar
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA 92690, California
| | - Trilochan Sahoo
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA 92690, California
| | - Jia-Chi Wang
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA 92690, California
| | - Morteza Hemmat
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA 92690, California
| | - Mary H Haddadin
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA 92690, California
| | - Renius Owen
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA 92690, California
| | - Arturo L Anguiano
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA 92690, California
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30
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Horn H, Bausinger J, Staiger AM, Sohn M, Schmelter C, Gruber K, Kalla C, Ott MM, Rosenwald A, Ott G. Numerical and structural genomic aberrations are reliably detectable in tissue microarrays of formalin-fixed paraffin-embedded tumor samples by fluorescence in-situ hybridization. PLoS One 2014; 9:e95047. [PMID: 24733537 PMCID: PMC3986364 DOI: 10.1371/journal.pone.0095047] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 03/23/2014] [Indexed: 11/23/2022] Open
Abstract
Few data are available regarding the reliability of fluorescence in-situ hybridization (FISH), especially for chromosomal deletions, in high-throughput settings using tissue microarrays (TMAs). We performed a comprehensive FISH study for the detection of chromosomal translocations and deletions in formalin-fixed and paraffin-embedded (FFPE) tumor specimens arranged in TMA format. We analyzed 46 B-cell lymphoma (B-NHL) specimens with known karyotypes for translocations of IGH-, BCL2-, BCL6- and MYC-genes. Locus-specific DNA probes were used for the detection of deletions in chromosome bands 6q21 and 9p21 in 62 follicular lymphomas (FL) and six malignant mesothelioma (MM) samples, respectively. To test for aberrant signals generated by truncation of nuclei following sectioning of FFPE tissue samples, cell line dilutions with 9p21-deletions were embedded into paraffin blocks. The overall TMA hybridization efficiency was 94%. FISH results regarding translocations matched karyotyping data in 93%. As for chromosomal deletions, sectioning artefacts occurred in 17% to 25% of cells, suggesting that the proportion of cells showing deletions should exceed 25% to be reliably detectable. In conclusion, FISH represents a robust tool for the detection of structural as well as numerical aberrations in FFPE tissue samples in a TMA-based high-throughput setting, when rigorous cut-off values and appropriate controls are maintained, and, of note, was superior to quantitative PCR approaches.
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Affiliation(s)
- Heike Horn
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Julia Bausinger
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Annette M. Staiger
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Maximilian Sohn
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | | | - Kim Gruber
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Claudia Kalla
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - M. Michaela Ott
- Institute of Pathology, Caritas-Hospital, Bad Mergentheim, Germany
| | | | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- * E-mail:
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31
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Kudesia R, Li M, Smith J, Patel A, Williams Z. Rescue karyotyping: a case series of array-based comparative genomic hybridization evaluation of archival conceptual tissue. Reprod Biol Endocrinol 2014; 12:19. [PMID: 24589081 PMCID: PMC3996014 DOI: 10.1186/1477-7827-12-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 02/27/2014] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Determination of fetal aneuploidy is central to evaluation of recurrent pregnancy loss (RPL). However, obtaining this information at the time of a miscarriage is not always possible or may not have been ordered. Here we report on "rescue karyotyping", wherein DNA extracted from archived paraffin-embedded pregnancy loss tissue from a prior dilation and curettage (D&C) is evaluated by array-based comparative genomic hybridization (aCGH). METHODS A retrospective case series was conducted at an academic medical center. Patients included had unexplained RPL and a prior pregnancy loss for which karyotype information would be clinically informative but was unavailable. After extracting DNA from slides of archived tissue, aCGH with a reduced stringency approach was performed, allowing for analysis of partially degraded DNA. Statistics were computed using STATA v12.1 (College Station, TX). RESULTS Rescue karyotyping was attempted on 20 specimens from 17 women. DNA was successfully extracted in 16 samples (80.0%), enabling analysis at either high or low resolution. The longest interval from tissue collection to DNA extraction was 4.2 years. There was no significant difference in specimen sufficiency for analysis in the collection-to-extraction interval (p=0.14) or gestational age at pregnancy loss (p=0.32). Eight specimens showed copy number variants: 3 trisomies, 2 partial chromosomal deletions, 1 mosaic abnormality and 2 unclassified variants. CONCLUSIONS Rescue karyotyping using aCGH on DNA extracted from paraffin-embedded tissue provides the opportunity to obtain critical fetal cytogenetic information from a prior loss, even if it occurred years earlier. Given the ubiquitous archiving of paraffin embedded tissue obtained during a D&C and the ease of obtaining results despite long loss-to-testing intervals or early gestational age at time of fetal demise, this may provide a useful technique in the evaluation of couples with recurrent pregnancy loss.
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Affiliation(s)
- Rashmi Kudesia
- Program for Early and Recurrent Pregnancy Loss (PEARL), Department of Obstetrics, Gynecology & Women’s Health, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Price Building, Room 474, Bronx, NY 10461, USA
| | - Marilyn Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop NAB 2015, Houston, TX 77030, USA
| | - Janice Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop NAB 2015, Houston, TX 77030, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop NAB 2015, Houston, TX 77030, USA
| | - Zev Williams
- Program for Early and Recurrent Pregnancy Loss (PEARL), Department of Obstetrics, Gynecology & Women’s Health, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Price Building, Room 474, Bronx, NY 10461, USA
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32
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Kooper AJA, Faas BHW, Feenstra I, de Leeuw N, Smeets DFCM. Best diagnostic approach for the genetic evaluation of fetuses after intrauterine death in first, second or third trimester: QF-PCR, karyotyping and/or genome wide SNP array analysis. Mol Cytogenet 2014; 7:6. [PMID: 24428858 PMCID: PMC3906897 DOI: 10.1186/1755-8166-7-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 12/17/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The aim of this study was to evaluate the best diagnostic approach for the genetic analysis of samples from first, second and third trimester intrauterine fetal deaths (IUFDs). We examined a total of 417 IUFD samples from fetuses with and without congenital anomalies. On 414 samples, karyotyping (N = 46) and/or rapid aneuploidy testing by QF-PCR (N = 371) was performed). One hundred sixty eight samples with a normal test result were subsequently tested by genome wide Single Nucleotide Polymorphism (SNP) array analysis. Three samples were only analyzed by array. RESULTS In 50 (12.0%) samples an aneuploidy was detected by QF-PCR and/or karyotyping, representing 47.1% of first, 13.2% of second and 3.4% of third trimester pregnancies. Karyotyping and QF-PCR failed in 4 (8.7%) and 7 (1.9%) samples, respectively, concerning mostly contaminated amniotic fluid samples from third trimester pregnancies.Clinically relevant aberrations were identified in 4.2% (all fetuses with malformations) of the 168 samples tested by SNP array. Inherited copy number variants (CNVs) were detected in 5.4% and 8.9% showed CNVs of unknown clinical relevance as parental inheritance could not be studied yet. In a sample from a fetus suspect for Meckel-Grüber syndrome, the genotype information from the SNP array revealed various stretches of homozygosity, including one stretch encompassing the CEP290 gene. Subsequent CEP290 mutation analysis revealed a homozygous, pathogenic mutation in this gene. CONCLUSIONS Based on our experience we recommend QF-PCR as the first-line test in IUFD samples of first and second trimester pregnancies to exclude aneuploidy before performing array analysis. The chance to detect aneuploidy in third trimester pregnancies is relatively low and therefore array analysis can be performed as a first-tier test. A tissue sample, instead of amniotic fluid, is preferred because of a higher success rate in testing.We emphasize the need for analysis of parental samples whenever a rare, unique CNV is detected to allow for better interpretation of such findings and to improve future pregnancy management. Furthermore, we illustrate the strength of SNP arrays for genotype analysis, even though we realize it is crucial to have detailed phenotypic information to make optimal use of the genotype data in finding candidate recessive genes that may be related to the fetal phenotype.
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Affiliation(s)
- Angelique JA Kooper
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Brigitte HW Faas
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Ilse Feenstra
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Dominique FCM Smeets
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
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Liehr T, Weise A, Hamid AB, Fan X, Klein E, Aust N, Othman MA, Mrasek K, Kosyakova N. Multicolor FISH methods in current clinical diagnostics. Expert Rev Mol Diagn 2013; 13:251-5. [PMID: 23570403 DOI: 10.1586/erm.12.146] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Multicolor FISH (mFISH) assays are currently indispensable for a precise description of derivative chromosomes. Routine application of such techniques on human chromosomes started in 1996 with the simultaneous use of all 24 human whole-chromosome painting probes in multiplex-FISH and spectral karyotyping. Since then, multiple approaches for chromosomal differentiation based on multicolor-FISH (MFISH) assays have been developed. Predominantly, they are applied to characterize marker or derivative chromosomes identified in conventional banding analysis. Since the introduction of array-based comparative genomic hybridization (aCGH), mFISH is also applied to verify and further delineate aCGH-detected aberrations. For the latter, it is important to consider the fact that aCGH cannot detect or characterize balanced rearrangements, which are important to be resolved in detail in infertility diagnostics. In addition, mFISH is necessary to distinguish different imbalanced situations detectable in aCGH; small supernumerary marker chromosomes have to be differentiated from insertions or unbalanced translocations. This review presents an overview on the available mFISH methods and their applications in pre- and post-natal clinical genetics.
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Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, Jena D-07743, Germany.
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Dhillon RK, Hillman SC, Morris RK, McMullan D, Williams D, Coomarasamy A, Kilby MD. Additional information from chromosomal microarray analysis (CMA) over conventional karyotyping when diagnosing chromosomal abnormalities in miscarriage: a systematic review and meta-analysis. BJOG 2013; 121:11-21. [DOI: 10.1111/1471-0528.12382] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2013] [Indexed: 02/03/2023]
Affiliation(s)
- RK Dhillon
- Academic Department; Birmingham Women's Foundation Trust; Edgbaston Birminghmam UK
| | - SC Hillman
- Academic Department; Birmingham Women's Foundation Trust; Edgbaston Birminghmam UK
- School of Clinical and Experimental Medicine; College of Medicine and Dentistry; University of Birmingham; Edgbaston Birmingham UK
| | - RK Morris
- Academic Department; Birmingham Women's Foundation Trust; Edgbaston Birminghmam UK
- School of Clinical and Experimental Medicine; College of Medicine and Dentistry; University of Birmingham; Edgbaston Birmingham UK
| | - D McMullan
- West Midlands Regional Genetics Laboratories and the Department of Clinical Genetics; Birmingham Women's Foundation Trust; Edgbaston Birmingham UK
| | - D Williams
- West Midlands Regional Genetics Laboratories and the Department of Clinical Genetics; Birmingham Women's Foundation Trust; Edgbaston Birmingham UK
| | - A Coomarasamy
- Academic Department; Birmingham Women's Foundation Trust; Edgbaston Birminghmam UK
- School of Clinical and Experimental Medicine; College of Medicine and Dentistry; University of Birmingham; Edgbaston Birmingham UK
| | - MD Kilby
- Academic Department; Birmingham Women's Foundation Trust; Edgbaston Birminghmam UK
- School of Clinical and Experimental Medicine; College of Medicine and Dentistry; University of Birmingham; Edgbaston Birmingham UK
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Sheath KL, Duffy L, Asquith P, Love DR, George AM. Bacterial artificial chromosomes (BACs)-on-Beads™ as a diagnostic platform for the rapid aneuploidy screening of products of conception. Mol Med Rep 2013; 8:650-4. [PMID: 23764829 DOI: 10.3892/mmr.2013.1519] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 05/28/2013] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to evaluate the use of KaryoLite™ bacterial artificial chromosomes (BACs)‑on‑Beads™ (BoBs) technology for the rapid screening of products of conception (POC). Validation and prospective studies were carried out on 85 and 95 patient samples, respectively. Validation studies had previously been analyzed using routine culture and G-banded karyotyping. BoBs resulted in an abnormality detection frequency of 27%, with a failure rate of <3%. The time required for processing was significantly lower compared with that of tissue culture. In conclusion, BoBs technology decreased the failure rate, while increasing the analytical sensitivity compared with G-banded karyotype analysis alone. Additionally, significant cost savings may be achieved with regard to the time of processing and analysis of specimens.
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Affiliation(s)
- Karen L Sheath
- Diagnostic Genetics, LabPlus, Auckland City Hospital, Auckland 1148, New Zealand
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