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Navarrete-Meneses MP, Ochoa-Mellado I, Gutiérrez-Álvarez R, Martínez-Anaya D, Juárez-Figueroa U, Durán-McKinster C, Lieberman-Hernández E, Yokoyama-Rebollar E, Gómez-Carmona S, Del Castillo-Ruiz V, Pérez-Vera P, Salas-Labadía C. Cytogenomic characterization of small supernumerary marker chromosomes in patients with pigmentary mosaicism. Front Genet 2024; 15:1356786. [PMID: 38711916 PMCID: PMC11071077 DOI: 10.3389/fgene.2024.1356786] [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: 12/16/2023] [Accepted: 03/21/2024] [Indexed: 05/08/2024] Open
Abstract
Introduction The combination of gene content on the marker chromosome, chromosomal origin, level of mosaicism, origin mechanism (chromothripsis), and uniparental disomy can influence the final characterization of sSMCs. Several chromosomal aberrations, including sSMCs, have been observed in 30%-60% of patients with pigmentary mosaicism, and in more than 80%, chromosomal abnormalities are present in the mosaic state. In patients with pigmentary mosaicism the most representative chromosomes involved in sSMCs are 3, 5, 6, 9, 10, 13, 15, 18, 20, and X. In this study, we included the complete clinical, cytogenetic, and molecular characterization of seven patients with pigmentary mosaicism associated with the presence of SMCs of different chromosomal origins. Methods The patients were diagnosed by the Genetics and Dermatology Department of three different hospitals. Cytogenetic and FISH analyses were performed on peripheral blood, light skin, and dark skin. FISH analysis was performed using different probes, depending on the marker chromosome description. Different array analysis was performed. Results To date, of the seven cases studied, the chromosomal origins of six were successfully identified by FISH or array analysis. The chromosomes involved in SMCs were 6, 9, 15, and 18, X. The most frequently found was the centric minute structure. Discussion To date, this group of seven patients constitutes the largest clinical and cytogenetically finely described study of cases with pigmentary mosaicism associated with sSMCs. Undoubtedly, analysis of the two skin types is a fundamental part of our study, as numerical differences may occur in the cell lines found in each skin type. The knowledge generated in this study will help delineate a very heterogeneous entity more accurately, and in the future, analyzing more patients with PM will likely establish a more definite association with the presence of this genetic alteration.
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Affiliation(s)
- M. P. Navarrete-Meneses
- Genetic and cancer Laboratory, National Institute of Pediatrics (Mexico), Mexico City, Mexico
| | - I. Ochoa-Mellado
- Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - R. Gutiérrez-Álvarez
- Genetic and cancer Laboratory, National Institute of Pediatrics (Mexico), Mexico City, Mexico
| | - D. Martínez-Anaya
- Genetic and cancer Laboratory, National Institute of Pediatrics (Mexico), Mexico City, Mexico
| | - U. Juárez-Figueroa
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - C. Durán-McKinster
- Departamento de Dermatología, Instituto Nacional de Pediatría, Mexico City, Mexico
| | | | | | - S. Gómez-Carmona
- Departamento de Genética Médica, Centro de Rehabilitación e Inclusión Infantil Teletón, Cancún, México
| | | | - P. Pérez-Vera
- Genetic and cancer Laboratory, National Institute of Pediatrics (Mexico), Mexico City, Mexico
| | - C. Salas-Labadía
- Genetic and cancer Laboratory, National Institute of Pediatrics (Mexico), Mexico City, Mexico
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Liehr T, Ziegler M, Person L, Kankel S, Padutsch N, Weise A, Weimer JP, Williams H, Ferreira S, Melo JB, Carreira IM. Small supernumerary marker chromosomes derived from human chromosome 11. Front Genet 2023; 14:1293652. [PMID: 38174048 PMCID: PMC10763568 DOI: 10.3389/fgene.2023.1293652] [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: 09/13/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction: With only 39 reported cases in the literature, carriers of a small supernumerary marker chromosome (sSMC) derived from chromosome 11 represent an extremely rare cytogenomic condition. Methods: Herein, we present a review of reported sSMC(11), add 18 previously unpublished cases, and closely review eight cases classified as 'centromere-near partial trisomy 11' and a further four suited cases from DECIPHER. Results and discussion: Based on these data, we deduced the borders of the pericentric regions associated with clinical symptoms into a range of 2.63 and 0.96 Mb for chromosome 11 short (p) and long (q) arms, respectively. In addition, the minimal pericentric region of chromosome 11 without triplo-sensitive genes was narrowed to positions 47.68 and 60.52 Mb (GRCh37). Furthermore, there are apparent differences in the presentation of signs and symptoms in carriers of larger sSMCs derived from chromosome 11 when the partial trisomy is derived from different chromosome arms. However, the number of informative sSMC(11) cases remains low, with overlapping presentation between p- and q-arm-imbalances. In addition, uniparental disomy (UPD) of 'normal' chromosome 11 needs to be considered in the evaluation of sSMC(11) carriers, as imprinting may be an influencing factor, although no such cases have been reported. Comprehensively, prenatal sSMC(11) cases remain a diagnostic and prognostic challenge.
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Affiliation(s)
- Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Monika Ziegler
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Luisa Person
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Stefanie Kankel
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Niklas Padutsch
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Jörg Paul Weimer
- Department of Gynecology and Obstetrics, University Hospital of Schleswig-Holstein, University Kiel, Kiel, Germany
| | | | - Susana Ferreira
- Cytogenetics and Genomics Laboratory, CACC, iCBR/CIMAGO, CIBB, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Joana B. Melo
- Cytogenetics and Genomics Laboratory, CACC, iCBR/CIMAGO, CIBB, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Isabel M. Carreira
- Cytogenetics and Genomics Laboratory, CACC, iCBR/CIMAGO, CIBB, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
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Lesieur-Sebellin M, Marzin P, Arnoux JB, Maurin ML, Receveur A, Cantagrel V, Rose S, Dorval G, Levy J, Malan V. Supernumerary chromosome 6 marker associated with paternal uniparental isodisomy of chromosome 6 in a patient with a syndromic disorder of insulin secretion. Eur J Med Genet 2023; 66:104848. [PMID: 37739061 DOI: 10.1016/j.ejmg.2023.104848] [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: 03/21/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
The association of both uniparental disomy and small supernumerary marker chromosomes is rare. Clinical impact depends on the presence of imprinted genes and/or the unmasking of a recessive mutation of the chromosome involved in the uniparental disomy and the euchromatic content of the sSMC. Here, we report on the second case of a patient harbouring a de novo supernumerary marker chromosome 6 causing partial trisomy 6p12.3p11.1 associated with a paternal uniparental isodisomy of chromosome 6. Our patient presented with intrauterine growth retardation, macroglossia, initial developmental delay and transient neonatal diabetes mellitus followed by a congenital hyperinsulinism. Diabetes and intrauterine growth retardation can be linked to the paternal isodisomy of the imprinted locus on chromosome 6q24 whereas developmental delay is probably due to the small supernumerary marker chromosome. However, the clinical impact of partial trisomy 6p is difficult to address due to a limited number of patients. The careful clinical examination and the molecular characterization of additional patients with trisomy 6p are needed to further predict the phenotype for genetic counselling. Finally, uniparental disomy should be considered when a sSMC involving a chromosome containing imprinted regions is detected, especially in the prenatal setting.
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Affiliation(s)
- Marion Lesieur-Sebellin
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, APHP.Centre, Hôpital Necker-Enfants Malades, Paris, France; Université Paris Cité, Génétique des Troubles du Neurodéveloppement, Institut Imagine, INSERM UMR_1163, F-75015, Paris, France
| | - Pauline Marzin
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, APHP.Centre, Hôpital Necker-Enfants Malades, Paris, France; Université Paris Cité, Bases Moléculaires et Physiopathologiques des Ostéochondrodysplasies, Institut Imagine, INSERM UMR_1163, F-75015, Paris, France
| | - Jean-Baptiste Arnoux
- Centre de Référence des Maladies Héréditaires du Métabolisme, service de Pédiatrie, Hôpital Necker-Enfants Malades, APHP, Université Paris Cité, Filière G2M, Paris, France
| | - Marie-Laure Maurin
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, APHP.Centre, Hôpital Necker-Enfants Malades, Paris, France
| | - Aline Receveur
- Service d'Histologie Embryologie Cytogénétique, APHP.Université Paris Saclay, Hôpital Antoine Béclère, 157 Rue de La Porte de Trivaux, 92141, Clamart Cedex, France
| | - Vincent Cantagrel
- Université Paris Cité, Génétique des Troubles du Neurodéveloppement, Institut Imagine, INSERM UMR_1163, F-75015, Paris, France
| | - Sylvia Rose
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, APHP.Centre, Hôpital Necker-Enfants Malades, Paris, France
| | - Guillaume Dorval
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, APHP.Centre, Hôpital Necker-Enfants Malades, Paris, France
| | - Jonathan Levy
- Département de Génétique, Hôpital Robert Debré, Paris, France
| | - Valérie Malan
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, APHP.Centre, Hôpital Necker-Enfants Malades, Paris, France; Université Paris Cité, Génétique des Troubles du Neurodéveloppement, Institut Imagine, INSERM UMR_1163, F-75015, Paris, France.
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Gavril EC, Nucă I, Pânzaru MC, Ivanov AV, Mihai CT, Antoci LM, Ciobanu CG, Rusu C, Popescu R. Genotype-Phenotype Correlations in 2q37-Deletion Syndrome: An Update of the Clinical Spectrum and Literature Review. Genes (Basel) 2023; 14:465. [PMID: 36833393 PMCID: PMC9957522 DOI: 10.3390/genes14020465] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
2q37 microdeletion/deletion syndrome (2q37DS) is one of the most common subtelomeric deletion disorders, caused by a 2q37 deletion of variable size. The syndrome is characterized by a broad and diverse spectrum of clinical findings: characteristic facial dysmorphism, developmental delay/intellectual disability (ID), brachydactyly type E, short stature, obesity, hypotonia in infancy, and abnormal behavior with autism spectrum disorder. Although numerous cases have been described so far, the exact mapping of the genotype and phenotype have not yet been achieved. MATERIALS AND METHODS In this study we analyzed nine newly diagnosed cases with 2q37 deletion (3 male/6 female, aged between 2 and 30 years old), and followed up at the Iasi Regional Medical Genetics Centre. All patients were tested first with MLPA using combined kits P036/P070 subtelomeric screening mix and follow-up mix P264; after, the deletion size and location were confirmed via CGH-array. We compared our findings with the data of other cases reported in the literature. RESULTS From nine cases, four had pure 2q37 deletions of variable sizes, and five presented deletion/duplication rearrangements (with chromosomes 2q, 9q, and 11p). In most cases, characteristic phenotypic aspects were observed: 9/9 facial dysmorphism, 8/9 global developmental delay and ID, 6/9 hypotonia, 5/9 behavior disorders, and 8/9 skeletal anomalies-especially brachydactyly type E. Two cases had obesity, one case had craniosynostosis, and four had heart defects. Other features found in our cases included translucent skin and telangiectasias (6/9), and a hump of fat on the upper thorax (5/9). CONCLUSIONS Our study enriches the literature data by describing new clinical features associated with 2q37 deletion, and possible genotype-phenotype correlations.
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Affiliation(s)
- Eva-Cristiana Gavril
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Investigatii Medicale Praxis, St. Moara de Vant No 35, 700376 Iasi, Romania
| | - Irina Nucă
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Investigatii Medicale Praxis, St. Moara de Vant No 35, 700376 Iasi, Romania
| | - Monica-Cristina Pânzaru
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Medical Genetics Department, “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | - Anca Viorica Ivanov
- Pediatrics Department, Grigore T. Popa University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
| | | | - Lucian-Mihai Antoci
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
| | - Cristian-Gabriel Ciobanu
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
| | - Cristina Rusu
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Medical Genetics Department, “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | - Roxana Popescu
- Medical Genetics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, University Street, No 16, 700115 Iasi, Romania
- Medical Genetics Department, “Saint Mary” Emergency Children’s Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
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Paternal UPD14 with sSMC derived from chromosome 14 in Kagami-Ogata syndrome. CHROMOSOME RESEARCH : AN INTERNATIONAL JOURNAL ON THE MOLECULAR, SUPRAMOLECULAR AND EVOLUTIONARY ASPECTS OF CHROMOSOME BIOLOGY 2023; 31:1. [PMID: 36656404 DOI: 10.1007/s10577-023-09712-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/27/2022] [Accepted: 01/02/2023] [Indexed: 01/20/2023]
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Molecular delineation of de novo small supernumerary marker chromosomes in prenatal diagnosis, a retrospective study. Taiwan J Obstet Gynecol 2023; 62:94-100. [PMID: 36720559 DOI: 10.1016/j.tjog.2022.06.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2022] [Indexed: 01/30/2023] Open
Abstract
OBJECTIVES To define the genotype-phenotype correlation of small supernumerary marker chromosomes (sSMCs) and conduct precise genetic counseling, we retrospectively searched and reviewed de novo sSMCs cases detected during prenatal diagnosis at The First Affiliated Hospital of Zhengzhou University. MATERIALS AND METHODS Chromosome karyotypes of 20,314 cases of amniotic fluid from pregnant women were performed. For 16 samples with de novo sSMCs, 10 were subjected to single-nucleotide polymorphism (SNP) array or low-coverage massively parallel copy number variation sequencing (CNV-seq) analysis. RESULTS Among the 10 sSMCs cases, two sSMCs derived from chromosome 9, and three sSMCs derived from chromosomes 12, 18 and 22. The remaining 5 cases were not identified by SNP array or CNV-seq because they lacked euchromatin or had a low proportion of mosaicism. Four of them with a karyotype of 47,XN,+mar presented normal molecular cytogenetic results (seq[hg19] 46,XN), and the remaining patient with a karyotype of 46,XN,+mar presented with Turner syndrome (seq[hg19] 45,X). Five sSMCs samples were mosaics of all 16 cases. CONCLUSION Considering the variable origins of sSMCs, further genetic testing of sSMCs should be performed by SNP array or CNV-seq. Detailed molecular characterization would allow precise genetic counseling for prenatal diagnosis.
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Kleinfinger P, Brechard M, Luscan A, Trost D, Boughalem A, Mylene Valduga, Serero DR S, Costa JM, Lohmann L. Case Report: How whole-genome sequencing-based cell-free DNA prenatal testing can help identify a marker mhromosome. Front Genet 2022; 13:926290. [PMID: 36226188 PMCID: PMC9549001 DOI: 10.3389/fgene.2022.926290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022] Open
Abstract
A supernumerary marker chromosome (SMC) is a structurally abnormal chromosome that cannot be characterized by conventional banding cytogenetics. Marker chromosomes are present in 0.075% of prenatal cases. They are associated with variable phenotypes, ranging from normal to severely abnormal, and the prognosis is largely dependent on the results of further cytogenomic analysis. Here, we report the identification and characterization of a marker chromosome following prenatal screening in a 39-year-old pregnant patient. The patient had a normal first trimester ultrasound but was high-risk for fetal chromosome anomalies based on the results of maternal serum parameters. Chorionic villus sampling was performed, and analysis of chorionic villi revealed the presence of two identical marker chromosomes. In the interest of a rapid identification of the markers, we performed noninvasive prenatal testing (NIPT) together with chorionic villus sampling. A pericentromeric 29 Mb duplication of chromosome 20: dup (20) (p13q11.21) was identified and thereafter confirmed by targeted metaphasic FISH. Whole-genome sequencing-based NIPT was instrumental in rapid characterization of the SMCs and allowed us to obviate the need for multiple expensive and time-consuming FISH analyses.
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Chien SC, Chen CP, Liou JD. Prenatal diagnosis and genetic counseling of uniparental disomy. Taiwan J Obstet Gynecol 2022; 61:210-215. [DOI: 10.1016/j.tjog.2022.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 10/18/2022] Open
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Prenatal diagnosis and molecular cytogenetic characterization of a familial small supernumerary marker chromosome derived from the acrocentric chromosome 14/22. Taiwan J Obstet Gynecol 2022; 61:364-367. [DOI: 10.1016/j.tjog.2022.02.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2022] [Indexed: 11/20/2022] Open
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Target enrichment long-read sequencing with adaptive sampling can determine the structure of the small supernumerary marker chromosomes. J Hum Genet 2022; 67:363-368. [PMID: 35027654 DOI: 10.1038/s10038-021-01004-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/05/2021] [Accepted: 12/04/2021] [Indexed: 12/23/2022]
Abstract
Structural analysis of small supernumerary marker chromosomes (sSMCs) has revealed that many have complex structures. Structural analysis of sSMCs by whole genome sequencing using short-read sequencers is challenging however because most present with a low level of mosaicism and consist of a small region of the involved chromosome. In this present study, we applied adaptive sampling using nanopore long-read sequencing technology to enrich the target region and thereby attempted to determine the structure of two sSMCs with complex structural rearrangements previously revealed by cytogenetic microarray. In adaptive sampling, simple specification of the target region in the FASTA file enables to identify whether or not the sequencing DNA is included in the target, thus promoting efficient long-read sequencing. To evaluate the target enrichment efficiency, we performed conventional pair-end short-read sequencing in parallel. Sequencing with adaptive sampling achieved a target enrichment at about a 11.0- to 11.5-fold higher coverage rate than conventional pair-end sequencing. This enabled us to quickly identify all breakpoint junctions and determine the exact sSMC structure as a ring chromosome. In addition to the microhomology and microinsertion at the junctions, we identified inverted repeat structure in both sSMCs, suggesting the common generation mechanism involving replication impairment. Adaptive sampling is thus an easy and beneficial method of determining the structures of complex chromosomal rearrangements.
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Whether to transfer mosaic embryos: a cytogenetic view of true mosaicism by amniocentesis. Reprod Biomed Online 2021; 43:33-43. [PMID: 33962907 DOI: 10.1016/j.rbmo.2021.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 11/21/2022]
Abstract
RESEARCH QUESTION Preimplantation genetic testing for aneuploidies has increasingly been employed for embryo selection, resulting in a recent surge in mosaic embryos. According to the cytogenetic results, which types of mosaic embryo survive early pregnancy, progress to the second trimester and finally result in a live birth? DESIGN This study evaluated 30,587 pregnant women undergoing amniocentesis from January 2004 to March 2020 at the cytogenic centre of Kaohsiung Chang Gung Memorial Hospital. Samples from amniocentesis were cultured using the in-situ method. The types and distribution of level III chromosomal mosaicism (two or more cells with the same abnormality in two or more colonies and both culture dishes, clinically referred to as 'true mosaicism') were retrospectively reviewed. RESULTS Among the 30,587 women, 78 cases (0.26%) of level III chromosomal mosaicism were identified. The types of chromosomal mosaicism were classified as sex chromosome mosaicism (SCM), autosomal chromosome mosaicism (ACM) and marker chromosome mosaicism (MCM), with SCM, ACM and MCM accounting for 58.97%, 32.05% and 8.97% of cases, respectively. The most common mosaic cell lines were monosomy X and trisomy 21. The most common mosaic cell line progressing to live birth was monosomy X. CONCLUSIONS Mosaic monosomy X and trisomy 21 are the most common cell lines of true mosaicism determined by amniocentesis. Monosomy X mosaicism is the most common cell line in live births. For women considering the transfer of these types of mosaic embryo in a circumstance where euploid embryos are unavailable, clinicians should provide careful prenatal counselling, detailed ultrasonography and amniocentesis.
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Liehr T, Williams HE, Ziegler M, Kankel S, Padutsch N, Al-Rikabi A. Small supernumerary marker chromosomes derived from chromosome 14 and/or 22. Mol Cytogenet 2021; 14:13. [PMID: 33632263 PMCID: PMC7908736 DOI: 10.1186/s13039-021-00533-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/27/2021] [Indexed: 12/28/2022] Open
Abstract
Small supernumerary marker chromosomes (sSMCs) are additional derivative chromosomes present in an otherwise numerically and structurally normal karyotype. They may derive from each of the 24 human chromosomes, and most contain a normal centromeric region with an alphoid sequence from a single chromosome. The majority of human chromosomes have a unique centromeric DNA-sequence enabling their indubitable characterization. However, chromosomes 14 and 22 share a common centromeric sequence D14/22Z1, and sSMCs with this DNA-stretch can derive from either chromosome. Euchromatin-carrying sSMCs(14 or 22) may be further characterized by molecular cytogenetics. However, in most diagnostic laboratories, heterochromatic sSMCs cannot be differentiated between chromosomes 14 or 22 derivation and are often reported as der(14 or 22). Still, heterochromatic sSMC(14 or 22) can be distinguished from each other using the D22Z4 probe (non-commercial) localized to 22p11.2. Herein, 355 sSMC(14 or 22) analyzed in the authors’ laboratory during the last ~ 20 years are summarized to address the questions: (1) What are the true frequencies of chromosome 14- and chromosome 22- derived sSMCs within D14/22Z1-positive cases? (2) Does sub-characterization of sSMC(14) and sSMC(22) make a difference in routine diagnostics? These questions could be answered as follows: (ad 1) within the studied group of sSMCs ~ 40% are derived from chromosome 14 and ~ 60% from chromosome 22; (ad 2) the knowledge on exact sSMC origin can help to save costs in routine diagnostics; i.e. in a clinically abnormal person with sSMC(14) a test for uniparental disomy is indicated, which is not necessary if a chromosome 22 origin for the sSMC was determined.
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Affiliation(s)
- Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, 07747, Jena, Germany.
| | - Heather E Williams
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, 622 West 168th Street, New York, NY, 10032, USA
| | - Monika Ziegler
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, 07747, Jena, Germany
| | - Stefanie Kankel
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, 07747, Jena, Germany
| | - Niklas Padutsch
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, 07747, Jena, Germany
| | - Ahmed Al-Rikabi
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, 07747, Jena, Germany
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Prenatal Detection of Uniparental Disomies (UPD): Intended and Incidental Finding in the Era of Next Generation Genomics. Genes (Basel) 2020; 11:genes11121454. [PMID: 33287348 PMCID: PMC7761756 DOI: 10.3390/genes11121454] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Prenatal detection of uniparental disomy (UPD) is a methodological challenge, and a positive testing result requires comprehensive considerations on the clinical consequences as well as ethical issues. Whereas prenatal testing for UPD in families which are prone to UPD formation (e.g., in case of chromosomal variants, imprinting disorders) is often embedded in genetic counselling, the incidental identification of UPD is often more difficult to manage. With the increasing application of high-resolution test systems enabling the identification of UPD, an increase in pregnancies with incidental detection of UPD can be expected. This paper will cover the current knowledge on uniparental disomies, their clinical consequences with focus on prenatal testing, genetic aspects and predispositions, genetic counselling, as well as methods (conventional tests and high-throughput assays).
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Deutsche Gesellschaft für Humangenetik e.V., Berufsverband Deutscher Humangenetiker e.V.. Leitlinien für die molekulare und zytogenetische Diagnostik bei Prader-Willi-Syndrom und Angelman-Syndrom. MED GENET-BERLIN 2020. [DOI: 10.1515/medgen-2020-2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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15
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Matsubara K, Yanagida K, Nagai T, Kagami M, Fukami M. De Novo Small Supernumerary Marker Chromosomes Arising From Partial Trisomy Rescue. Front Genet 2020; 11:132. [PMID: 32174976 PMCID: PMC7056893 DOI: 10.3389/fgene.2020.00132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/03/2020] [Indexed: 11/24/2022] Open
Abstract
Small supernumerary marker chromosomes (SMCs) are rare cytogenetic abnormalities. De novo small SMCs, particularly those combined with uniparental disomy (UPD), are assumed to result from incomplete trisomy rescue. Recently, a one-off cellular event designated as chromothripsis was reported as a mechanism for trisomy rescue in micronuclei. This Perspective article aims to highlight a possible association among trisomy rescue, chromothripsis, and SMCs. We propose that chromothripsis-mediated incomplete trisomy rescue in micronuclei underlies various chromosomal rearrangements including SMCs, although other mechanisms such as U-type exchange may also yield SMCs. These assumptions are primarily based on observations of previously reported patients with complex rearrangements and our patient with a small SMC. Given the high frequency of trisomic cells in human preimplantation embryos, chromothripsis-mediated trisomy rescue may be a physiologically important phenomenon. Nevertheless, trisomy rescue has a potential to produce UPD, SMCs, and other chromosomal rearrangements. The concepts of trisomy rescue, chromothripsis, and micronuclei provide novel insights into the mechanism for the maintenance and modification of human chromosomes.
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Affiliation(s)
- Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | | | | | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
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16
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Liehr T, Al-Rikabi A. Mosaicism: Reason for Normal Phenotypes in Carriers of Small Supernumerary Marker Chromosomes With Known Adverse Outcome. A Systematic Review. Front Genet 2019; 10:1131. [PMID: 31781176 PMCID: PMC6859531 DOI: 10.3389/fgene.2019.01131] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 10/17/2019] [Indexed: 01/01/2023] Open
Abstract
Small supernumerary marker chromosomes (sSMCs) are present in ∼3.3 million of presently living human beings. The majority of these sSMC carriers (i.e. ∼2.1 million) will never know about their condition, as they are perfectly healthy and just may learn by chance about it, e.g. if chromosomal analysis is done for some reason during their life time. The remainder ∼1.2 million of sSMC carriers are clinically affected either due to adverse effects of gained genetic material being present on the sSMC and/or by uniparental disomy of the sSMC’s sister chromosomes. Influence of mosaicism being present in 50% of sSMC carriers is controversy discussed in the literature. Even though genotype–phenotype correlation for sSMCs progressed during last years, still there are only eight sSMC-associated syndromes characterized yet, which may go together with mosaicism. Here we summarize presently available data for carriers of sSMCs normally leading to these well-defined syndromes, however, showing (almost) no clinical signs. This can be observed in ∼1 to 30% of the corresponding sSMC-carriers, thus, a high impact for counselling in corresponding prenatal de novo cases is not to be neglected.
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Affiliation(s)
- Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Ahmed Al-Rikabi
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
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17
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Kurtas NE, Xumerle L, Leonardelli L, Delledonne M, Brusco A, Chrzanowska K, Schinzel A, Larizza D, Guerneri S, Natacci F, Bonaglia MC, Reho P, Manolakos E, Mattina T, Soli F, Provenzano A, Al-Rikabi AH, Errichiello E, Nazaryan-Petersen L, Giglio S, Tommerup N, Liehr T, Zuffardi O. Small supernumerary marker chromosomes: A legacy of trisomy rescue? Hum Mutat 2018; 40:193-200. [PMID: 30412329 DOI: 10.1002/humu.23683] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 11/07/2018] [Accepted: 11/07/2018] [Indexed: 11/11/2022]
Abstract
We studied by a whole genomic approach and trios genotyping, 12 de novo, nonrecurrent small supernumerary marker chromosomes (sSMC), detected as mosaics during pre- or postnatal diagnosis and associated with increased maternal age. Four sSMCs contained pericentromeric portions only, whereas eight had additional non-contiguous portions of the same chromosome, assembled together in a disordered fashion by repair-based mechanisms in a chromothriptic event. Maternal hetero/isodisomy was detected with a paternal origin of the sSMC in some cases, whereas in others two maternal alleles in the sSMC region and biparental haplotypes of the homologs were detected. In other cases, the homologs were biparental while the sSMC had the same haplotype of the maternally inherited chromosome. These findings strongly suggest that most sSMCs are the result of a multiple-step mechanism, initiated by maternal meiotic nondisjunction followed by postzygotic anaphase lagging of the supernumerary chromosome and its subsequent chromothripsis.
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Affiliation(s)
| | - Luciano Xumerle
- Department of Biotechnology, University of Verona, Verona, Italy
| | | | | | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, Torino, Italy
| | - Krystyna Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Albert Schinzel
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Daniela Larizza
- Pediatrics and Adolescentology Unit, University of Pavia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Silvana Guerneri
- Laboratory of Medical Genetics, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Federica Natacci
- Laboratory of Medical Genetics, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Maria Clara Bonaglia
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Paolo Reho
- Biomedical Experimental and Clinical Sciences "Mario Serio", University of Florence, Firenze, Italy
| | | | - Teresa Mattina
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Fiorenza Soli
- Department of Genetics, Santa Chiara Hospital, Trento, Italy
| | - Aldesia Provenzano
- Biomedical Experimental and Clinical Sciences "Mario Serio", University of Florence, Firenze, Italy.,Azienda Ospedaliero-Universitaria Meyer, Firenze, Italy
| | - Ahmed H Al-Rikabi
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | | | | | - Sabrina Giglio
- Biomedical Experimental and Clinical Sciences "Mario Serio", University of Florence, Firenze, Italy.,Azienda Ospedaliero-Universitaria Meyer, Firenze, Italy
| | - Niels Tommerup
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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18
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Tesner P, Vlckova M, Drabova J, Vseticka J, Klimova A, Lastuvkova J, Zidovska J, Kremlikova Pourova R, Hancarova M, Sedlacek Z, Kocarek E. Molecular Cytogenetic Diagnostics of Marker Chromosomes: Analysis in Four Prenatal Cases and Long-Term Clinical Evaluation of Carriers. Cytogenet Genome Res 2018; 154:187-195. [DOI: 10.1159/000488790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2018] [Indexed: 01/15/2023] Open
Abstract
The prenatal finding of a small supernumerary marker chromosome (sSMC) is a challenge for genetic counseling. Our analytic algorithm is based on sSMC frequencies and multicolor FISH to accelerate the procedure. The chromosomal origin, size, and degree of mosaicism of the sSMC then determine the prognosis. We illustrate the effectiveness on 4 prenatally identified de novo mosaic sSMCs derived from chromosomes 13/21, X, 3, and 17. Three sSMC carriers had a good prognosis and apparently healthy children were born, showing no abnormality till the last examination at the age of 4 years. One case had a poor prognosis, and the parents decided to terminate the pregnancy. Our work contributes to the laboratory and clinical management of prenatally detected sSMCs. FISH is a reliable method for fast sSMC evaluation and prognosis assessment; it prevents unnecessary delays and uncertainty, allows informed decision making, and reduces unnecessary pregnancy terminations.
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Chromothripsis Detectable in Small Supernumerary Marker Chromosomes (sSMC) Using Fluorescence In Situ Hybridization (FISH). Methods Mol Biol 2018. [PMID: 29564819 DOI: 10.1007/978-1-4939-7780-2_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The formation of small supernumerary marker chromosomes (sSMC) still remains enigmatic. However, it is suggested that majority of all kinds of de novo sSMC (inverted duplication-, ring-, and centric-minute-shaped ones) are products of incomplete trisomic rescue during early embryogenesis. Recent work, based on molecular cytogenetics, suggests that these trisomic rescue events are going together with chromothripsis, directed against the supernumerary chromosome to be degraded. Here we present a protocol how to characterize so-called discontinuous sSMC by means of fluorescence in situ hybridization (FISH).
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20
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Li X, Liu Y, Yue S, Wang L, Zhang T, Guo C, Hu W, Kagan KO, Wu Q. Uniparental disomy and prenatal phenotype: Two case reports and review. Medicine (Baltimore) 2017; 96:e8474. [PMID: 29137034 PMCID: PMC5690727 DOI: 10.1097/md.0000000000008474] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
RATIONALE Uniparental disomy (UPD) gives a description of the inheritance of both homologues of a chromosome pair from the same parent. The consequences of UPD depend on the specific chromosome/segment involved and its parental origin. PATIENT CONCERNS We report prenatal phenotypes of 2 rare cases of UPD. DIAGNOSES The prenatal phenotype of case 1 included sonographic markers such as enlarged nuchal translucency (NT), absent nasal bone, short femur and humerus length, and several structural malformations involving Dandy-Walker malformation and congenital heart defects. The prenatal phenotype of Case 2 are sonographic markers, including enlarged NT, thickened nuchal fold, ascites, and polyhydramnios without apparent structural malformations. INTERVENTIONS Conventional G-band karyotype appears normal in case 1, while it shows normal chromosomes with a small supernumerary marker chromosome (sSMC) in case 2. Genetic etiology was left unknown until single-nucleotide polymorphism-based array (SNP-array) was performed, and segmental paternal UPD 22 was identified in case 1 and segmental paternal UPD 14 was found in case 2. OUTCOMES The parents of case 1 chose termination of pregnancy. The neonate of case 2 was born prematurely with a bellshaped small thorax and died within a day. LESSONS UPD cases are rare and the phenotypes are different, which depend on the origin and affected chromosomal part. If a fetus shows multiple anomalies that cannot be attributed to a common aneuploidy or a genetic syndrome, or manifests some features possibly related to an UPD syndrome, such as detection of sSMC, SNP-array should be considered.
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Affiliation(s)
| | - Yan Liu
- Department of Obstetrics, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | | | | | | | | | | | - Karl-Oliver Kagan
- Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany
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21
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22
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Ahram DF, Stambouli D, Syrogianni A, Al‐Sarraj Y, Gerou S, El‐Shanti H, Kambouris M. Mosaic partial pericentromeric trisomy 8 and maternal uniparental disomy in a male patient with autism spectrum disorder. Clin Case Rep 2016; 4:1125-1131. [PMID: 27980747 PMCID: PMC5134130 DOI: 10.1002/ccr3.705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 08/28/2016] [Accepted: 08/29/2016] [Indexed: 01/06/2023] Open
Abstract
Various chromosomal anomalies including small supernumerary marker chromosome (sSMC) and Uniparental disomy (UPD) have been described in association with intellectual disability and autism spectrum disorder. Based on our reported findings, we recommend that patients with sSMC(8) be evaluated for autism spectrum disorder (ASD) for early institution of therapy. In the presence of an identifiable sSMC, exploration of UPD is also recommended to further investigate the role of chromosome 8 UPD in ASD.
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Affiliation(s)
- Dina F. Ahram
- Medical Genetics CenterQatar Biomedical Research InstituteHamad Bin Khalifa UniversityDohaQatar
| | | | | | - Yasser Al‐Sarraj
- Medical Genetics CenterQatar Biomedical Research InstituteHamad Bin Khalifa UniversityDohaQatar
| | | | - Hatem El‐Shanti
- Medical Genetics CenterQatar Biomedical Research InstituteHamad Bin Khalifa UniversityDohaQatar
- PediatricsUniversity of Jordan School of MedicineAmmanJordan
- PediatricsUniversity of IowaIowa CityIowaUSA
| | - Marios Kambouris
- Pathology‐GeneticsSidra Medical and Research CenterDohaQatar
- GeneticsYale University School of MedicineNew HavenConnecticutUSA
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23
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Grafodatskaya D, Choufani S, Basran R, Weksberg R. An Update on Molecular Diagnostic Testing of Human Imprinting Disorders. J Pediatr Genet 2016; 6:3-17. [PMID: 28180023 DOI: 10.1055/s-0036-1593840] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 05/16/2016] [Indexed: 01/07/2023]
Abstract
Imprinted genes are expressed in a parent of origin manner. Dysregulation of imprinted genes expression causes various disorders associated with abnormalities of growth, neurodevelopment, and metabolism. Molecular mechanisms leading to imprinting disorders and strategies for their diagnosis are discussed in this review article.
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Affiliation(s)
- Daria Grafodatskaya
- Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Sanaa Choufani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Raveen Basran
- Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada; Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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24
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Zhang LN, Meng Z, He ZW, Li DF, Luo XY, Liang LY. [Clinical phenotypes and copy number variations in children with microdeletion and microduplication syndromes: an analysis of 50 cases]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2016; 18:840-845. [PMID: 27655541 PMCID: PMC7389961 DOI: 10.7499/j.issn.1008-8830.2016.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/14/2016] [Indexed: 06/06/2023]
Abstract
OBJECTIVE To investigate the association between genotype and phenotype of microdeletion and microduplication syndromes (MMSs) and the pathogenesis of pathogenic copy number variations (CNVs). METHODS A total of 50 children with MMSs diagnosed by chromosomal microarray analysis (CMA) from June 2013 to September 2015 were enrolled, and the clinical manifestations and features of pathogenic CNVs were analyzed. RESULTS The main clinical manifestations of children with MMSs included mental retardation, developmental delay, short stature, and unusual facies, with the presence of abnormalities in multiple systems. There were 54 pathogenic CNVs in total, consisting of 36 microdeletion segments and 18 microduplication segments, with sizes ranging from 28 kb to 48.5 Mb (mean 13.86 Mb). Pathogenic CNVs often occurred in chromosomes X, 15, and 1. CONCLUSIONS The clinical manifestations of MMSs are not specific, and a genotype-first approach can be used for diagnosis. Mode of inheritance, type of recombination (deletion or duplication), size of segment, and functional genes included helps with the interpretation of CNVs of de novo mutations, and in-depth research on rare pathogenesis may become breakthrough points for the identification of new MMSs.
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Affiliation(s)
- Li-Na Zhang
- Department of Pediatric Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510260, China.
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25
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Zhang S, Qin H, Wang J, OuYang L, Luo S, Fu C, Fan X, Su J, Chen R, Xie B, Hu X, Chen S, Shen Y. Maternal uniparental disomy 14 and mosaic trisomy 14 in a Chinese boy with moderate to severe intellectual disability. Mol Cytogenet 2016; 9:66. [PMID: 27559361 PMCID: PMC4995659 DOI: 10.1186/s13039-016-0274-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/02/2016] [Indexed: 11/10/2022] Open
Abstract
Background Both maternal uniparental disomy 14 (UPD(14)mat) and mosaic trisomy 14 are rare events in live individuals. A combination of the two events in one individual is rarely encountered. Only six live-born cases have so far been reported. Case presentation Here we reported a case of concomitant UPD(14)mat and mosaic trisomy 14 in a 10-year-old Chinese patient. Most clinical features of our patient were consistent with those previous reported for UPD(14)mat cases, which include prenatal and postnatal growth retardation, neonatal hypotonia, feeding difficulty, intellectual disability, truncal obesity, small hands and feet, short stature, and mild facial dysmorphism, but our patient showed more severe intellectual disability and no sign of precocious puberty. SNP array analysis revealed a mixture of chromosome 14 maternal isodisomy with heterodisomy and a low level trisomy mosaicism of whole chromsome 14 in blood and hyperpigmented skin samples, whereas only UPD(14)mat was detected in normal skin sample. Cytogenetic analysis identified one trisomy 14 cell in 100 metaphase of peripheral blood lymphocytes (47,XX, +14[1]/46,XX[99]). Conclusions To our knowledge, this is the first case of a patient with UPD(14)mat and mosaic trisomy 14 reported in a Chinese patient. The definitive genetic diagnosis is beneficial for genetic counseling and clinical management of our patient, and for improving our understanding of the genotype-phenotype correlations of concomitant UPD(14)mat and mosaic trisomy 14. Electronic supplementary material The online version of this article (doi:10.1186/s13039-016-0274-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shujie Zhang
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, No.59, Xiangzhu Road, Nanning, China
| | - Haisong Qin
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, No.59, Xiangzhu Road, Nanning, China
| | - Jin Wang
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, No.59, Xiangzhu Road, Nanning, China
| | - Luping OuYang
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, No.59, Xiangzhu Road, Nanning, China
| | - Shiyu Luo
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, No.59, Xiangzhu Road, Nanning, China
| | - Chunyun Fu
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, No.59, Xiangzhu Road, Nanning, China
| | - Xin Fan
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, No.59, Xiangzhu Road, Nanning, China
| | - Jiasun Su
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, No.59, Xiangzhu Road, Nanning, China
| | - Rongyu Chen
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, No.59, Xiangzhu Road, Nanning, China
| | - Bobo Xie
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, No.59, Xiangzhu Road, Nanning, China
| | - Xuyun Hu
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, No.59, Xiangzhu Road, Nanning, China
| | - Shaoke Chen
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, No.59, Xiangzhu Road, Nanning, China
| | - Yiping Shen
- Department of Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, No.59, Xiangzhu Road, Nanning, China.,Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115 USA
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26
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Hochstenbach R, Nowakowska B, Volleth M, Ummels A, Kutkowska-Kaźmierczak A, Obersztyn E, Ziemkiewicz K, Gerloff C, Schanze D, Zenker M, Muschke P, Schanze I, Poot M, Liehr T. Multiple Small Supernumerary Marker Chromosomes Resulting from Maternal Meiosis I or II Errors. Mol Syndromol 2016; 6:210-21. [PMID: 26997941 PMCID: PMC4772618 DOI: 10.1159/000441408] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2015] [Indexed: 01/11/2023] Open
Abstract
We present 2 cases with multiple de novo supernumerary marker chromosomes (sSMCs), each derived from a different chromosome. In a prenatal case, we found mosaicism for an sSMC(4), sSMC(6), sSMC(9), sSMC(14) and sSMC(22), while a postnatal case had an sSMC(4), sSMC(8) and an sSMC(11). SNP-marker segregation indicated that the sSMC(4) resulted from a maternal meiosis II error in the prenatal case. Segregation of short tandem repeat markers on the sSMC(8) was consistent with a maternal meiosis I error in the postnatal case. In the latter, a boy with developmental/psychomotor delay, autism, hyperactivity, speech delay, and hypotonia, the sSMC(8) was present at the highest frequency in blood. By comparison to other patients with a corresponding duplication, a minimal region of overlap for the phenotype was identified, with CHRNB3 and CHRNA6 as dosage-sensitive candidate genes. These genes encode subunits of nicotinic acetylcholine receptors (nAChRs). We propose that overproduction of these subunits leads to perturbed component stoichiometries with dominant negative effects on the function of nAChRs, as was shown by others in vitro. With the limitation that in each case only one sSMC could be studied, our findings demonstrate that different meiotic errors lead to multiple sSMCs. We relate our findings to age-related aneuploidy in female meiosis and propose that predivision sister-chromatid separation during meiosis I or II, or both, may generate multiple sSMCs.
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Affiliation(s)
- Ron Hochstenbach
- Division of Biomedical Genetics, Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Beata Nowakowska
- Department of Medical Genetics, Institute of the Mother and Child, Warsaw, Poland
| | | | - Amber Ummels
- Division of Biomedical Genetics, Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Ewa Obersztyn
- Department of Medical Genetics, Institute of the Mother and Child, Warsaw, Poland
| | - Kamila Ziemkiewicz
- Department of Medical Genetics, Institute of the Mother and Child, Warsaw, Poland
| | - Claudia Gerloff
- University Women's Clinic, Otto-von-Guericke University, Magdeburg, Germany
| | | | | | | | - Ina Schanze
- Department of Human Genetics, Magdeburg, Germany
| | - Martin Poot
- Division of Biomedical Genetics, Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Thomas Liehr
- Department of Human Genetics, University Clinic, Jena, Germany
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27
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Unrevealed mosaicism in the next-generation sequencing era. Mol Genet Genomics 2015; 291:513-30. [PMID: 26481646 PMCID: PMC4819561 DOI: 10.1007/s00438-015-1130-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 10/07/2015] [Indexed: 12/19/2022]
Abstract
Mosaicism refers to the presence in an individual of normal and abnormal cells that are genotypically distinct and are derived from a single zygote. The incidence of mosaicism events in the human body is underestimated as the genotypes in the mosaic ratio, especially in the low-grade mosaicism, stay unrevealed. This review summarizes various research outcomes and diagnostic questions in relation to different types of mosaicism. The impact of both tested biological material and applied method on the mosaicism detection rate is especially highlighted. As next-generation sequencing technologies constitute a promising methodological solution in mosaicism detection in the coming years, revisions in current diagnostic protocols are necessary to increase the detection rate of the unrevealed mosaicism events. Since mosaicism identification is a complex process, numerous examples of multistep mosaicism investigations are presented and discussed.
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28
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Armanet N, Tosca L, Brisset S, Liehr T, Tachdjian G. Small Supernumerary Marker Chromosomes in Human Infertility. Cytogenet Genome Res 2015; 146:100-108. [PMID: 26398339 DOI: 10.1159/000438718] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2015] [Indexed: 11/19/2022] Open
Abstract
Small supernumerary marker chromosomes (sSMC) are structurally abnormal chromosomes that cannot be unambiguously identified by banding cytogenetics. The objective of this study was to provide an overview of sSMC frequency and characterization in a context of infertility and to review the literature describing sSMC in relation with male and female infertility. Therefore, a systematic literature review on sSMC associated with infertility was conducted by means of a PubMed literature and a sSMC database (http://ssmc-tl.com/sSMC.html) search. A total of 234 patients with infertility were identified as carriers of sSMC. All chromosomes, except chromosomes 10, 19 and the X, were involved in sSMC, and in 72% the sSMC originated from acrocentric chromosomes. Euchromatic imbalances were caused by the presence of sSMC in 30% of the cases. Putative genes have been identified in only 1.2% of sSMC associated with infertility. The implication of sSMC in infertility could be due to a partial trisomy of some genes but also to mechanical effects perturbing meiosis. Further precise molecular and interphase-architecture studies on sSMC are needed in the future to characterize the relationship between this chromosomal anomaly and human infertility.
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Affiliation(s)
- Narjes Armanet
- Service d'Histologie, Embryologie et Cytogénétique, Hôpital Antoine Béclère, Hôpitaux Universitaires Paris-Sud, Clamart, France
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Izumi K, Kubota N, Arakawa M, Takayama M, Harada Y, Nakamura T, Nishi E, Hidaka E. Dissecting the phenotype of supernumerary marker chromosome 20 in a patient with syndromic Pierre Robin sequence: combinatorial effect of gene dosage and uniparental disomy. Am J Med Genet A 2015; 167:1289-93. [PMID: 25847371 DOI: 10.1002/ajmg.a.36921] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 11/23/2014] [Indexed: 11/12/2022]
Abstract
Clinical phenotypes in individuals with a supernumerary marker chromosome (SMC) are mainly caused by gene dosage effects due to the genes located on the SMC. An additional effect may result from uniparental disomy (UPD). Consequently, the occurrence of UPD may be a confounding factor in identifying genotype-phenotype correlations in SMC syndromes. Here, we report on a patient that illustrates this problem; the phenotype of this patient was a consequence of a combined effect of gene dosage and UPD. The proband showed facial dysmorphisms, growth retardation and developmental delay. G-band karyotype of the proband's peripheral blood showed the presence of mosaic SMC. A SNP array analysis documented maternal UPD20 and 20p duplication. It is known that maternal UPD20 causes prenatal onset growth retardation and feeding difficulties. By contrast, duplication of 20p causes facial dysmorphisms, micrognathia, cleft palate, developmental delay and vertebral anomalies. Our classification of the proband's phenotype showed a mixture of these two effects. Therefore, we suggest the routine use of genome-wide SNP array towards the detailed genotype-phenotype correlations for SMC syndromes.
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Affiliation(s)
- Kosuke Izumi
- Division of Medical Genetics, Nagano Children's Hospital, Azumino, Japan.,Research Center for Epigenetic Disease, Institute for Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Noriko Kubota
- Department of Laboratory Medicine, Nagano Children's Hospital, Azumino, Japan.,Life Science Research Center, Nagano Children's Hospital, Azumino, Japan
| | - Michiko Arakawa
- Division of Medical Genetics, Nagano Children's Hospital, Azumino, Japan
| | | | - Yukiko Harada
- Department of Pediatrics, Inariyama Medical Walfare Center, Chikuma, Japan
| | - Tomohiko Nakamura
- Life Science Research Center, Nagano Children's Hospital, Azumino, Japan.,Division of Neonatology, Nagano Children's Hospital, Azumino, Japan
| | - Eriko Nishi
- Division of Medical Genetics, Nagano Children's Hospital, Azumino, Japan.,Life Science Research Center, Nagano Children's Hospital, Azumino, Japan.,Department of Medical Genetics, Shinshu University Graduate School of Medicine, Matsumoto, Japan
| | - Eiko Hidaka
- Department of Laboratory Medicine, Nagano Children's Hospital, Azumino, Japan.,Life Science Research Center, Nagano Children's Hospital, Azumino, Japan
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30
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Eggermann T, Soellner L, Buiting K, Kotzot D. Mosaicism and uniparental disomy in prenatal diagnosis. Trends Mol Med 2015; 21:77-87. [DOI: 10.1016/j.molmed.2014.11.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/18/2014] [Accepted: 11/26/2014] [Indexed: 01/21/2023]
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31
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Papenhausen PR, Kelly CA, Zvereff V, Schwartz S. Four-copy number intervals in SNP microarray analysis: unique patterns and positions. Cytogenet Genome Res 2014; 144:92-103. [PMID: 25401283 DOI: 10.1159/000368859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2014] [Indexed: 11/19/2022] Open
Abstract
Over the past several years, the utility of microarray technology in delineating copy number changes has become well established. In the past 4 years, we have used the SNP array to detect and analyze allele ratios in 150 cases with 4-copy intervals, confirmed by FISH, offering insight into the underlying mechanisms of formation. These cases may be divided into 5 allele patterns--the first 4 of which involve a single homologue--as detected by the genotyping aspects of the microarray: (1) triplications combining homozygous and heterozygous alleles, with a 3:1 ratio of heterozygotes; (2) triplications with allele patterns combining homozygous and heterozygous alleles, with heterozygote ratios of both 3:1 and 2:2; (3) triplications that have homozygous alleles combined with only 2:2 heterozygous alleles; (4) triplications that are completely homozygous; and (5) homozygous duplications on each homologue with no heterozygous alleles. The implications of copy number variants with diverse allelic segregations are presented in this study.
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Affiliation(s)
- Peter R Papenhausen
- Department of Cytogenetics, Laboratory Corporation of America, Research Triangle Park, N.C., USA
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32
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Salas-Labadía C, Lieberman E, Cruz-Alcívar R, Navarrete-Meneses P, Gómez S, Cantú-Reyna C, Buiting K, Durán-McKinster C, Pérez-Vera P. Partial and complete trisomy 14 mosaicism: clinical follow-up, cytogenetic and molecular analysis. Mol Cytogenet 2014; 7:65. [PMID: 25276227 PMCID: PMC4180134 DOI: 10.1186/s13039-014-0065-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/07/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Trisomy 14 mosaicism is a rare chromosomal abnormality. It is associated with multiple congenital anomalies. We report a 15 year-old female with an unusual karyotype with three cell lines: 47,XX,+mar/47,XX,+14/46,XX. At six months old she had short stature, cleft palate, hyperpigmented linear spots in arms and legs and developmental delay. At present, she has mild facial dysmorphism and moderate mental retardation. METHODS Cytogenetic analysis was performed in peripheral blood lymphocytes and in the light and dark skin following standard methods. DNAarray - Oligo 180 k was carried out using Agilent Technologies and FISH analysis was accomplished using DNA BACs probes to confirm the result obtained by DNAarray. Methylation-Specific PCR (MS-PCR) of the MEG3 promoter and microsatellite analysis were performed. RESULTS Microarray analysis confirmed partial trisomy 14 mosaicism; the marker chromosome was found to be from chromosome 14, the result was confirmed with FISH. Methylation (14q32.3) and microsatellite (14q11-14q32.33) analysis were carried out and UPD was discarded. The global result was: mos 47,XX,+del(14)(q11.2)[45]/47,XX,+14[10]/46,XX[45]. CONCLUSIONS This is a unique case because of the coexistence of two abnormal cell lines, including one with +14 and another with +del(14)(q11.2). To our knowledge, only three patients have been reported with trisomy 14 and another abnormal cell line. The array analysis identified the marker chromosome and characterized the breakpoint. The del(14)(q11.2) does not seem to be related to any particular phenotypic characteristic of the patient; the clinical features of our patient observed until now, can be attributed to trisomy 14 mosaicism. Nevertheless, we cannot discard the manifestation of new symptoms related to her karyotype in the future.
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Affiliation(s)
- Consuelo Salas-Labadía
- />Departamento de Genética Humana, Laboratorio de Cultivo de Tejidos, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C, México, DF C.P. 04530 Mexico
| | - Esther Lieberman
- />Departamento de Genética Humana, Instituto Nacional de Pediatría, México, DF Mexico
| | - Roberto Cruz-Alcívar
- />Departamento de Genética Humana, Laboratorio de Cultivo de Tejidos, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C, México, DF C.P. 04530 Mexico
| | - Pilar Navarrete-Meneses
- />Departamento de Genética Humana, Laboratorio de Cultivo de Tejidos, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C, México, DF C.P. 04530 Mexico
| | - Samuel Gómez
- />Departamento de Genética Humana, Instituto Nacional de Pediatría, México, DF Mexico
| | | | - Karin Buiting
- />Institut für Humangenetik Universitätsklinikum, Essen, Germany
| | | | - Patricia Pérez-Vera
- />Departamento de Genética Humana, Laboratorio de Cultivo de Tejidos, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C, México, DF C.P. 04530 Mexico
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33
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Hussein SS, Kreskowski K, Ziegler M, Klein E, Hamid AB, Kosyakova N, Volleth M, Liehr T, Fan X, Piaszinski K. Mitotic stability of small supernumerary marker chromosomes depends on their shape and telomeres - a long term in vitro study. Gene 2014; 552:246-8. [PMID: 25245454 DOI: 10.1016/j.gene.2014.09.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/19/2014] [Indexed: 12/23/2022]
Abstract
Mosaicism is present in more than 50% of the cases with small supernumerary marker chromosomes (sSMCs) and karyotype 47,XX,+mar/46,XX or 47,XY,+mar/46,XY. Recently we provided first evidence that the mitotic stability of sSMC is dependent on their structure, i.e. their shape. Thus, here we performed a long term in vitro study on 12 selected cell lines from the Else Kröner-Fresenius-sSMC-cellbank (http://ssmc-tl.com/ekf-cellbank.html) to test mitotic sSMC stability systematically. The obtained results showed that inverted duplicated shaped and also the so-called complex sSMCs (group 1) are by far more stable, than centric-minute- or ring-shaped sSMCs (groups 2). Generally speaking, the percentage of cells with group-1-sSMCs remained stable over 90 days of cell culture, while that of group-2-sSMCs in parts dramatically decreased. In one group-2-cell line the sSMC was even lost completely after 30 days of in vitro culture, in others the sSMC was depleted in up to 40% of the cells. Still the highest rate of sSMC loss was recorded during EBV-transformation. Overall, the major difference between groups 1 and 2 was the number of telomeres per sSMC. In group 1 the sSMCs had "original" telomeres at both of their ends; in group 2 the sSMCs had either no, possibly secondary acquired and/or only one original telomere. This absence of protective telomeric sequences in group 2 seems to make sSMC more susceptible for loss during cell division. Still, also a growth advantage of cells without sSMC cannot be neglected entirely.
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Affiliation(s)
- Shaymaa Subhi Hussein
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Katharina Kreskowski
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Monika Ziegler
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Elisabeth Klein
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Ahmed B Hamid
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Marianne Volleth
- Institut für Humangenetik, Universitätsklinikum, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany.
| | - Xiaobo Fan
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Katja Piaszinski
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
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34
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Regions of homozygosity identified by oligonucleotide SNP arrays: evaluating the incidence and clinical utility. Eur J Hum Genet 2014; 23:663-71. [PMID: 25118026 DOI: 10.1038/ejhg.2014.153] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 06/03/2014] [Accepted: 07/10/2014] [Indexed: 11/09/2022] Open
Abstract
Copy neutral segments with allelic homozygosity, also known as regions of homozygosity (ROHs), are frequently identified in cases interrogated by oligonucleotide single-nucleotide polymorphism (oligo-SNP) microarrays. Presence of ROHs may be because of parental relatedness, chromosomal recombination or rearrangements and provides important clues regarding ancestral homozygosity, consanguinity or uniparental disomy. In this study of 14 574 consecutive cases, 832 (6%) were found to harbor one or more ROHs over 10 Mb, of which 651 cases (78%) had multiple ROHs, likely because of identity by descent (IBD), and 181 cases (22%) with ROHs involving a single chromosome. Parental relatedness was predicted to be first degree or closer in 5%, second in 9% and third in 19%. Of the 181 cases, 19 had ROHs for a whole chromosome revealing uniparental isodisomy (isoUPD). In all, 25 cases had significant ROHs involving a single chromosome; 5 cases were molecularly confirmed to have a mixed iso- and heteroUPD15 and 1 case each with segmental UPD9pat and segmental UPD22mat; 17 cases were suspected to have a mixed iso- and heteroUPD including 2 cases with small supernumerary marker and 2 cases with mosaic trisomy. For chromosome 15, 12 (92%) of 13 molecularly studied cases had either Prader-Willi or Angelman syndrome. Autosomal recessive disorders were confirmed in seven of nine cases from eight families because of the finding of suspected gene within a ROH. This study demonstrates that ROHs are much more frequent than previously recognized and often reflect parental relatedness, ascertain autosomal recessive diseases or unravel UPD in many cases.
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35
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Sahoo T, Wang JC, Elnaggar MM, Sanchez-Lara P, Ross LP, Mahon LW, Hafezi K, Deming A, Hinman L, Bruno Y, Bartley JA, Liehr T, Anguiano A, Jones M. Concurrent triplication and uniparental isodisomy: evidence for microhomology-mediated break-induced replication model for genomic rearrangements. Eur J Hum Genet 2014; 23:61-6. [PMID: 24713661 DOI: 10.1038/ejhg.2014.53] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 02/17/2014] [Accepted: 02/19/2014] [Indexed: 12/11/2022] Open
Abstract
Whole-genome oligonucleotide single-nucleotide polymorphism (oligo-SNP) arrays enable simultaneous interrogation of copy number variations (CNVs), copy neutral regions of homozygosity (ROH) and uniparental disomy (UPD). Structural variation in the human genome contributes significantly to genetic variation, and often has deleterious effects leading to disease causation. Co-occurrence of CNV and regions of allelic homozygosity in tandem involving the same chromosomal arm are extremely rare. Replication-based mechanisms such as microhomology-mediated break-induced replication (MMBIR) are recent models predicted to induce structural rearrangements and gene dosage aberrations; however, supportive evidence in humans for one-ended DNA break repair coupled with MMBIR giving rise to interstitial copy number gains and distal loss of heterozygosity has not been documented. We report on the identification and characterization of two cases with interstitial triplication followed by uniparental isodisomy (isoUPD) for remainder of the chromosomal arm. Case 1 has a triplication at 9q21.11-q21.33 and segmental paternal isoUPD for 9q21.33-qter, and presented with citrullinemia with a homozygous mutation in the argininosuccinate synthetase gene (ASS1 at 9q34.1). Case 2 has a triplication at 22q12.1-q12.2 and segmental maternal isoUPD 22q12.2-qter, and presented with hearing loss, mild dysmorphic features and bilateral iris coloboma. Interstitial triplication coupled with distal segmental isoUPD is a novel finding that provides human evidence for one-ended DNA break and replication-mediated repair. Both copy number gains and isoUPD may contribute to the phenotype. Significantly, these cases represent the first detailed genomic analysis that provides support for a MMBIR mechanism inducing copy number gains and segmental isoUPD in tandem.
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Affiliation(s)
- Trilochan Sahoo
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Jia-Chi Wang
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | | | - Pedro Sanchez-Lara
- Children's Hospital Los Angeles, Division of Medical Genetics, Los Angeles, CA, USA
| | - Leslie P Ross
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Loretta W Mahon
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Katayoun Hafezi
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Abigail Deming
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Lynne Hinman
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Yovana Bruno
- White Memorial Medical Center, Los Angeles, CA, USA
| | - James A Bartley
- Children's Hospital Los Angeles, Division of Medical Genetics, Los Angeles, CA, USA
| | | | - Arturo Anguiano
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Marilyn Jones
- 1] Rady Children's Hospital, Division of Genetics/Dysmorphology, San Diego, CA, USA [2] University of California, San Diego, CA, USA
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36
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Malvestiti F, De Toffol S, Grimi B, Chinetti S, Marcato L, Agrati C, Di Meco AM, Frascoli G, Trotta A, Malvestiti B, Ruggeri A, Dulcetti F, Maggi F, Simoni G, Grati FR. De novo
small supernumerary marker chromosomes detected on 143 000 consecutive prenatal diagnoses: chromosomal distribution, frequencies, and characterization combining molecular cytogenetics approaches. Prenat Diagn 2014; 34:460-8. [DOI: 10.1002/pd.4330] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 01/08/2014] [Accepted: 01/08/2014] [Indexed: 01/13/2023]
Affiliation(s)
- Francesca Malvestiti
- Research and Development, Cytogenetics and Molecular Biology; TOMA Advanced Biomedical Assays; Busto Arsizio Varese Italy
| | - Simona De Toffol
- Research and Development, Cytogenetics and Molecular Biology; TOMA Advanced Biomedical Assays; Busto Arsizio Varese Italy
| | - Beatrice Grimi
- Research and Development, Cytogenetics and Molecular Biology; TOMA Advanced Biomedical Assays; Busto Arsizio Varese Italy
| | - Sara Chinetti
- Research and Development, Cytogenetics and Molecular Biology; TOMA Advanced Biomedical Assays; Busto Arsizio Varese Italy
| | - Livia Marcato
- Research and Development, Cytogenetics and Molecular Biology; TOMA Advanced Biomedical Assays; Busto Arsizio Varese Italy
| | - Cristina Agrati
- Research and Development, Cytogenetics and Molecular Biology; TOMA Advanced Biomedical Assays; Busto Arsizio Varese Italy
| | - Anna Maria Di Meco
- Research and Development, Cytogenetics and Molecular Biology; TOMA Advanced Biomedical Assays; Busto Arsizio Varese Italy
| | - Giuditta Frascoli
- Research and Development, Cytogenetics and Molecular Biology; TOMA Advanced Biomedical Assays; Busto Arsizio Varese Italy
| | - Anna Trotta
- Research and Development, Cytogenetics and Molecular Biology; TOMA Advanced Biomedical Assays; Busto Arsizio Varese Italy
| | - Barbara Malvestiti
- Research and Development, Cytogenetics and Molecular Biology; TOMA Advanced Biomedical Assays; Busto Arsizio Varese Italy
| | - Anna Ruggeri
- Research and Development, Cytogenetics and Molecular Biology; TOMA Advanced Biomedical Assays; Busto Arsizio Varese Italy
| | - Francesca Dulcetti
- Research and Development, Cytogenetics and Molecular Biology; TOMA Advanced Biomedical Assays; Busto Arsizio Varese Italy
| | - Federico Maggi
- Research and Development, Cytogenetics and Molecular Biology; TOMA Advanced Biomedical Assays; Busto Arsizio Varese Italy
| | - Giuseppe Simoni
- Research and Development, Cytogenetics and Molecular Biology; TOMA Advanced Biomedical Assays; Busto Arsizio Varese Italy
| | - Francesca Romana Grati
- Research and Development, Cytogenetics and Molecular Biology; TOMA Advanced Biomedical Assays; Busto Arsizio Varese Italy
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37
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Neira VA, Romero-Espinoza P, Rojas-Martínez A, Ortiz-López R, Córdova-Fletes C, Plaja A, Barros-Núñez P. De novo MECP2 disomy in a Mexican male carrying a supernumerary marker chromosome and no typical Lubs syndrome features. Gene 2013; 524:381-5. [PMID: 23639959 DOI: 10.1016/j.gene.2013.04.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 04/02/2013] [Accepted: 04/03/2013] [Indexed: 10/26/2022]
Abstract
Xq28 duplication, including the MECP2 gene, is among the most frequently identified Xq subtelomeric rearrangements. The resulting clinical phenotype is named Lubs syndrome and mainly consists of intellectual disability, congenital hypotonia, absent speech, recurrent infections, and seizures. Here we report a Mexican male patient carrying a supernumerary marker chromosome with de novo Xq28 gain. By MLPA, duplication of MECP2, GDI1, and SLC6A8 was found and a subsequent a-CGH analysis demonstrated that the gain spanned ~2.1Mb. Despite gain of the MECP2 gene, the features of this patient do not evoke Lubs syndrome. Probably the mosaicism of the supernumerary marker chromosome is modifying the phenotype in this patient.
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Affiliation(s)
- Vivian Alejandra Neira
- División de Genética, Centro de Investigación Biomédica de Occidente, CMNO-IMSS, Guadalajara, Jalisco, Mexico
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38
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Wang JC, Vaccarello-Cruz M, Ross L, Owen R, Pratt VM, Lightman K, Liu Y, Hafezi K, Cherif D, Sahoo T. Mosaic isochromosome 15q and maternal uniparental isodisomy for chromosome 15 in a patient with morbid obesity and variant PWS-like phenotype. Am J Med Genet A 2013; 161A:1695-701. [DOI: 10.1002/ajmg.a.35939] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 02/18/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Jia-Chi Wang
- Cytogenetics Laboratory, Quest Diagnostics Nichols Institute; San Juan Capistrano, California
| | | | - Leslie Ross
- Cytogenetics Laboratory, Quest Diagnostics Nichols Institute; San Juan Capistrano, California
| | - Renius Owen
- Cytogenetics Laboratory, Quest Diagnostics Nichols Institute; San Juan Capistrano, California
| | - Victoria M. Pratt
- Molecular Genetics, Quest Diagnostics Nichols Institute; Chantilly, Virginia
| | | | - Yan Liu
- Cytogenetics Laboratory, Quest Diagnostics Nichols Institute; San Juan Capistrano, California
| | - Katayoun Hafezi
- Cytogenetics Laboratory, Quest Diagnostics Nichols Institute; San Juan Capistrano, California
| | - Dhia Cherif
- Cytogenetics Laboratory, Quest Diagnostics Nichols Institute; San Juan Capistrano, California
| | - Trilochan Sahoo
- Cytogenetics Laboratory, Quest Diagnostics Nichols Institute; San Juan Capistrano, California
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39
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Liehr T, Klein E, Mrasek K, Kosyakova N, Guilherme R, Aust N, Venner C, Weise A, Hamid A. Clinical Impact of Somatic Mosaicism in Cases with Small Supernumerary Marker Chromosomes. Cytogenet Genome Res 2013; 139:158-63. [DOI: 10.1159/000346026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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40
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Ou J, Wang W, Liehr T, Klein E, Hamid AB, Wang F, Duan C, Li H. Characterization of three small supernumerary marker chromosomes (sSMC) in humans. J Matern Fetal Neonatal Med 2012; 26:106-8. [PMID: 23013067 DOI: 10.3109/14767058.2012.732129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In the present study, three prenatally detected small supernumerary marker chromosomes (sSMC) were identified by banding cytogenetics and characterized in detail by molecular cytogenetics. In one case an sSMC(10) leading to a pericentric partial trisomy and in two cases heterochromatic sSMC derived from chromosome 22 were characterized. Outcomes were reportedly normal for two of the three cases for whom this information was known.
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Affiliation(s)
- Jian Ou
- Nanjing Medical University Affiliated Suzhou Hospital, Suzhou Municipal Hospital, Jiangsu, China
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41
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Reddy KS, Aradhya S, Meck J, Tiller G, Abboy S, Bass H. A systematic analysis of small supernumerary marker chromosomes using array CGH exposes unexpected complexity. Genet Med 2012; 15:3-13. [PMID: 22935720 DOI: 10.1038/gim.2012.78] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
PURPOSE A small supernumerary marker chromosome is often seen in patients with developmental disorders. Prior to array-based comparative genomic hybridization markers were rarely genotyped end to end. In this study, a valid genotype-to-phenotype correlation was possible because the supernumerary marker chromosomes were fully characterized by array-based comparative genomic hybridization in a genome-wide analysis. METHODS Ten consecutive de novo small supernumerary marker chromosome cases were systematically genotyped using G-banding, C-banding, AgNOR staining, whole-genome array-based comparative genomic hybridization, and fluorescence in situ hybridization. RESULTS Among 10 small supernumerary marker chromosome cases studied, 4 (40%) were not identified by array-based comparative genomic hybridization because of low-level mosaicism or because they lacked euchromatin. One case (10%) was a simple pericentromeric marker extending from 5p13.3 to 5q11.2. Five (50%) markers showed unexpected complexity. Two cases had markers that were derivative acrocentric (AgNOR+) chromosomes with the euchromatin from chromosomes 18p or 19p. Each of the other three cases with complex markers had unusual characteristics including a marker from noncontiguous segments of chromosome 19q, a highly complex rearrangement involving a chromosome 20 homolog as well as the small supernumerary marker chromosome, and a mosaic duplication of a proximal 8p marker. CONCLUSION Small supernumerary marker chromosomes are frequently complex on the basis of our small sample. Whole-genome array-based comparative genomic hybridization characterization of the small supernumerary marker chromosome provided informed genetic counseling.
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Affiliation(s)
- Kavita S Reddy
- Medical Genetics and Genomics Laboratory, Kaiser Permanente Southern California, Los Angeles, California, USA.
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42
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Klein E, Manvelyan M, Simonyan I, Hamid AB, Guilherme RS, Liehr T, Karamysheva T. Centromeric association of small supernumerary marker chromosomes with their sister-chromosomes detected by three dimensional molecular cytogenetics. Mol Cytogenet 2012; 5:15. [PMID: 22413994 PMCID: PMC3313875 DOI: 10.1186/1755-8166-5-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 03/14/2012] [Indexed: 11/19/2022] Open
Abstract
Background Small supernumerary marker chromosomes (sSMC) are detected in 0.043% of general population and can be characterized for their chromosomal origin, genetic content and shape by molecular cytogenetic approaches. Even though recently progress was achieved towards genotype-phenotype-correlations of sSMC, nothing is known on the influence that an additional derivative extra chromosome has on the nuclear architecture. Results Here we present the first three-dimensional interphase fluorescence in situ hybridization (FISH) studies for the nuclear architecture of sSMC. It could be shown that sSMC derived from chromosomes 15, 16 or 18 preferentially colocalized with one of their corresponding sister chromosomes. This was true in B- and T-lymphocytes as well as in skin fibroblasts. Additionally, a case with a complex sSMC with a karyotype 47,XY,+der(18)t(8;18)(8p23.2 ~ 23.1;18q11.1) was studied. Here the sSMC co-localized with one homologous chromosome 8 instead of 18. Conclusion Overall, there is a kind of "attraction" between an sSMC and one of its homologous sister chromosomes. This seems to be transmitted by the euchromatic part of the sSMC rather than its heterochromatic one.
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Affiliation(s)
- Elisabeth Klein
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany.
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Weise A, Mrasek K, Klein E, Mulatinho M, Llerena JC, Hardekopf D, Pekova S, Bhatt S, Kosyakova N, Liehr T. Microdeletion and microduplication syndromes. J Histochem Cytochem 2012; 60:346-58. [PMID: 22396478 DOI: 10.1369/0022155412440001] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The widespread use of whole genome analysis based on array comparative genomic hybridization in diagnostics and research has led to a continuously growing number of microdeletion and microduplication syndromes (MMSs) connected to certain phenotypes. These MMSs also include increasing instances in which the critical region can be reciprocally deleted or duplicated. This review catalogues the currently known MMSs and the corresponding critical regions including phenotypic consequences. Besides the pathogenic pathways leading to such rearrangements, the different detection methods and their limitations are discussed. Finally, the databases available for distinguishing between reported benign or pathogenic copy number alterations are highlighted. Overall, a review of MMSs that previously were also denoted "genomic disorders" or "contiguous gene syndromes" is given.
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Affiliation(s)
- Anja Weise
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany.
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Yu S, Fiedler S, Brawner S, Joyce J, Zhou X, Liu H. Characterizing Small Supernumerary Marker Chromosomes with Combination of Multiple Techniques. Cytogenet Genome Res 2011; 136:6-14. [DOI: 10.1159/000334271] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2011] [Indexed: 01/24/2023] Open
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