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Vasilyeva OY, Tolmacheva EN, Dmitriev AE, Darkova YA, Sazhenova EA, Nikitina TV, Lebedev IN, Vasilyev SA. Aberrant methylation of placental development genes in chorionic villi of spontaneous abortions with trisomy 16. Vavilovskii Zhurnal Genet Selektsii 2024; 28:198-203. [PMID: 38680176 PMCID: PMC11043499 DOI: 10.18699/vjgb-24-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/18/2024] [Accepted: 01/18/2023] [Indexed: 05/01/2024] Open
Abstract
In humans, aneuploidy is incompatible with the birth of healthy children and mainly leads to the death of embryos in the early stages of development in the first trimester of pregnancy. Trisomy 16 is the most common aneuploidy among spontaneous abortions of the first trimester of pregnancy. However, the mechanisms leading to the death of embryos with trisomy 16 remain insufficiently investigated. One of these potential mechanisms is abnormal placental development, including aberrant remodeling of spiral arteries. Spiral artery remodeling involves the migration of trophoblast cells into the maternal spiral arteries, replacing their endothelium and remodeling to ensure a stable embryonic nutrition and oxygen supply. This is a complex process which depends on many factors from both the embryo and the mother. We analyzed the methylation level of seven genes (ADORA2B, NPR3, PRDM1, PSG2, PHTLH, SV2C, and TICAM2) involved in placental development in the chorionic villi of spontaneous abortions with trisomy 16 (n = 14), compared with spontaneous abortions with a normal karyotype (n = 31) and the control group of induced abortions (n = 10). To obtain sequencing libraries, targeted amplification of individual gene regions using designed oligonucleotide primers for bisulfite-converted DNA was used. The analysis was carried out using targeted bisulfite massive parallel sequencing. In the group of spontaneous abortions with trisomy 16, the level of methylation of the PRDM1 and PSG2 genes was significantly increased compared to induced abortions (p = 0.0004 and p = 0.0015, respectively). In the group of spontaneous abortions, there was no increase in the level of methylation of the PRDM1 and PSG2 genes, but the level of methylation of the ADORA2B gene was significantly increased compared to the induced abortions (p = 0.032). The results obtained indicate the potential mechanisms of the pathogenetic effect of trisomy 16 on the placental development with the participation of the studied genes.
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Affiliation(s)
- O Yu Vasilyeva
- Research Institute of Medical Genetics of the Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - E N Tolmacheva
- Research Institute of Medical Genetics of the Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - A E Dmitriev
- National Research Tomsk State University, Tomsk, Russia
| | - Ya A Darkova
- National Research Tomsk State University, Tomsk, Russia
| | - E A Sazhenova
- Research Institute of Medical Genetics of the Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - T V Nikitina
- Research Institute of Medical Genetics of the Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - I N Lebedev
- Research Institute of Medical Genetics of the Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - S A Vasilyev
- Research Institute of Medical Genetics of the Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
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Maksiutenko EM, Barbitoff YA, Nasykhova YA, Pachuliia OV, Lazareva TE, Bespalova ON, Glotov AS. The Landscape of Point Mutations in Human Protein Coding Genes Leading to Pregnancy Loss. Int J Mol Sci 2023; 24:17572. [PMID: 38139401 PMCID: PMC10743817 DOI: 10.3390/ijms242417572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Pregnancy loss is the most frequent complication of a pregnancy which is devastating for affected families and poses a significant challenge for the health care system. Genetic factors are known to play an important role in the etiology of pregnancy loss; however, despite advances in diagnostics, the causes remain unexplained in more than 30% of cases. In this review, we aggregated the results of the decade-long studies into the genetic risk factors of pregnancy loss (including miscarriage, termination for fetal abnormality, and recurrent pregnancy loss) in euploid pregnancies, focusing on the spectrum of point mutations associated with these conditions. We reviewed the evolution of molecular genetics methods used for the genetic research into causes of pregnancy loss, and collected information about 270 individual genetic variants in 196 unique genes reported as genetic cause of pregnancy loss. Among these, variants in 18 genes have been reported by multiple studies, and two or more variants were reported as causing pregnancy loss for 57 genes. Further analysis of the properties of all known pregnancy loss genes showed that they correspond to broadly expressed, highly evolutionary conserved genes involved in crucial cell differentiation and developmental processes and related signaling pathways. Given the features of known genes, we made an effort to construct a list of candidate genes, variants in which may be expected to contribute to pregnancy loss. We believe that our results may be useful for prediction of pregnancy loss risk in couples, as well as for further investigation and revealing genetic etiology of pregnancy loss.
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Affiliation(s)
| | - Yury A. Barbitoff
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.N.); (O.V.P.); (T.E.L.); (O.N.B.)
| | | | | | | | | | - Andrey S. Glotov
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.N.); (O.V.P.); (T.E.L.); (O.N.B.)
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Essers R, Lebedev IN, Kurg A, Fonova EA, Stevens SJC, Koeck RM, von Rango U, Brandts L, Deligiannis SP, Nikitina TV, Sazhenova EA, Tolmacheva EN, Kashevarova AA, Fedotov DA, Demeneva VV, Zhigalina DI, Drozdov GV, Al-Nasiry S, Macville MVE, van den Wijngaard A, Dreesen J, Paulussen A, Hoischen A, Brunner HG, Salumets A, Zamani Esteki M. Prevalence of chromosomal alterations in first-trimester spontaneous pregnancy loss. Nat Med 2023; 29:3233-3242. [PMID: 37996709 PMCID: PMC10719097 DOI: 10.1038/s41591-023-02645-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/11/2023] [Indexed: 11/25/2023]
Abstract
Pregnancy loss is often caused by chromosomal abnormalities of the conceptus. The prevalence of these abnormalities and the allocation of (ab)normal cells in embryonic and placental lineages during intrauterine development remain elusive. In this study, we analyzed 1,745 spontaneous pregnancy losses and found that roughly half (50.4%) of the products of conception (POCs) were karyotypically abnormal, with maternal and paternal age independently contributing to the increased genomic aberration rate. We applied genome haplarithmisis to a subset of 94 pregnancy losses with normal parental and POC karyotypes. Genotyping of parental DNA as well as POC extra-embryonic mesoderm and chorionic villi DNA, representing embryonic and trophoblastic tissues, enabled characterization of the genomic landscape of both lineages. Of these pregnancy losses, 35.1% had chromosomal aberrations not previously detected by karyotyping, increasing the rate of aberrations of pregnancy losses to 67.8% by extrapolation. In contrast to viable pregnancies where mosaic chromosomal abnormalities are often restricted to chorionic villi, such as confined placental mosaicism, we found a higher degree of mosaic chromosomal imbalances in extra-embryonic mesoderm rather than chorionic villi. Our results stress the importance of scrutinizing the full allelic architecture of genomic abnormalities in pregnancy loss to improve clinical management and basic research of this devastating condition.
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Affiliation(s)
- Rick Essers
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW-Research Institute for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Igor N Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Ants Kurg
- Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Elizaveta A Fonova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW-Research Institute for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Rebekka M Koeck
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW-Research Institute for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Ulrike von Rango
- Department of Anatomy & Embryology, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Lloyd Brandts
- Department of Clinical Epidemiology and Medical Technology Assessment (KEMTA), Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
| | - Spyridon Panagiotis Deligiannis
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Obstetrics and Gynecology, University of Helsinki, Helsinki, Finland
| | - Tatyana V Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Elena A Sazhenova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Ekaterina N Tolmacheva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Anna A Kashevarova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Dmitry A Fedotov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Viktoria V Demeneva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Daria I Zhigalina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Gleb V Drozdov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Salwan Al-Nasiry
- Department of Genetics and Cell Biology, GROW-Research Institute for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
- Department of Obstetrics and Gynaecology, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
| | - Merryn V E Macville
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW-Research Institute for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Arthur van den Wijngaard
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW-Research Institute for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Jos Dreesen
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
| | - Aimee Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW-Research Institute for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Internal Medicine, Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW-Research Institute for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andres Salumets
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.
- Competence Center on Health Technologies, Tartu, Estonia.
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.
| | - Masoud Zamani Esteki
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands.
- Department of Genetics and Cell Biology, GROW-Research Institute for Oncology and Reproduction, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, The Netherlands.
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.
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Demeneva VV, Tolmacheva EN, Nikitina TV, Sazhenova EA, Yuriev SY, Makhmutkhodzhaev AS, Zuev AS, Filatova SA, Dmitriev AE, Darkova YA, Nazarenko LP, Lebedev IN, Vasilyev SA. Expression of the NUP153 and YWHAB genes from their canonical promoters and alternative promoters of the LINE-1 retrotransposon in the placenta of the first trimester of pregnancy. Vavilovskii Zhurnal Genet Selektsii 2023; 27:63-71. [PMID: 36923475 PMCID: PMC10009475 DOI: 10.18699/vjgb-23-09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/26/2022] [Accepted: 12/30/2022] [Indexed: 03/11/2023] Open
Abstract
The placenta has a unique hypomethylated genome. Due to this feature of the placenta, there is a potential possibility of using regulatory elements derived from retroviruses and retrotransposons, which are suppressed by DNA methylation in the adult body. In addition, there is an abnormal increase in the level of methylation of the LINE-1 retrotransposon in the chorionic trophoblast in spontaneous abortions with both normal karyotype and aneuploidy on different chromosomes, which may be associated with impaired gene transcription using LINE-1 regulatory elements. To date, 988 genes that can be expressed from alternative LINE-1 promoters have been identified. Using the STRING tool, genes (NUP153 and YWHAB) were selected, the products of which have significant functional relationships with proteins highly expressed in the placenta and involved in trophoblast differentiation. This study aimed to analyze the expression of the NUP153 and YWHAB genes, highly active in the placenta, from canonical and alternative LINE-1 promoters in the germinal part of the placenta of spontaneous and induced abortions. Gene expression analysis was performed using real-time PCR in chorionic villi and extraembryonic mesoderm of induced abortions (n = 10), adult lymphocytes (n = 10), spontaneous abortions with normal karyotype (n = 10), and with the most frequent aneuploidies in the first trimester of pregnancy (trisomy 16 (n = 8) and monosomy X (n = 6)). The LINE-1 methylation index was assessed in the chorionic villi of spontaneous abortions using targeted bisulfite massive parallel sequencing. The level of expression of both genes from canonical promoters was higher in blood lymphocytes than in placental tissues (p < 0.05). However, the expression level of the NUP153 gene from the alternative LINE-1 promoter was 17 times higher in chorionic villi and 23 times higher in extraembryonic mesoderm than in lymphocytes (p < 0.05). The expression level of NUP153 and YWHAB from canonical promoters was higher in the group of spontaneous abortions with monosomy X compared to all other groups (p <0.05). The LINE-1 methylation index negatively correlated with the level of gene expression from both canonical (NUP153 - R = -0.59, YWHAB - R = -0.52, p < 0.05) and alternative LINE-1 promoters (NUP153 - R = -0.46, YWHAB - R = -0.66, p < 0.05). Thus, the observed increase in the LINE-1 methylation index in the placenta of spontaneous abortions is associated with the level of expression of the NUP153 and YWHAB genes not only from alternative but also from canonical promoters, which can subsequently lead to negative consequences for normal embryogenesis.
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Affiliation(s)
- V V Demeneva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - E N Tolmacheva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - T V Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - E A Sazhenova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - S Yu Yuriev
- Siberian State Medical University, Tomsk, Russia
| | | | - A S Zuev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - S A Filatova
- National Research Tomsk State University, Tomsk, Russia
| | - A E Dmitriev
- National Research Tomsk State University, Tomsk, Russia
| | - Ya A Darkova
- National Research Tomsk State University, Tomsk, Russia
| | - L P Nazarenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - I N Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia Siberian State Medical University, Tomsk, Russia
| | - S A Vasilyev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia National Research Tomsk State University, Tomsk, Russia
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Nikitina TV, Lebedev IN. Stem Cell-Based Trophoblast Models to Unravel the Genetic Causes of Human Miscarriages. Cells 2022; 11:1923. [PMID: 35741051 PMCID: PMC9221414 DOI: 10.3390/cells11121923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 02/01/2023] Open
Abstract
Miscarriage affects approximately 15% of clinically recognized pregnancies, and 1-3% of couples experience pregnancy loss recurrently. Approximately 50-60% of miscarriages result from chromosomal abnormalities, whereas up to 60% of euploid recurrent abortions harbor variants in candidate genes. The growing number of detected genetic variants requires an investigation into their role in adverse pregnancy outcomes. Since placental defects are the main cause of first-trimester miscarriages, the purpose of this review is to provide a survey of state-of-the-art human in vitro trophoblast models that can be used for the functional assessment of specific abnormalities/variants implicated in pregnancy loss. Since 2018, when primary human trophoblast stem cells were first derived, there has been rapid growth in models of trophoblast lineage. It has been found that a proper balance between self-renewal and differentiation in trophoblast progenitors is crucial for the maintenance of pregnancy. Different responses to aneuploidy have been shown in human embryonic and extra-embryonic lineages. Stem cell-based models provide a powerful tool to explore the effect of a specific aneuploidy/variant on the fetus through placental development, which is important, from a clinical point of view, for deciding on the suitability of embryos for transfer after preimplantation genetic testing for aneuploidy.
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Affiliation(s)
- Tatiana V. Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, 634050 Tomsk, Russia;
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Tolmacheva EN, Vasilyev SA, Nikitina TV, Lytkina ES, Sazhenova EA, Zhigalina DI, Vasilyeva OY, Markov AV, Demeneva VV, Tashireva LA, Kashevarova AA, Lebedev IN. Identification of differentially methylated genes in first-trimester placentas with trisomy 16. Sci Rep 2022; 12:1166. [PMID: 35064135 PMCID: PMC8782849 DOI: 10.1038/s41598-021-04107-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 12/10/2021] [Indexed: 12/20/2022] Open
Abstract
The presence of an extra chromosome in the embryo karyotype often dramatically affects the fate of pregnancy. Trisomy 16 is the most common aneuploidy in first-trimester miscarriages. The present study identified changes in DNA methylation in chorionic villi of miscarriages with trisomy 16. Ninety-seven differentially methylated sites in 91 genes were identified (false discovery rate (FDR) < 0.05 and Δβ > 0.15) using DNA methylation arrays. Most of the differentially methylated genes encoded secreted proteins, signaling peptides, and receptors with disulfide bonds. Subsequent analysis using targeted bisulfite massive parallel sequencing showed hypermethylation of the promoters of specific genes in miscarriages with trisomy 16 but not miscarriages with other aneuploidies. Some of the genes were responsible for the development of the placenta and embryo (GATA3-AS1, TRPV6, SCL13A4, and CALCB) and the formation of the mitotic spindle (ANKRD53). Hypermethylation of GATA3-AS1 was associated with reduced expression of GATA3 protein in chorionic villi of miscarriages with trisomy 16. Aberrant hypermethylation of genes may lead to a decrease in expression, impaired trophoblast differentiation and invasion, mitotic disorders, chromosomal mosaicism and karyotype self-correction via trisomy rescue mechanisms.
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Affiliation(s)
- Ekaterina N Tolmacheva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia.
| | - Stanislav A Vasilyev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - Tatiana V Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | | | - Elena A Sazhenova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - Daria I Zhigalina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - Oksana Yu Vasilyeva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - Anton V Markov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - Victoria V Demeneva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - Liubov A Tashireva
- Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Anna A Kashevarova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - Igor N Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
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Lebedev IN, Zhigalina DI. From contemplation to classification of chromosomal mosaicism in human preimplantation embryos. J Assist Reprod Genet 2021; 38:2833-2848. [PMID: 34518954 PMCID: PMC8609036 DOI: 10.1007/s10815-021-02304-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022] Open
Abstract
Chromosomal mosaicism is a hallmark of early human embryo development. The last decade yielded an enormous amount of information about diversity and prevalence of mosaicism in preimplantation embryos due to progress in preimplantation genetic testing of aneuploidies (PGT-A) based exclusively on molecular karyotyping of trophectoderm biopsy. However, the inner cell mass karyotype is still missing for mosaic embryos affecting the success rate of assisted reproductive medicine. Here, a classification model of chromosomal mosaicism is proposed based on the analysis of the primary zygote karyotype, the timing and types of primary and secondary chromosome segregation errors, and the distribution of mosaic cell clones between different embryonic and extraembryonic compartments of the blastocyst. Five basic principles for mosaicism analysis are introduced, namely, the estimation of the primary zygote karyotype, the investigation of additional sample point, the requirement of the second time point analysis, the delineating of reciprocity of chromosome segregation, and comprehensive chromosome screening at the single-cell level. The suggested model allows the prediction of the inner cell mass karyotype of the blastocyst and its developmental potential based on information from trophectoderm biopsy and non-invasive PGT-A using blastocoele fluid sample or spent culture medium as additional sample and time points for analysis and considering the reciprocity as a basic process in chromosome segregation errors between daughter cells in postzygotic cell divisions.
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Affiliation(s)
- Igor N. Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika Street 10, Tomsk, 634050 Russia
| | - Daria I. Zhigalina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika Street 10, Tomsk, 634050 Russia
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Sazhenova EA, Nikitina TV, Vasilyev SA, Tolmacheva EN, Vasilyeva OY, Markov AV, Yuryev SY, Skryabin NA, Zarubin AA, Kolesnikov NA, Stepanov VA, Lebedev IN. NLRP7 variants in spontaneous abortions with multilocus imprinting disturbances from women with recurrent pregnancy loss. J Assist Reprod Genet 2021; 38:2893-2908. [PMID: 34554362 PMCID: PMC8608992 DOI: 10.1007/s10815-021-02312-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 09/02/2021] [Indexed: 11/25/2022] Open
Abstract
PURPOSE Comparative analysis of multilocus imprinting disturbances (MLIDs) in miscarriages from women with sporadic (SPL) and recurrent pregnancy loss (RPL) and identification of variants in the imprinting control gene NLRP7 that may lead to MLIDs. METHODS Chorionic cytotrophoblast and extraembryonic mesoderm samples from first-trimester miscarriages were evaluated in 120 women with RPL and 134 women with SPL; 100 induced abortions were analyzed as a control group. All miscarriages had a normal karyotype. Epimutations in 7 imprinted genes were detected using methyl-specific PCR and confirmed with DNA pyrosequencing. Sequencing of all 13 exons and adjusted intron regions of the NLRP7 gene was performed. RESULTS Epimutations in imprinted genes were more frequently detected (p < 0.01) in the placental tissues of miscarriages from women with RPL (7.1%) than in those of women with SPL (2.7%). The predominant epimutation was postzygotic hypomethylation of maternal alleles of imprinted genes (RPL, 5.0%; SPL, 2.1%; p < 0.01). The frequency of MLID was higher among miscarriages from women with RPL than among miscarriages from women with SPL (1.7% and 0.4%, respectively, p < 0.01). Variants in NLRP7 were detected only in miscarriages from women with RPL. An analysis of the parental origin of NLRP7 variants revealed heterozygous carriers in families with RPL who exhibited spontaneous abortions with MLIDs and compound heterozygosity for NLRP7 variants. CONCLUSION RPL is associated with NLRP7 variants that lead to germinal and postzygotic MLIDs that are incompatible with normal embryo development. TRIAL REGISTRATION Not applicable.
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Affiliation(s)
- Elena A Sazhenova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika str., 10, Tomsk, Russia.
| | - Tatyana V Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika str., 10, Tomsk, Russia
| | - Stanislav A Vasilyev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika str., 10, Tomsk, Russia
| | - Ekaterina N Tolmacheva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika str., 10, Tomsk, Russia
| | - Oksana Yu Vasilyeva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika str., 10, Tomsk, Russia
| | - Anton V Markov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika str., 10, Tomsk, Russia
| | | | - Nikolay A Skryabin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika str., 10, Tomsk, Russia
| | - Alexey A Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika str., 10, Tomsk, Russia
| | - Nikita A Kolesnikov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika str., 10, Tomsk, Russia
| | - Vadim A Stepanov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika str., 10, Tomsk, Russia
| | - Igor N Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Ushaika str., 10, Tomsk, Russia
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Wen J, Grommisch B, DiAdamo A, Chai H, Ng SME, Hui P, Bale A, Mak W, Wang G, Li P. Detection of cytogenomic abnormalities by OncoScan microarray assay for products of conception from formalin-fixed paraffin-embedded and fresh fetal tissues. Mol Cytogenet 2021; 14:21. [PMID: 33810806 PMCID: PMC8019165 DOI: 10.1186/s13039-021-00542-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/17/2021] [Indexed: 12/02/2022] Open
Abstract
Background The OncoScan microarray assay (OMA) using highly multiplexed molecular inversion probes for single nucleotide polymorphism (SNP) loci enabled the detection of cytogenomic abnormalities of chromosomal imbalances and pathogenic copy number variants (pCNV). The small size of molecular inversion probes is optimal for SNP genotyping of fragmented DNA from fixed tissues. This retrospective study evaluated the clinical utility of OMA as a uniform platform to detect cytogenomic abnormalities for pregnancy loss from fresh and fixed tissues of products of conception (POC). Results Fresh specimens of POC were routinely subjected to cell culture and then analyzed by karyotyping. POC specimens with a normal karyotype (NK) or culture failure (CF) and from formalin-fixed paraffin-embedded (FFPE) tissues were subjected to DNA extraction for OMA. The abnormality detection rate (ADR) by OMA on 94 cases of POC-NK, 38 cases of POC-CF, and 35 cases of POC-FFPE tissues were 2% (2/94), 26% (10/38), and 57% (20/35), respectively. The detected cytogenomic abnormalities of aneuploidies, triploidies and pCNV accounted for 50%, 40% and 10% in POC-CF and 85%, 10% and 5% in POC-FFPE, respectively. False negative result from cultured maternal cells and maternal cell contamination were each detected in one case. OMA on two cases with unbalanced structural chromosome abnormalities further defined genomic imbalances and breakpoints. Conclusion OMA on POC-CF and POC-FFPE showed a high diagnostic yield of cytogenomic abnormalities. This approach circumvented the obstacles of CF from fresh specimens and fragmented DNA from fixed tissues and provided a reliable and effective platform for detecting cytogenomic abnormalities and monitoring true fetal result from maternal cell contamination.
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Affiliation(s)
- Jiadi Wen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Brittany Grommisch
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Autumn DiAdamo
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Hongyan Chai
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Sok Meng Evelyn Ng
- Yale Center for Genome Analysis, Yale University School of Medicine, New Haven, CT, USA
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Allen Bale
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Winifred Mak
- Department of Women's Health, Dell Medical School, The University of Texas At Austin, Austin, TX, USA
| | - Guilin Wang
- Yale Center for Genome Analysis, Yale University School of Medicine, New Haven, CT, USA.
| | - Peining Li
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
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10
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Vasilyev SA, Tolmacheva EN, Vasilyeva OY, Markov AV, Zhigalina DI, Zatula LA, Lee VA, Serdyukova ES, Sazhenova EA, Nikitina TV, Kashevarova AA, Lebedev IN. LINE-1 retrotransposon methylation in chorionic villi of first trimester miscarriages with aneuploidy. J Assist Reprod Genet 2021; 38:139-149. [PMID: 33170392 PMCID: PMC7823001 DOI: 10.1007/s10815-020-02003-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 11/02/2020] [Indexed: 01/15/2023] Open
Abstract
PURPOSE High frequency of aneuploidy in meiosis and cleavage stage coincides with waves of epigenetic genome reprogramming that may indicate a possible association between epigenetic mechanisms and aneuploidy occurrence. This study aimed to assess the methylation level of the long interspersed repeat element 1 (LINE-1) retrotransposon in chorionic villi of first trimester miscarriages with a normal karyotype and aneuploidy. METHODS The methylation level was assessed at 19 LINE-1 promoter CpG sites in chorionic villi of 141 miscarriages with trisomy of chromosomes 2, 6, 8-10, 13-15, 16, 18, 20-22, and monosomy X using massive parallel sequencing. RESULTS The LINE-1 methylation level was elevated statistically significant in chorionic villi of miscarriages with both trisomy (45.2 ± 4.3%) and monosomy X (46.9 ± 4.2%) compared with that in induced abortions (40.0 ± 2.4%) (p < 0.00001). The LINE-1 methylation levels were specific for miscarriages with different aneuploidies and significantly increased in miscarriages with trisomies 8, 14, and 18 and monosomy X (p < 0.05). The LINE-1 methylation level increased with gestational age both for group of miscarriages regardless of karyotype (R = 0.21, p = 0.012) and specifically for miscarriages with trisomy 16 (R = 0.48, p = 0.007). LINE-1 methylation decreased with maternal age in miscarriages with a normal karyotype (R = - 0.31, p = 0.029) and with trisomy 21 (R = - 0.64, p = 0.024) and increased with paternal age for miscarriages with trisomy 16 (R = 0.38, p = 0.048) and monosomy X (R = 0.73, p = 0.003). CONCLUSION Our results indicate that the pathogenic effects of aneuploidy in human embryogenesis can be supplemented with significant epigenetic changes in the repetitive sequences.
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Affiliation(s)
- Stanislav A Vasilyev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Nab. R. Ushaiki, 10, Tomsk, Russia.
- Biological Institute, National Research Tomsk State University, Lenina, 36, Tomsk, Russia.
| | - Ekaterina N Tolmacheva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Nab. R. Ushaiki, 10, Tomsk, Russia
| | - Oksana Yu Vasilyeva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Nab. R. Ushaiki, 10, Tomsk, Russia
| | - Anton V Markov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Nab. R. Ushaiki, 10, Tomsk, Russia
| | - Daria I Zhigalina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Nab. R. Ushaiki, 10, Tomsk, Russia
| | - Lada A Zatula
- Department of Medical Genetics, Siberian State Medical University, Moskovskiy Trakt, 2, Tomsk, Russia
| | - Vasilissa A Lee
- Department of Medical Genetics, Siberian State Medical University, Moskovskiy Trakt, 2, Tomsk, Russia
| | - Ekaterina S Serdyukova
- Biological Institute, National Research Tomsk State University, Lenina, 36, Tomsk, Russia
| | - Elena A Sazhenova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Nab. R. Ushaiki, 10, Tomsk, Russia
| | - Tatyana V Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Nab. R. Ushaiki, 10, Tomsk, Russia
| | - Anna A Kashevarova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Nab. R. Ushaiki, 10, Tomsk, Russia
| | - Igor N Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Nab. R. Ushaiki, 10, Tomsk, Russia
- Department of Medical Genetics, Siberian State Medical University, Moskovskiy Trakt, 2, Tomsk, Russia
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11
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Zhang Y, Lei Q, Liu J, Lin M, Luo L, Li T, Wang Q, Zhou C. Selective growth of mosaic cells in chromosomal analysis of chorionic villi by conventional karyotyping. Mol Cell Probes 2020; 51:101532. [DOI: 10.1016/j.mcp.2020.101532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/01/2020] [Accepted: 02/09/2020] [Indexed: 10/25/2022]
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12
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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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13
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Karyotype evaluation of repeated abortions in primary and secondary recurrent pregnancy loss. J Assist Reprod Genet 2020; 37:517-525. [PMID: 32009222 DOI: 10.1007/s10815-020-01703-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/27/2020] [Indexed: 12/19/2022] Open
Abstract
PURPOSE To study the contribution of embryo chromosomal abnormalities in primary and secondary recurrent pregnancy loss (RPL) and to analyze the recurrence of chromosomal constitution in miscarriages from the same couple. METHODS Retrospective study of abortion karyotypes in RPL families based on the mother's primary or secondary RPL status (563 embryo specimens, 335 samples from primary, and 228 samples from secondary RPL). RPL was defined as two or more consecutive miscarriages. One hundred eight cases of recurrent embryo/fetal loss in 51 families were analyzed to assess the probability of having the same karyotype pattern (recurrent normal or recurrent abnormal) in both previous and subsequent pregnancy loss. The karyotypes of abortions were established using standard cytogenetic analysis, as well as interphase fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH). RESULTS The frequency of aberrations was 43.9% in abortions from primary RPL versus 52.6% in secondary RPL (p = 0.041). Women 35 years of age or older were the main contributors to this difference. The odds ratio of a subsequent abortion having the same karyotype pattern (normal or abnormal) as the previous one was 6.98 (p = 0.0013). CONCLUSION The frequency of abnormalities is higher in abortions from the secondary RPL versus primary RPL group, and this difference is due to the relative deficiency of miscarriages with abnormal karyotypes in older women with primary RPL. The probability of having the same karyotype pattern (recurrent normal or recurrent abnormal) in the previous and subsequent abortion is increased significantly compared with chance.
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14
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Mandrioli D, Belpoggi F, Silbergeld EK, Perry MJ. Aneuploidy: a common and early evidence-based biomarker for carcinogens and reproductive toxicants. Environ Health 2016; 15:97. [PMID: 27729050 PMCID: PMC5059969 DOI: 10.1186/s12940-016-0180-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 09/28/2016] [Indexed: 05/29/2023]
Abstract
Aneuploidy, defined as structural and numerical aberrations of chromosomes, continues to draw attention as an informative effect biomarker for carcinogens and male reproductive toxicants. It has been well documented that aneuploidy is a hallmark of cancer. Aneuploidies in oocytes and spermatozoa contribute to infertility, pregnancy loss and a number of congenital abnormalities, and sperm aneuploidy is associated with testicular cancer. It is striking that several carcinogens induce aneuploidy in somatic cells, and also adversely affect the chromosome compliment of germ cells. In this paper we review 1) the contributions of aneuploidy to cancer, infertility, and developmental abnormalities; 2) techniques for assessing aneuploidy in precancerous and malignant lesions and in sperm; and 3) the utility of aneuploidy as a biomarker for integrated chemical assessments of carcinogenicity, and reproductive and developmental toxicity.
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Affiliation(s)
- Daniele Mandrioli
- Cesare Maltoni Cancer Research Center, Ramazzini Institute, 40010 Bentivoglio, Bologna, Italy
| | - Fiorella Belpoggi
- Cesare Maltoni Cancer Research Center, Ramazzini Institute, 40010 Bentivoglio, Bologna, Italy
| | - Ellen K. Silbergeld
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, 21205 Baltimore, MD USA
| | - Melissa J. Perry
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, The George Washington University, 950 New Hampshire Ave. NW, 4th Floor, Washington, DC 20052 USA
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15
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Nikitina TV, Sazhenova EA, Tolmacheva EN, Sukhanova NN, Kashevarova AA, Skryabin NA, Vasilyev SA, Nemtseva TN, Yuriev SY, Lebedev IN. Comparative Cytogenetic Analysis of Spontaneous Abortions in Recurrent and Sporadic Pregnancy Losses. Biomed Hub 2016; 1:1-11. [PMID: 31988885 PMCID: PMC6945958 DOI: 10.1159/000446099] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background The majority of miscarriages are sporadic; however, 1–5% of couples experience recurrent pregnancy loss (RPL). Approximately 50–60% of miscarriages result from chromosomal abnormalities. Currently, there are conflicting reports regarding the rates of chromosomal abnormalities between recurrent and sporadic pregnancy losses. Methods A retrospective comparative cytogenetic analysis of 442 RPL and 466 sporadic abortions (SA) was performed. Maternal age and medical background were evaluated, and chromosomal abnormality rates were compared between groups. Results The frequency of embryos with abnormal karyotypes was significantly higher in SA compared to RPL (56.7 and 46.6%, respectively), and abortions from women under 30 years of age were the main contributor to this difference. An age-dependent increase in the abnormal karyotype rate was observed in two groups of women - those with SA [53.0 and 70.1% for younger and older (≥35-year-old) mothers, respectively] and those with idiopathic RPL without any concomitant reproductive pathology (46.5 and 78.4% for younger and older mothers) - but not in the group of women with RPL associated with concomitant reproductive pathology. The incidence of recurrent abnormal karyotypes in subsequent miscarriages was significantly higher than random probability (odds ratio = 22.75). Conclusion Our findings highlight the variability in the risk of aneuploidy in recurrent abortion.
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Affiliation(s)
- Tatiana V Nikitina
- Laboratory of Cytogenetics, Institute of Medical Genetics, Siberian State Medical University, Tomsk, Russia
| | - Elena A Sazhenova
- Laboratory of Cytogenetics, Institute of Medical Genetics, Siberian State Medical University, Tomsk, Russia
| | - Ekaterina N Tolmacheva
- Laboratory of Cytogenetics, Institute of Medical Genetics, Siberian State Medical University, Tomsk, Russia
| | - Natalia N Sukhanova
- Laboratory of Cytogenetics, Institute of Medical Genetics, Siberian State Medical University, Tomsk, Russia
| | - Anna A Kashevarova
- Laboratory of Cytogenetics, Institute of Medical Genetics, Siberian State Medical University, Tomsk, Russia.,Laboratory of Ontogenetics, Tomsk State University, Siberian State Medical University, Tomsk, Russia
| | - Nikolay A Skryabin
- Laboratory of Cytogenetics, Institute of Medical Genetics, Siberian State Medical University, Tomsk, Russia.,Laboratory of Ontogenetics, Tomsk State University, Siberian State Medical University, Tomsk, Russia
| | - Stanislav A Vasilyev
- Laboratory of Cytogenetics, Institute of Medical Genetics, Siberian State Medical University, Tomsk, Russia.,Laboratory of Ontogenetics, Tomsk State University, Siberian State Medical University, Tomsk, Russia
| | - Tatiana N Nemtseva
- Center of Perinatal Health, Siberian State Medical University, Tomsk, Russia
| | - Sergey Y Yuriev
- Center of Perinatal Health, Siberian State Medical University, Tomsk, Russia.,Departments of Obstetrics and Gynecology, Siberian State Medical University, Tomsk, Russia
| | - Igor N Lebedev
- Laboratory of Cytogenetics, Institute of Medical Genetics, Siberian State Medical University, Tomsk, Russia.,Laboratory of Ontogenetics, Tomsk State University, Siberian State Medical University, Tomsk, Russia.,Departments of Medical Genetics, Siberian State Medical University, Tomsk, Russia
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16
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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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17
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Russo R, Sessa AM, Fumo R, Gaeta S. Chromosomal anomalies in early spontaneous abortions: interphase FISH analysis on 855 FFPE first trimester abortions. Prenat Diagn 2016; 36:186-91. [PMID: 26716606 DOI: 10.1002/pd.4768] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 12/15/2015] [Accepted: 12/23/2015] [Indexed: 11/11/2022]
Abstract
OBJECTIVE Cytogenetic analysis of spontaneous abortuses presents at least two main challenges, cell culture failure, and excess of normal female karyotypes related to maternal cell contamination (MCC). Molecular cytogenetic techniques using uncultured cell suspension overcome cell culture failure, but do not resolve MCC at all. The aim of the present study is to demonstrate that interphase fluorescence in situ hybridization (FISH) on routine formalin-fixed paraffin embedded (FFPE) abortive materials is an efficient method to identify chromosomal anomalies in abortuses and to detect MCC. METHOD Interphase FISH with a panel of eight probes was applied on 855 FFPE consecutive early spontaneous abortions. RESULTS Male/female ratio was 0.88 in the complete sample, 0.9 in the group of negative FISH result, and 0.8 in the group with abnormal FISH results, suggesting that no gender predominance was present in our data. The aneuploidy rate was 50.3%. Autosomal trisomies were 60%, polyploidies 23.2%, and X monosomy 14%. Chromosomal mosaicism was discovered in 1.9% with six cases of confined placental mosaicism. CONCLUSION FISH on FFPE abortion materials appears to be a successful approach to detect chromosomal anomalies in abortions. Moreover, the preservation of the tissue morphology allows the analysis of only the fetal cells, making the presence of maternal tissues irrelevant.
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Affiliation(s)
- Rosa Russo
- Department of Pathology, Molecular Genetics Laboratory, University Medical Hospital, S. Giovanni di Dio e Ruggi D'Aragona, Salerno, Italy
| | - Anna Maria Sessa
- Department of Pathology, Molecular Genetics Laboratory, University Medical Hospital, S. Giovanni di Dio e Ruggi D'Aragona, Salerno, Italy
| | - Rosalba Fumo
- Department of Pathology, Molecular Genetics Laboratory, University Medical Hospital, S. Giovanni di Dio e Ruggi D'Aragona, Salerno, Italy
| | - Sara Gaeta
- Department of Pathology, Molecular Genetics Laboratory, University Medical Hospital, S. Giovanni di Dio e Ruggi D'Aragona, Salerno, Italy
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18
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Daughtry BL, Chavez SL. Chromosomal instability in mammalian pre-implantation embryos: potential causes, detection methods, and clinical consequences. Cell Tissue Res 2016; 363:201-225. [PMID: 26590822 PMCID: PMC5621482 DOI: 10.1007/s00441-015-2305-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 09/24/2015] [Indexed: 01/08/2023]
Abstract
Formation of a totipotent blastocyst capable of implantation is one of the first major milestones in early mammalian embryogenesis, but less than half of in vitro fertilized embryos from most mammals will progress to this stage of development. Whole chromosomal abnormalities, or aneuploidy, are key determinants of whether human embryos will arrest or reach the blastocyst stage. Depending on the type of chromosomal abnormality, however, certain embryos still form blastocysts and may be morphologically indistinguishable from chromosomally normal embryos. Despite the implementation of pre-implantation genetic screening and other advanced in vitro fertilization (IVF) techniques, the identification of aneuploid embryos remains complicated by high rates of mosaicism, atypical cell division, cellular fragmentation, sub-chromosomal instability, and micro-/multi-nucleation. Moreover, several of these processes occur in vivo following natural human conception, suggesting that they are not simply a consequence of culture conditions. Recent technological achievements in genetic, epigenetic, chromosomal, and non-invasive imaging have provided additional embryo assessment approaches, particularly at the single-cell level, and clinical trials investigating their efficacy are continuing to emerge. In this review, we summarize the potential mechanisms by which aneuploidy may arise, the various detection methods, and the technical advances (such as time-lapse imaging, "-omic" profiling, and next-generation sequencing) that have assisted in obtaining this data. We also discuss the possibility of aneuploidy resolution in embryos via various corrective mechanisms, including multi-polar divisions, fragment resorption, endoreduplication, and blastomere exclusion, and conclude by examining the potential implications of these findings for IVF success and human fecundity.
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Affiliation(s)
- Brittany L Daughtry
- Department of Cell, Developmental & Cancer Biology, Graduate Program in Molecular & Cellular Biosciences, Oregon Health & Science University School of Medicine, Portland, Ore., USA
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, 505 NW 185th Avenue, Beaverton, OR 97006, USA
| | - Shawn L Chavez
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, 505 NW 185th Avenue, Beaverton, OR 97006, USA.
- Physiology & Pharmacology, Oregon Health & Science University School of Medicine, Portland, Ore., USA.
- Department of Obstetrics & Gynecology, Oregon Health & Science University School of Medicine, Portland, Ore., USA.
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19
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Figueroa ZI, Young HA, Meeker JD, Martenies SE, Barr DB, Gray G, Perry MJ. Dialkyl phosphate urinary metabolites and chromosomal abnormalities in human sperm. ENVIRONMENTAL RESEARCH 2015; 143:256-265. [PMID: 26519831 PMCID: PMC4743645 DOI: 10.1016/j.envres.2015.10.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/16/2015] [Accepted: 10/19/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND The past decade has seen numerous human health studies seeking to characterize the impacts of environmental exposures, such as organophosphate (OP) insecticides, on male reproduction. Despite an extensive literature on OP toxicology, many hormone-mediated effects on the testes are not well understood. OBJECTIVES This study investigated environmental exposures to OPs and their association with the frequency of sperm chromosomal abnormalities (i.e., disomy) among adult men. METHODS Men (n=159) from a study assessing the impact of environmental exposures on male reproductive health were included in this investigation. Multi-probe fluorescence in situ hybridization (FISH) for chromosomes X, Y, and 18 was used to determine XX18, YY18, XY18 and total disomy in sperm nuclei. Urine was analyzed using gas chromatography coupled with mass spectrometry for concentrations of dialkyl phosphate (DAP) metabolites of OPs [dimethylphosphate (DMP); dimethylthiophosphate (DMTP); dimethyldithiophosphate (DMDTP); diethylphosphate (DEP); diethylthiophosphate (DETP); and diethyldithiophosphate (DEDTP)]. Poisson regression was used to model the association between OP exposures and disomy measures. Incidence rate ratios (IRRs) were calculated for each disomy type by exposure quartiles for most metabolites, controlling for age, race, BMI, smoking, specific gravity, total sperm concentration, motility, and morphology. RESULTS A significant positive trend was seen for increasing IRRs by exposure quartiles of DMTP, DMDTP, DEP and DETP in XX18, YY18, XY18 and total disomy. A significant inverse association was observed between DMP and total disomy. Findings for total sum of DAP metabolites concealed individual associations as those results differed from the patterns observed for each individual metabolite. Dose-response relationships appeared nonmonotonic, with most of the increase in disomy rates occurring between the second and third exposure quartiles and without additional increases between the third and fourth exposure quartiles. CONCLUSIONS This is the first epidemiologic study of this size to examine the relationship between environmental OP exposures and human sperm disomy outcomes. Our findings suggest that increased disomy rates were associated with specific DAP metabolites, suggesting that the impacts of OPs on testis function need further characterization in epidemiologic studies.
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Affiliation(s)
- Zaida I Figueroa
- Department of Environmental and Occupational Health, George Washington University, Milken Institute School of Public Health, 950 New Hampshire Ave. NW (4th Floor), Washington, DC 20052, United States.
| | - Heather A Young
- Department of Epidemiology and Biostatistics, George Washington University, Milken Institute School of Public Health, 950 New Hampshire Ave. NW (5th Floor), Washington, DC 20052, United States.
| | - John D Meeker
- Department of Environmental Health Sciences, University of Michigan, School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109-2029, United States.
| | - Sheena E Martenies
- Department of Environmental and Occupational Health, George Washington University, Milken Institute School of Public Health, 950 New Hampshire Ave. NW (4th Floor), Washington, DC 20052, United States.
| | - Dana Boyd Barr
- Department of Environmental Health, Emory University, Rollins School of Public Health, 1518 Clifton Road, NE, Atlanta, GA 30322, United States.
| | - George Gray
- Department of Environmental and Occupational Health, George Washington University, Milken Institute School of Public Health, 950 New Hampshire Ave. NW (4th Floor), Washington, DC 20052, United States.
| | - Melissa J Perry
- Department of Environmental and Occupational Health, George Washington University, Milken Institute School of Public Health, 950 New Hampshire Ave. NW (4th Floor), Washington, DC 20052, United States.
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20
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Carbone L, Chavez SL. Mammalian pre-implantation chromosomal instability: species comparison, evolutionary considerations, and pathological correlations. Syst Biol Reprod Med 2015; 61:321-35. [PMID: 26366555 DOI: 10.3109/19396368.2015.1073406] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Pre-implantation embryo development in mammals begins at fertilization with the migration and fusion of the maternal and paternal pro-nuclei, followed by the degradation of inherited factors involved in germ cell specification and the activation of embryonic genes required for subsequent cell divisions, compaction, and blastulation. The majority of studies on early embryogenesis have been conducted in the mouse or non-mammalian species, often requiring extrapolation of the findings to human development. Given both conserved similarities and species-specific differences, however, even comparison between closely related mammalian species may be challenging as certain aspects, including susceptibility to chromosomal aberrations, varies considerably across mammals. Moreover, most human embryo studies are limited to patient samples obtained from in vitro fertilization (IVF) clinics and donated for research, which are generally of poorer quality and produced with germ cells that may be sub-optimal. Recent technical advances in genetic, epigenetic, chromosomal, and time-lapse imaging analyses of high quality whole human embryos have greatly improved our understanding of early human embryogenesis, particularly at the single embryo and cell level. This review summarizes the major characteristics of mammalian pre-implantation development from a chromosomal perspective, in addition to discussing the technological achievements that have recently been developed to obtain this data. We also discuss potential translation to clinical applications in reproductive medicine and conclude by examining the broader implications of these findings for the evolution of mammalian species and cancer pathology in somatic cells.
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Affiliation(s)
- Lucia Carbone
- a Division of Neuroscience , Oregon National Primate Research Center .,b Department of Behavioral Neuroscience .,c Department of Molecular & Medical Genetics .,d Bioinformatics & Computational Biology, Oregon Health & Science University
| | - Shawn L Chavez
- e Division of Reproductive & Developmental Sciences , Oregon National Primate Research Center .,f Department of Obstetrics & Gynecology , and.,g Department of Physiology & Pharmacology , Oregon Health & Science University , Portland , Oregon , USA
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Vasilyev SA, Tolmacheva EN, Kashevarova AA, Sazhenova EA, Lebedev IN. Methylation status of LINE-1 retrotransposon in chromosomal mosaicism during early stages of human embryonic development. Mol Biol 2015. [DOI: 10.1134/s0026893314060193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Tsai MC, Cheng HY, Su MT, Chen M, Kuo PL. Partial trisomy 8 mosaicism not detected by cultured amniotic-fluid cells. Taiwan J Obstet Gynecol 2014; 53:598-601. [DOI: 10.1016/j.tjog.2014.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2014] [Indexed: 12/31/2022] Open
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Schmid M, Steinlein C, Tian Q, Hanlon Newell AE, Gessler M, Olson SB, Rosenwald A, Kneitz B, Fedorov LM. Mosaic variegated aneuploidy in mouse BubR1 deficient embryos and pregnancy loss in human. Chromosome Res 2014; 22:375-92. [DOI: 10.1007/s10577-014-9432-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/13/2014] [Accepted: 06/17/2014] [Indexed: 12/23/2022]
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Chen S, Li S, Xie W, Li X, Zhang C, Jiang H, Zheng J, Pan X, Zheng H, Liu JS, Deng Y, Chen F, Jiang H. Performance comparison between rapid sequencing platforms for ultra-low coverage sequencing strategy. PLoS One 2014; 9:e92192. [PMID: 24651575 PMCID: PMC3961333 DOI: 10.1371/journal.pone.0092192] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 02/19/2014] [Indexed: 12/03/2022] Open
Abstract
Ultra-low coverage sequencing (ULCS) is one of the most promising strategies for sequencing based clinical application. These clinical applications, especially prenatal diagnosis, have a strict requirement of turn-around-time; therefore, the application of ULCS is restricted by current high throughput sequencing platforms. Recently, the emergence of rapid sequencing platforms, such as MiSeq and Ion Proton, brings ULCS strategy into a new era. The comparison of their performance could shed lights on their potential application in large-scale clinic trials. In this study, we performed ULCS (<0.1X coverage) on both MiSeq and Ion Proton platforms for 18 spontaneous abortion fetuses carrying aneuploidy and compared their performance on different levels. Overall basic data and GC bias showed no significant difference between these two platforms. We also found the sex and aneuploidy detection indicated 100% sensitivity and 100% specificity on both platforms. Our study generated essential data from these two rapid sequencing platforms, which provides useful reference for later research and potentially accelerates the clinical applications of ULCS.
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Affiliation(s)
- Shengpei Chen
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Municipal Key Laboratory of Birth Defects Screening and Engineering, BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Diseases Genome, BGI-Shenzhen, Guangdong, China
- BGI-Nanjing, Nanjing, China
- The Key Technology R&D Program of Jiangsu Province, Nanjing, China
| | - Sheng Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | - Haojun Jiang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | - Jia Sophie Liu
- Research Group, Complete Genomics, Mountain View, California, United States of America
| | - Yongqiang Deng
- Department of Stomatology, The Second People’s Hospital of Shenzhen, Shenzhen, China
| | | | - Hui Jiang
- BGI-Shenzhen, Shenzhen, China
- * E-mail:
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Abstract
Genome instability has long been implicated as the main causal factor in aging. Somatic cells are continuously exposed to various sources of DNA damage, from reactive oxygen species to UV radiation to environmental mutagens. To cope with the tens of thousands of chemical lesions introduced into the genome of a typical cell each day, a complex network of genome maintenance systems acts to remove damage and restore the correct base pair sequence. Occasionally, however, repair is erroneous, and such errors, as well as the occasional failure to correctly replicate the genome during cell division, are the basis for mutations and epimutations. There is now ample evidence that mutations accumulate in various organs and tissues of higher animals, including humans, mice, and flies. What is not known, however, is whether the frequency of these random changes is sufficient to cause the phenotypic effects generally associated with aging. The exception is cancer, an age-related disease caused by the accumulation of mutations and epimutations. Here, we first review current concepts regarding the relationship between DNA damage, repair, and mutation, as well as the data regarding genome alterations as a function of age. We then describe a model for how randomly induced DNA sequence and epigenomic variants in the somatic genomes of animals can result in functional decline and disease in old age. Finally, we discuss the genetics of genome instability in relation to longevity to address the importance of alterations in the somatic genome as a causal factor in aging and to underscore the opportunities provided by genetic approaches to develop interventions that attenuate genome instability, reduce disease risk, and increase life span.
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Affiliation(s)
- Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, New York, NY 10461, USA.
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Tolmacheva EN, Kashevarova AA, Skryabin NA, Lebedev IN. Epigenetic effects of trisomy 16 in human placenta. Mol Biol 2013. [DOI: 10.1134/s0026893313030175] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mantikou E, Wong KM, Repping S, Mastenbroek S. Molecular origin of mitotic aneuploidies in preimplantation embryos. Biochim Biophys Acta Mol Basis Dis 2012; 1822:1921-30. [DOI: 10.1016/j.bbadis.2012.06.013] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 06/14/2012] [Accepted: 06/26/2012] [Indexed: 01/06/2023]
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Baffero GM, Somigliana E, Crovetto F, Paffoni A, Persico N, Guerneri S, Lalatta F, Fogliani R, Fedele L. Confined placental mosaicism at chorionic villous sampling: risk factors and pregnancy outcome. Prenat Diagn 2012; 32:1102-8. [PMID: 22961322 DOI: 10.1002/pd.3965] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 07/31/2012] [Accepted: 08/01/2012] [Indexed: 11/06/2022]
Abstract
OBJECTIVE This study aims to investigate the clinical relevance of confined placental mosaicism (CPM) detected at chorionic villous sampling (CVS) and to identify risk factors for this condition. METHOD Women diagnosed with CPM between January 2005 and December 2009 were identified. They were matched to women with unremarkable CVS in a 1 : 2 ratio by study period and contacted by phone for interview. RESULTS One hundred fifteen exposed and 230 unexposed women were selected. Baseline characteristics did not differ between the study groups apart from maternal body mass index, which is mildly higher in the CPM group (+0.6 kg/m(2), p = 0.047), and maternal age, which is higher in women with type III CPM (39.7 ± 2.6 vs 37.1 ± 3.2 years, p = 0.005). A higher frequency of gestational hypertension was observed in exposed women (10% vs 2%) (p = 0.003). Small for gestational age newborns were more frequent in women with type I CPM (15% vs 5%, p = 0.03). The incidence of other main complications of pregnancy (stillbirth, prematurity, preeclampsia and gestational diabetes mellitus) was similar. Neonatal complications and subsequent infant health and development did not also differ. CONCLUSION Women with the diagnosis of CPM at CVS can be generally reassured regarding the course of pregnancy and infant health and development.
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van den Berg MMJ, van Maarle MC, van Wely M, Goddijn M. Genetics of early miscarriage. Biochim Biophys Acta Mol Basis Dis 2012; 1822:1951-9. [PMID: 22796359 DOI: 10.1016/j.bbadis.2012.07.001] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 05/11/2012] [Accepted: 07/06/2012] [Indexed: 12/15/2022]
Abstract
A miscarriage is the most frequent complication of a pregnancy. Poor chromosome preparations, culture failure, or maternal cell contamination may hamper conventional karyotyping. Techniques such as chromosomal comparative genomic hybridization (chromosomal-CGH), array-comparative genomic hybridization (array-CGH), fluorescence in situ hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA) and quantitative fluorescent polymerase chain reaction (QF-PCR) enable us to trace submicroscopic abnormalities. We found the prevalence of chromosome abnormalities in women facing a single sporadic miscarriage to be 45% (95% CI: 38-52; 13 studies, 7012 samples). The prevalence of chromosome abnormalities in women experiencing a subsequent miscarriage after preceding recurrent miscarriage proved to be comparable: 39% (95% CI: 29-50; 6 studies 1359 samples). More chromosome abnormalities are detected by conventional karyotyping compared to FISH or MLPA only (chromosome region specific techniques), and the same amount of abnormalities compared to QF-PCR (chromosome region specific techniques) and chromosomal-CGH and array-CGH (whole genome techniques) only. Molecular techniques could play a role as an additional technique when culture failure or maternal contamination occurs: recent studies show that by using array-CGH, an additional 5% of submicroscopic chromosome variants can be detected. Because of the small sample size as well as the unknown clinical relevance of these molecular aberrations, more and larger studies should be performed of submicroscopic chromosome abnormalities among sporadic miscarriage samples. For recurrent miscarriage samples molecular technique studies are relatively new. It has often been suggested that miscarriages are due to chromosomal abnormalities in more than 50%, but the present review has determined that chromosomal and submicroscopic genetic abnormalities on average are prevalent in maximally half of the miscarriage samples. This article is part of a Special Issue entitled: Molecular Genetics of Human Reproductive Failure.
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Toutain J, Labeau-Gaüzere C, Barnetche T, Horovitz J, Saura R. Confined placental mosaicism and pregnancy outcome: a distinction needs to be made between types 2 and 3. Prenat Diagn 2011; 30:1155-64. [PMID: 20936639 DOI: 10.1002/pd.2631] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
OBJECTIVE To study the influence of types 2 and 3 confined placental mosaicism (CPM) on pregnancy outcome. METHOD From 13 809 chorionic villus samplings (CVSs), karyotype after long-term cultured villi (LTC-villi) was systematically performed. Next, in case of suspicion of CPM, karyotype after short-term cultured villi (STC-villi) was established to define type 2 CPM (chromosomal abnormality limited to the mesenchymal core) or type 3 CPM (chromosomal abnormality found both in the cytotrophoblast and the mesenchymal core). Confirmatory amniocentesis was performed to exclude fetal mosaicism. Uniparental disomy (UPD) testing was carried out when the abnormal cell line involved chromosomes 5, 6, 7, 15 or 16. RESULTS Fifty-seven CPM cases were observed (57/13 809 = 0.41%) and of these, 37 were type 2 and 20 were type 3 CPM. Incidence of preterm infants, neonatal hypotrophy and adverse pregnancy outcome were comparable between patients in whom type 2 CPM was demonstrated and the control population. In contrast, for the type 3 CPM the incidence of these factors was higher than for the control population. CONCLUSION When a CPM is suspected, it appears essential to determine type, since type 2 has no effect on fetal development and type 3 is associated with preterm infants, low birth weight and adverse pregnancy outcome.
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Affiliation(s)
- Jérôme Toutain
- Department of Medical Genetics, Pellegrin University Hospitals (Maternity), Bordeaux, France.
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Tolmacheva EN, Kashevarova AA, Sukhanova NN, Kharkov VN, Lebedev IN. Skewed X-chromosome inactivation in human embryos with mosaic trisomy 16. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795411020189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Robberecht C, Vanneste E, Pexsters A, D’Hooghe T, Voet T, Vermeesch JR. Somatic genomic variations in early human prenatal development. Curr Genomics 2010; 11:397-401. [PMID: 21358983 PMCID: PMC3018719 DOI: 10.2174/138920210793175967] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 05/26/2010] [Accepted: 05/28/2010] [Indexed: 11/22/2022] Open
Abstract
Only 25 to 30% of conceptions result in a live birth. There is mounting evidence that the cause for this low fecundity is an extremely high incidence of chromosomal rearrangements occurring in the cleavage stage embryo. In this review, we gather all recent evidence for an extraordinary degree of mosaicisms in early embryogenesis. The presence of the rearrangements seen in the cleavage stage embryos can explain the origins of the placental mosaicisms seen during chorion villi sampling as well as the chromosomal anomalies seen in early miscarriages. Whereas these rearrangements often lead to implantation failure and early miscarriages, natural selection of the fittest cells in the embryo is the likely mechanism leading to healthy fetuses.
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Affiliation(s)
| | | | - Anne Pexsters
- University Hospitals Leuven, Leuven University Fertility Center, Leuven, Belgium
| | - Thomas D’Hooghe
- University Hospitals Leuven, Leuven University Fertility Center, Leuven, Belgium
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Dória S, Carvalho F, Ramalho C, Lima V, Francisco T, Machado AP, Brandão O, Sousa M, Matias A, Barros A. An efficient protocol for the detection of chromosomal abnormalities in spontaneous miscarriages or foetal deaths. Eur J Obstet Gynecol Reprod Biol 2009; 147:144-50. [DOI: 10.1016/j.ejogrb.2009.07.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 06/25/2009] [Accepted: 07/31/2009] [Indexed: 10/20/2022]
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Kashevarova AA, Tolmacheva EN, Sukhanova NN, Sazhenova EA, Lebedev IN. Estimation of the mehylation status of the promoter region of the cell cycle control gene P14ARF in placental tissues of spontaneous abortions with chromosomal mosaicism. RUSS J GENET+ 2009. [DOI: 10.1134/s1022795409060155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Tolmacheva EN, Kashevarova AA, Sukhanova NN, Sazhenova EA, Lebedev IN. Epigenetic inactivation of the RB1 gene as a factor of genomic instability: A possible contribution to etiology of chromosomal mosaicism during human embryo development. RUSS J GENET+ 2009. [DOI: 10.1134/s1022795408110033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Zhang YX, Zhang YP, Gu Y, Guan FJ, Li SL, Xie JS, Shen Y, Wu BL, Ju W, Jenkins EC, Brown WT, Zhong N. Genetic analysis of first-trimester miscarriages with a combination of cytogenetic karyotyping, microsatellite genotyping and arrayCGH. Clin Genet 2009; 75:133-40. [DOI: 10.1111/j.1399-0004.2008.01131.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Abstract
PURPOSE OF REVIEW Preimplantation genetic diagnosis is widely used for the detection of embryo aneuploidy before implantation, with the aim of avoiding miscarriage or pregnancy termination of an aneuploid fetus. The majority of first trimester miscarriages occur due to chromosomal imbalances. The aim of this review is to assess whether preimplantation genetic diagnosis can help women who suffer from recurrent pregnancy loss. RECENT FINDINGS Several in-vitro fertilization clinics have employed preimplantation genetic diagnosis in women with recurrent pregnancy loss. Patients were classified into groups according to their age. Preimplantation genetic diagnosis was very successful in treating couples where one of the parents was a carrier of a balanced chromosomal abnormality such as a translocation. Similarly, recurrent pregnancy loss rate was reduced in women more than 35 years in age with a normal karyotype. On the other hand, in younger patients the beneficial effect of this procedure is debatable. In general, women with recurrent pregnancy loss produced more abnormal embryos than control groups. SUMMARY Preimplantation genetic diagnosis can be beneficial for three major subgroups of patients with recurrent pregnancy loss: couples carrying chromosomal translocations; women more than 35 years of age; women of any age whose previous miscarriages were due to fetal aneuploidy. It is likely that the rate of miscarriage will be further reduced with the new advances in methods of performing preimplantation genetic diagnosis for more chromosomes.
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Paparistidis N, Papadopoulou C, Chioti A, Papaioannou D, Tsekoura C, Keramitsoglou T, Kontopoulou-Antonopoulou V, Agapitos E, Balafoutas C, Varla-Leftherioti M. How valuable is measurement of peripheral blood natural killer cells at the time of abortion? Am J Reprod Immunol 2008; 59:306-15. [PMID: 18294356 DOI: 10.1111/j.1600-0897.2007.00547.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
PROBLEM Increased peripheral blood natural killer (NK) cells are associated to immune-mediated abortion, but their diagnostic value when measured at the time of miscarriage is unknown. METHOD OF STUDY In women with therapeutic (A = 79) or elective (C = 34) pregnancy termination, the NK-cell percentage was measured before and 5 days after curettage. Additionally, immune-mediated lesions (scored 0-3) and CD56(+) and CD16(+) decidual NKs (scored 1-3) were detected on the abortion material. RESULTS Aborters differed from controls in histological scores (P = 0.000) and in NK percentage (>12%) only in the measurement 5 days after the operation (P = 0.038). In comparison to histological lesions, NK measurement was found to have sensitivity 70%, specificity 73.68%, positive prognostic value 89.39% and negative prognostic value 43.75%. CONCLUSION An Increased NK-cell percentage 5 days after the pregnancy termination could be a marker of immune aetiology of miscarriage, as the probability of an aborter with NK >12% to have an immune-mediated abortion is almost 90%.
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Affiliation(s)
- Nikolaos Paparistidis
- Department of Obstetrics and Gynaecology, Helena Venizelou Maternity Hospital of Athens, Athens, Greece
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Borovik CL, Perez ABA, Silva LRD, Krepischi-Santos ACV, Costa SS, Rosenberg C. Array-CGH testing in spontaneous abortions with normal karyotypes. Genet Mol Biol 2008. [DOI: 10.1590/s1415-47572008000300004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Delhanty JDA. Mechanisms of aneuploidy induction in human oogenesis and early embryogenesis. Cytogenet Genome Res 2006; 111:237-44. [PMID: 16192699 DOI: 10.1159/000086894] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2004] [Accepted: 02/25/2005] [Indexed: 11/19/2022] Open
Abstract
The mechanisms of aneuploidy induction in human oogenesis mainly involve nondisjunction arising during the first and second meiotic divisions. Nondisjunction equally affects both whole chromosomes and chromatids, in the latter case it is facilitated by "predivision" or precocious centromere division. Karyotyping and CGH studies show an excess of hypohaploidy, which is confirmed in studies of preimplantation embryos, providing evidence in favour of anaphase lag as a mechanism. Preferential involvement of the smaller autosomes has been clearly shown but the largest chromosomes are also abnormal in many cases. Overall, the rate of chromosomal imbalance in oocytes from women aged between 30 and 35 has been estimated at 11% from recent karyotyping data but accruing CGH results suggest that the true figure should be considerably higher. Clear evidence has been obtained in favour of germinal or gonadal mosaicism as a predisposing factor. Constitutional aneuploidy in embryos is most frequent for chromosomes 22, 16, 21 and 15; least frequently involved are chromosomes 14, X and Y, and 6. However, embryos of women under 37 are far more likely to be affected by mosaic aneuploidy, which is present in over 50% of 3-day-old embryos. There are two main types, diploid/aneuploid and chaotic mosaics. Chaotic mosaics arise independently of maternal age and may be related to centrosome anomalies and hence of male origin. Aneuploid mosaics most commonly arise by chromosome loss, followed by chromosome gain and least frequently by mitotic nondisjunction. All may be related to maternal age as well as to lack of specific gene products in the embryo. Partial aneuploidy as a result of chromosome breakage affects a minimum of 10% of embryos.
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Affiliation(s)
- J D A Delhanty
- UCL Centre for Preimplantation Diagnosis, Department of Obstetrics & Gynaecology, University College London, London, UK.
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Nikitina TV, Lebedev IN, Sukhanova NN, Sazhenova EA, Nazarenko SA. A mathematical model for evaluation of maternal cell contamination in cultured cells from spontaneous abortions: significance for cytogenetic analysis of prenatal selection factors. Fertil Steril 2005; 83:964-72. [PMID: 15820808 DOI: 10.1016/j.fertnstert.2004.12.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2004] [Revised: 12/08/2004] [Accepted: 12/08/2004] [Indexed: 11/21/2022]
Abstract
OBJECTIVE To develop a mathematical model for more precise estimation of the incidence of chromosomal abnormalities and the sex ratio among spontaneous abortions masked by maternal cell contamination. DESIGN Retrospective analysis. SETTING Academic medical center. PATIENT(S) One hundred twelve samples of spontaneous abortion with a "46,XX" karyotype and 97 parents with aborted embryos. INTERVENTION(S) The presence of Y chromosome DNA in native tissues of "46,XX" spontaneous abortions was detected by amelogenin locus analysis. Detection of aneuploidies in noncultured tissues of "46,XX" abortions was performed by microsatellite DNA analysis and confirmed by fluorescence in situ hybridization. MAIN OUTCOME MEASURE(S) Accuracy of cytogenetic evaluation of spontaneous abortions. RESULT(S) Y chromosome DNA was revealed in 16% of the embryos with a "46,XX" karyotype. According to the mathematical model proposed, the frequency of chromosomal abnormalities in a sample of 478 abortions increased from 54.6% to 60.3%, and the sex ratio in embryos with normal karyotype changed from 0.66 to 1.02. The experimental validation of the model has shown that the observed and expected incidences of chromosomal abnormalities in "46,XX" abortions were in good agreement. CONCLUSION(S) Maternal cell contamination clearly affects the incidence of registered chromosomal abnormalities and the sex ratio in spontaneous abortions. Correction for maternal cell contamination should be taken into account before invoking biological explanations of sex ratio bias and might be useful to include in diagnostic reporting.
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Affiliation(s)
- Tatyana V Nikitina
- Cytogenetics Laboratory, Institute of Medical Genetics, Tomsk Scientific Center, Russian Academy of Medical Sciences, Ushaika Street 10, Tomsk 634050, Russia
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Menasha J, Levy B, Hirschhorn K, Kardon NB. Incidence and spectrum of chromosome abnormalities in spontaneous abortions: New insights from a 12-year study. Genet Med 2005; 7:251-63. [PMID: 15834243 DOI: 10.1097/01.gim.0000160075.96707.04] [Citation(s) in RCA: 172] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
PURPOSE Despite advances in harvesting and culturing techniques, analysis of the impact of these improvements on the observed frequency of chromosomal abnormalities in spontaneous abortions (SAB) has not been determined. We sought to evaluate the effect of these refinements on the success rate of our cultures and on the resulting frequency of detected chromosomal abnormalities. METHODS Between 1990 and 2002, 2301 specimens obtained from the products of conception (POC) of SABs were submitted to our laboratory for cytogenetic analysis. Due to refinements in specimen processing and culture techniques introduced at the end of 1997, our data were analyzed for two periods: Period A from 1990 through 1997 with 907 eligible specimens and Period B from 1998 through 2002 with 1273 eligible specimens. RESULTS Modifications in physician communication and sample processing contributed to significant improvements in the culture success rate and in the ratio of male-to-female cases with normal karyotypes. Additionally, increased detection of trisomic, triploid, and multiple aneuploid cases in Period B resulted in a significant increase in the percentage of cases with abnormal karyotypes (42.8% in Period A vs. 65.8% in Period B). Monosomy X accounted for < 10% of all abnormalities in Period B. Eighty five multiple aneuploid karyotypes, including 57 double trisomies, comprised 7.7% of our 1099 abnormal cases. These karyotypes were detected predominantly in POCs from the older women in our study. This collection of multiple aneuploidies is the largest published to date and includes abnormalities not reported in prior studies. We also present a table empirically derived from the data in Period B that indicates the likelihood of a specific abnormal karyotype based on maternal age. The table can be utilized by health care providers, who counsel patients after a spontaneous miscarriage. CONCLUSION Improvements in laboratory technique have led to reduced contamination and growth failure of POCs, irrespective of maternal age. This in turn has led to a more balanced male-to-female ratio and to the detection of an increased number of abnormal cases.
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Affiliation(s)
- Joshua Menasha
- Department of Human Genetics, Mount Sinai School of Medicine, New York, New York 10029, USA
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Scheuerle A, Heller K, Elder F. Complete trisomy 1q with mosaic Y;1 translocation: A recurrent aneuploidy presenting diagnostic dilemmas. Am J Med Genet A 2005; 138A:166-70. [PMID: 16152651 DOI: 10.1002/ajmg.a.30940] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We present a case of a liveborn male with complete trisomy 1q in mosaic form due to a de novo unbalanced translocation. There are seven previously documented cases of complete trisomy for 1q, which demonstrate that this is a lethal condition. All cases have similar phenotype including weights greater than 50th centile for gestational age, hydrocephalus, microphthalmia, abnormal ears, small mouth or jaw, and abnormal fingers. Single umbilical artery, imperforate anus, and dysplastic kidneys are also seen in more than one patient. Five of the eight translocation cases have identical chromosomal breakpoints involving 1q and Yq. This suggests the possibility of sequence similarities on these two chromosomes as has been documented with several other recurrent chromosomal rearrangements. Further, this case demonstrates the need for postnatal genetics evaluation following prenatal diagnosis. In postnatal testing, the aneuploidy could not be demonstrated in metaphase cells from cultured lymphocytes. More detailed testing prompted by abnormal amniocentesis and neonatal dysmorphology was necessary to confirm the cytogenetic diagnosis. Without the prenatal diagnosis, it is likely that the true cytogenetic aberration would have gone undetected.
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MESH Headings
- Abnormalities, Multiple/diagnosis
- Abnormalities, Multiple/genetics
- Abnormalities, Multiple/pathology
- Aneuploidy
- Anus, Imperforate/pathology
- Chromosomes, Human, Pair 1/genetics
- Chromosomes, Human, Y/genetics
- Ear/abnormalities
- Fatal Outcome
- Female
- Fetal Diseases/diagnosis
- Fetal Diseases/genetics
- Fetal Diseases/pathology
- Fingers/abnormalities
- Humans
- Hydrocephalus/pathology
- In Situ Hybridization, Fluorescence
- Infant, Newborn
- Karyotyping
- Kidney/abnormalities
- Lip/abnormalities
- Male
- Microphthalmos/pathology
- Mosaicism
- Pregnancy
- Prenatal Diagnosis
- Toes/abnormalities
- Translocation, Genetic
- Trisomy
- Umbilical Arteries/abnormalities
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Current awareness in prenatal diagnosis. Prenat Diagn 2004; 24:1025-30. [PMID: 15828089 DOI: 10.1002/pd.784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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