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El Amrani Z, Elalaoui SC, Jdioui W, Sbiti A, Ratbi I, Liehr T, Sefiani A, Natiq A. Complex translocation leading to13q interstitial deletion in a Moroccan child with retinoblastoma and intellectual disability. Ophthalmic Genet 2022; 43:689-692. [PMID: 35658784 DOI: 10.1080/13816810.2022.2083183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Retinoblastoma (RB) is the most common malignant intraocular tumor in children; it affects their eyes often even prenatally. RB may be sporadic or familial, due to germinal mutation in RB1 gene or by abnormal chromosomal abnormalities involving RB1 gene, located in 13q14. Monosomy of subband 13q14 as a partial deletion can also be responsible for RB with additional symptoms. The latter may be RB associated with psychomotor retardation, macrocephaly, broad forehead, thick earlobes, and bulbous nose. MATERIALS AND METHODS We present here the case of a boy from a consanguineous marriage with bilateral retinoblastoma, intellectual disability and facial dysmorphic features. Classical and molecular cytogenetics were used to recognize genotype-phenotype association. RESULTS The karyotype showed a three way translocation involving chromosomes 5, 12 and 13. Further molecular cytogenetics analysis revealed a deletion of 13q14 involving the tumor suppressor gene RB1. CONCLUSION This case highlights the impact of classical and molecular cytogenetics in diagnosis of rare genetic syndromes and for the genetic counselling of patients and their families. Pure molecular karyotyping analyses would miss the underlying chromosomal mechanism leading to the rearrangement.
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Affiliation(s)
- Zhour El Amrani
- RABAT Research team in genomics and molecular epidemiology of genetic diseases, Genomics Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco.,Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Morocco
| | - Siham Chafai Elalaoui
- RABAT Research team in genomics and molecular epidemiology of genetic diseases, Genomics Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco.,Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Morocco
| | - Wafae Jdioui
- médicale, Centre des consultations et des explorations externes, Hopital d'enfants, CHU Ibn SinaConsultation de génétique, Rabat, Marocco
| | - Aziza Sbiti
- RABAT Research team in genomics and molecular epidemiology of genetic diseases, Genomics Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco.,Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Morocco
| | - Ilham Ratbi
- RABAT Research team in genomics and molecular epidemiology of genetic diseases, Genomics Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco.,Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Morocco
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Abdelaziz Sefiani
- RABAT Research team in genomics and molecular epidemiology of genetic diseases, Genomics Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco.,Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Morocco
| | - Abdelhafid Natiq
- RABAT Research team in genomics and molecular epidemiology of genetic diseases, Genomics Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco.,Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Morocco
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2
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Moysés-Oliveira M, Giannuzzi G, Fish RJ, Rosenfeld JA, Petit F, Soares MDF, Kulikowski LD, Di-Battista A, Zamariolli M, Xia F, Liehr T, Kosyakova N, Carvalheira G, Parker M, Seaby EG, Ennis S, Gilbert RD, Hagelstrom RT, Cremona ML, Li WL, Malhotra A, Chandrasekhar A, Perry DL, Taft RJ, McCarrier J, Basel DG, Andrieux J, Stumpp T, Antunes F, Pereira GJ, Neerman-Arbez M, Meloni VA, Drummond-Borg M, Melaragno MI, Reymond A. Inactivation of AMMECR1 is associated with growth, bone, and heart alterations. Hum Mutat 2017; 39:281-291. [PMID: 29193635 DOI: 10.1002/humu.23373] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/18/2017] [Accepted: 11/18/2017] [Indexed: 01/26/2023]
Abstract
We report five individuals with loss-of-function of the X-linked AMMECR1: a girl with a balanced X-autosome translocation and inactivation of the normal X-chromosome; two boys with maternally inherited and de novo nonsense variants; and two half-brothers with maternally inherited microdeletion variants. They present with short stature, cardiac and skeletal abnormalities, and hearing loss. Variants of unknown significance in AMMECR1 in four male patients from two families with partially overlapping phenotypes were previously reported. AMMECR1 is coexpressed with genes implicated in cell cycle regulation, five of which were previously associated with growth and bone alterations. Our knockdown of the zebrafish orthologous gene resulted in phenotypes reminiscent of patients' features. The increased transcript and encoded protein levels of AMMECR1L, an AMMECR1 paralog, in the t(X;9) patient's cells indicate a possible partial compensatory mechanism. AMMECR1 and AMMECR1L proteins dimerize and localize to the nucleus as suggested by their nucleic acid-binding RAGNYA folds. Our results suggest that AMMECR1 is potentially involved in cell cycle control and linked to a new syndrome with growth, bone, heart, and kidney alterations with or without elliptocytosis.
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Affiliation(s)
- Mariana Moysés-Oliveira
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Giuliana Giannuzzi
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Richard J Fish
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Florence Petit
- Clinique de Génétique, CHU Lille - Hôpital Jeanne de Flandre, Lille, France
| | | | - Leslie Domenici Kulikowski
- Department of Pathology, Laboratório de Citogenômica, LIM 03, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Adriana Di-Battista
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Thomas Liehr
- Universitätsklinikum Jena, Institut für Humangenetik, Jena, Germany
| | | | - Gianna Carvalheira
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Michael Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Sheffield, United Kingdom
| | - Eleanor G Seaby
- Genomic Informatics Group, University Hospital Southampton, Southampton, United Kingdom
| | - Sarah Ennis
- Genomic Informatics Group, University Hospital Southampton, Southampton, United Kingdom
| | - Rodney D Gilbert
- Southampton Children's Hospital, University Hospital Southampton, Southampton, United Kingdom
| | | | - Maria L Cremona
- Illumina Clinical Services Laboratory, San Diego, California
| | - Wenhui L Li
- Illumina Clinical Services Laboratory, San Diego, California
| | - Alka Malhotra
- Illumina Clinical Services Laboratory, San Diego, California
| | | | - Denise L Perry
- Illumina Clinical Services Laboratory, San Diego, California
| | - Ryan J Taft
- Illumina Clinical Services Laboratory, San Diego, California
| | - Julie McCarrier
- Department of Pediatrics, Section of Genetics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Donald G Basel
- Department of Pediatrics, Section of Genetics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Joris Andrieux
- Institut de Génétique Médicale, CHU Lille - Hôpital Jeanne de Flandre, Lille, France
| | - Taiza Stumpp
- Developmental Biology Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fernanda Antunes
- Department of Pharmacology, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gustavo José Pereira
- Department of Pharmacology, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Marguerite Neerman-Arbez
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Vera Ayres Meloni
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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3
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Savić I, Ćirović D, Bugarski-Stanojević V. Exceptional Chromosomal Evolution and Cryptic Speciation of Blind Mole Rats Nannospalax leucodon (Spalacinae, Rodentia) from South-Eastern Europe. Genes (Basel) 2017; 8:E292. [PMID: 29068425 PMCID: PMC5704205 DOI: 10.3390/genes8110292] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/12/2017] [Accepted: 10/17/2017] [Indexed: 01/13/2023] Open
Abstract
Mole rats are exclusively subterranean and highly specialized rodents. Their long lifespans, remarkable anti-cancer mechanisms, and various distinctive adaptive features make them a useful research model. Moreover, opposing convergence of morphological traits, they have developed extremely high karyotype variability. Thus, 74 chromosomal forms have been described so far and new ones are being revealed continuously. These evolved during the process of rapid radiation and occur in different biogeographical regions. During research into their reproductive biology we have already provided substantial evidence for species-level separation of these taxa. Here, we review diverse chromosomal forms of the lesser blind mole rat, Mediterranean Nannospalax leucodon, distributed in South-eastern Europe, their karyotype records, biogeography, origin, and phylogeny from our extensive research. In the light of new data from molecular genetic studies, we question some former valuations and propose a cryptospecies rank for seven reproductively isolated chromosomal forms with sympatric and parapatric distribution and clear ecogeographical discrepances in their habitats, as well as new experimental and theoretical methods for understanding the courses of speciation of these unique fossorial mammals.
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Affiliation(s)
- Ivo Savić
- Biological Faculty, University of Belgrade, 11000 Belgrade, Serbia.
| | - Duško Ćirović
- Biological Faculty, University of Belgrade, 11000 Belgrade, Serbia.
| | - Vanja Bugarski-Stanojević
- Institute for Biological Research "Siniša Stanković", University of Belgrade, 11060 Belgrade, Serbia.
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4
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Donat M, Louis A, Kreskowski K, Ziegler M, Weise A, Schreyer I, Liehr T. X-autosome and X-Y Translocations in Female Carriers: X-chromosome Inactivation Easily Detectable by 5-ethynyl-2-deoxyuridine (EdU). Balkan J Med Genet 2017; 20:87-90. [PMID: 28924545 PMCID: PMC5596826 DOI: 10.1515/bjmg-2017-0012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Here we report one new case each of an X-autosome translocation (maternally derived), and an X-Y-chromosome translocation. Besides characterizing the involved breakpoints and/or imbalances in detail by molecular cyto-genetics, also skewed X-chromosome inactivation was determined on single cell level using 5-ethynyl-2-deoxyuridine (EdU). Thus, we confirmed that the recently suggested EdU approach can be simply adapted for routine diagnostic use. The latter is important, as only by knowing the real pattern of the skewed X-chromosome inactivation, correct interpretation of obtained results and subsequent reliable genetic counseling, can be done.
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Affiliation(s)
- M Donat
- Universtätsklinikum Jena, Institut für Humangenetik, Jena, Germany
| | - A Louis
- Labor für Humangenetische Diagnostik, Heidelberg, Germany
| | - K Kreskowski
- Universtätsklinikum Jena, Institut für Humangenetik, Jena, Germany
| | - M Ziegler
- Universtätsklinikum Jena, Institut für Humangenetik, Jena, Germany
| | - A Weise
- Universtätsklinikum Jena, Institut für Humangenetik, Jena, Germany
| | - I Schreyer
- Universtätsklinikum Jena, Institut für Humangenetik, Jena, Germany.,Jena University Hospital, Center for Ambulant Medicine, Jena, Germany
| | - T Liehr
- Universtätsklinikum Jena, Institut für Humangenetik, Jena, Germany
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5
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Liehr T, Othman MAK, Rittscher K. Multicolor Karyotyping and Fluorescence In Situ Hybridization-Banding (MCB/mBAND). Methods Mol Biol 2017; 1541:181-187. [PMID: 27910024 DOI: 10.1007/978-1-4939-6703-2_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Multicolor fluorescence in situ hybridization (mFISH) approaches are routine applications in tumor as well as clinical cytogenetics nowadays. The first approach when thinking about mFISH is multicolor karyotyping using human whole chromosome paints as probes; this can be achieved by narrow-band filter-based multiplex-FISH (M-FISH) or interferometer/spectroscopy-based spectral karyotyping (SKY). Besides, various FISH-based banding approaches were reported in the literature, including multicolor banding (MCB/mBAND) the latter being evaluated by narrow-band filters, and using specific software. Here, we describe the combined application of multicolor karyotyping and MCB/mBAND for the characterization of simple and complex acquired chromosomal changes in cancer cytogenetics.
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Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743, Jena, Germany.
| | - Moneeb A K Othman
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743, Jena, Germany
| | - Katharina Rittscher
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743, Jena, Germany
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6
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Amasdl S, Natiq A, Elalaoui SC, Sbiti A, Liehr T, Sefiani A. Insulin-like growth factor type 1 deficiency in a Moroccan patient with de novo inverted duplication 9p24p12 and developmental delay: a case report. J Med Case Rep 2016; 10:122. [PMID: 27178284 PMCID: PMC4868013 DOI: 10.1186/s13256-016-0830-x] [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: 01/22/2016] [Accepted: 02/11/2016] [Indexed: 11/30/2022] Open
Abstract
Background 9p duplication is a structural chromosome abnormality, described in more than 150 patients to date. In most cases the duplicated segment was derived from a parent being a reciprocal translocation carrier. However, about 15 cases with de novo 9p duplication have been reported previously. Clinically, this condition is characterized by mental retardation, short stature, developmental delay, facial dysmorphism, hand and toe anomalies, heart defects and/or ocular manifestations. Case presentation We report here the case of a 2-year-old Moroccan girl with a de novo duplication of 9p24 to p12. Clinical manifestations included failure to thrive, psychomotor delay, microcephaly, dysmorphic features, equinus feet, and umbilical hernia. Further clinical investigations showed an insulin-like growth factor type 1 deficiency. Banding cytogenetics identified a derivative chromosome 9, with an abnormally elongated short arm. Molecular cytogenetics based on multicolor banding probes characterized an inverted duplication 9p24 to p12 involving several genes especially an insulin-like growth factor binding protein named insulin-like growth factor binding protein-like 1, which seemed to be overexpressed, leading to the insulin-like growth factor deficiency in our patient. Conclusions This study showed that insulin-like growth factor type 1 deficiency can be another feature of 9p duplication, suggesting a likely involvement of insulin-like growth factor binding protein-like 1 overexpression in growth delay. However, further studies of the gene expressions are needed to better understand the phenotype-karyotype correlations.
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Affiliation(s)
- Saadia Amasdl
- Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie, Université Mohammed V Souissi, Rabat, Morocco. .,Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Morocco.
| | - Abdelhafid Natiq
- Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Morocco.,Faculté des Sciences, Université Mohammed V, Agdal, Rabat, Morocco
| | | | - Aziza Sbiti
- Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Morocco
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Abdelaziz Sefiani
- Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie, Université Mohammed V Souissi, Rabat, Morocco.,Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Morocco
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Liehr T, Othman MAK, Rittscher K, Alhourani E. The current state of molecular cytogenetics in cancer diagnosis. Expert Rev Mol Diagn 2015; 15:517-26. [PMID: 25664836 DOI: 10.1586/14737159.2015.1013032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Cytogenetics and molecular cytogenetics are and will continue to be indispensable tools in cancer diagnostics. Leukemia and lymphoma diagnostics are still emphases of routine (molecular) cytogenetics and corresponding studies of solid tumors gain more and more prominence. Here, first a historical perspective of molecular tumor cytogenetics is provided, which is followed by the basic principles of the fluorescence in situ hybridization (FISH) approach. Finally the current state of molecular cytogenetics in cancer diagnostics is discussed. Nowadays routine diagnostics includes basic FISH approaches rather than multicolor-FISH. The latter together with modern high-throughput methods have their impact on research to identify new tumor-associated genomic regions.
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Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, Postfach, D-07743 Jena, Germany
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New BAC probe set to narrow down chromosomal breakpoints in small and large derivative chromosomes, especially suited for mosaic conditions. Methods Mol Biol 2014; 1227:279-87. [PMID: 25239752 DOI: 10.1007/978-1-4939-1652-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Fluorescence in situ hybridization (FISH) and/or array-comparative genomic hybridization (aCGH) performed after initial banding cytogenetics is still the gold standard for detection of chromosomal rearrangements. Although aCGH provides a higher resolution, FISH has two main advantages over the array-based approaches: (1) it can be applied to characterize balanced as well as unbalanced rearrangements, whereas aCGH is restricted to unbalanced ones, and (2) chromosomal aberrations present in low level or complex mosaics can be characterized by FISH without any problems, while aCGH requires presence of over 50 % of aberrant cells in the sample for detection. Recently, a new FISH-based probe set was presented: the so-called pericentric-ladder-FISH (PCL-FISH) that enables characterization of chromosomal breakpoints especially in mosaic small supernumerary marker chromosomes (sSMC). It can also be applied on large inborn or acquired derivative chromosomes. The main feature of this set is that the probes are applied in a chromosome-specific manner and they align along the chromosome in average intervals of ten megabasepairs. Hence PCL-FISH provides denser coverage and a more precise anchorage on the human DNA-sequence than most other FISH-banding approaches.
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van Binsbergen E, Ellis RJ, Abdelmalik N, Jarvis J, Randhawa K, Wyatt-Ashmead J, Canham N, Thorpe-Beeston JG, Mancini GMS, Van Haelst MM. A fetus with de novo 2q33.2q35 deletion including MAP2 with brain anomalies, esophageal atresia, and laryngeal stenosis. Am J Med Genet A 2013; 164A:194-8. [PMID: 24243657 DOI: 10.1002/ajmg.a.36202] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 08/02/2013] [Indexed: 12/29/2022]
Abstract
Deletions of the long arm of chromosome 2 are rare. Few cases of interstitial deletions of the 2q33q35 region have been reported. Individuals with deletions in this region have growth retardation, psychomotor retardation, micrognathia, microcephaly, and apparently low-set ears. We describe a female fetus with a de novo deletion of 2q33.2 to q35 with delayed gyral formation with widespread neuronal heterotopia of the white matter, small cerebellum, esophageal atresia, laryngeal stenosis, micrognathia, and intrauterine growth retardation. With the use of karyotyping and high-resolution array comparative genomic hybridization the boundaries and gene content of the deletion were identified. Our aim was to determine whether a candidate gene for the brain phenotype was present in the deletion. By this means and based on literature we pinpointed the microtubule associated gene MAP2 as a candidate for the brain anomalies.
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Affiliation(s)
- Ellen van Binsbergen
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
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10
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Castronovo C, Valtorta E, Crippa M, Tedoldi S, Romitti L, Amione MC, Guerneri S, Rusconi D, Ballarati L, Milani D, Grosso E, Cavalli P, Giardino D, Bonati MT, Larizza L, Finelli P. Design and validation of a pericentromeric BAC clone set aimed at improving diagnosis and phenotype prediction of supernumerary marker chromosomes. Mol Cytogenet 2013; 6:45. [PMID: 24171812 PMCID: PMC4176193 DOI: 10.1186/1755-8166-6-45] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 10/08/2013] [Indexed: 12/17/2022] Open
Abstract
Background Small supernumerary marker chromosomes (sSMCs) are additional, structurally abnormal chromosomes, generally smaller than chromosome 20 of the same metaphase spread. Due to their small size, they are difficult to characterize by conventional cytogenetics alone. In regard to their clinical effects, sSMCs are a heterogeneous group: in particular, sSMCs containing pericentromeric euchromatin are likely to be associated with abnormal outcomes, although exceptions have been reported. To improve characterization of the genetic content of sSMCs, several approaches might be applied based on different molecular and molecular-cytogenetic assays, e.g., fluorescent in situ hybridization (FISH), array-based comparative genomic hybridization (array CGH), and multiplex ligation-dependent probe amplification (MLPA). To provide a complementary tool for the characterization of sSMCs, we constructed and validated a new, FISH-based, pericentromeric Bacterial Artificial Chromosome (BAC) clone set that with a high resolution spans the most proximal euchromatic sequences of all human chromosome arms, excluding the acrocentric short arms. Results By FISH analysis, we assayed 561 pericentromeric BAC probes and excluded 75 that showed a wrong chromosomal localization. The remaining 486 probes were used to establish 43 BAC-based pericentromeric panels. Each panel consists of a core, which with a high resolution covers the most proximal euchromatic ~0.7 Mb (on average) of each chromosome arm and generally bridges the heterochromatin/euchromatin junction, as well as clones located proximally and distally to the core. The pericentromeric clone set was subsequently validated by the characterization of 19 sSMCs. Using the core probes, we could rapidly distinguish between heterochromatic (1/19) and euchromatic (11/19) sSMCs, and estimate the euchromatic DNA content, which ranged from approximately 0.13 to more than 10 Mb. The characterization was not completed for seven sSMCs due to a lack of information about the covered region in the reference sequence (1/19) or sample insufficiency (6/19). Conclusions Our results demonstrate that this pericentromeric clone set is useful as an alternative tool for sSMC characterization, primarily in cases of very small SMCs that contain either heterochromatin exclusively or a tiny amount of euchromatic sequence, and also in cases of low-level or cryptic mosaicism. The resulting data will foster knowledge of human proximal euchromatic regions involved in chromosomal imbalances, thereby improving genotype–phenotype correlations.
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Affiliation(s)
- Chiara Castronovo
- Laboratorio di Citogenetica Medica e Genetica Molecolare, IRCCS Istituto Auxologico Italiano, via Ariosto 13, 20145, Milano, Italy.
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11
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Liehr T, Weise A, Hamid AB, Fan X, Klein E, Aust N, Othman MA, Mrasek K, Kosyakova N. Multicolor FISH methods in current clinical diagnostics. Expert Rev Mol Diagn 2013; 13:251-5. [PMID: 23570403 DOI: 10.1586/erm.12.146] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Multicolor FISH (mFISH) assays are currently indispensable for a precise description of derivative chromosomes. Routine application of such techniques on human chromosomes started in 1996 with the simultaneous use of all 24 human whole-chromosome painting probes in multiplex-FISH and spectral karyotyping. Since then, multiple approaches for chromosomal differentiation based on multicolor-FISH (MFISH) assays have been developed. Predominantly, they are applied to characterize marker or derivative chromosomes identified in conventional banding analysis. Since the introduction of array-based comparative genomic hybridization (aCGH), mFISH is also applied to verify and further delineate aCGH-detected aberrations. For the latter, it is important to consider the fact that aCGH cannot detect or characterize balanced rearrangements, which are important to be resolved in detail in infertility diagnostics. In addition, mFISH is necessary to distinguish different imbalanced situations detectable in aCGH; small supernumerary marker chromosomes have to be differentiated from insertions or unbalanced translocations. This review presents an overview on the available mFISH methods and their applications in pre- and post-natal clinical genetics.
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Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, Jena D-07743, Germany.
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12
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van Binsbergen E, Hochstenbach R, Giltay J, Swinkels M. Unstable transmission of a familial complex chromosome rearrangement. Am J Med Genet A 2012; 158A:2888-93. [DOI: 10.1002/ajmg.a.35580] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 06/25/2012] [Indexed: 02/06/2023]
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Hamid AB, Kreskowski K, Weise A, Kosayakova N, Mrasek K, Voigt M, Guilherme RS, Wagner R, Hardekopf D, Pekova S, Karamysheva T, Liehr T, Klein E. How to narrow down chromosomal breakpoints in small and large derivative chromosomes – a new probe set. J Appl Genet 2012; 53:259-69. [DOI: 10.1007/s13353-012-0098-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 04/05/2012] [Indexed: 01/07/2023]
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14
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Bucksch M, Ziegler M, Kosayakova N, Mulatinho MV, Mulhatino MV, Llerena JC, Morlot S, Fischer W, Polityko AD, Kulpanovich AI, Petersen MB, Belitz B, Trifonov V, Weise A, Liehr T, Hamid AB. A new multicolor fluorescence in situ hybridization probe set directed against human heterochromatin: HCM-FISH. J Histochem Cytochem 2012; 60:530-6. [PMID: 22511603 DOI: 10.1369/0022155412441708] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A new multicolor fluorescence in situ hybridization (mFISH) probe set is presented, and its possible applications are highlighted in 25 clinical cases. The so-called heterochromatin-M-FISH (HCM-FISH) probe set enables a one-step characterization of the large heterochromatic regions within the human genome. HCM-FISH closes a gap in the now available mFISH probe sets, as those do not normally cover the acrocentric short arms; the large pericentric regions of chromosomes 1, 9, and 16; as well as the band Yq12. Still, these regions can be involved in different kinds of chromosomal rearrangements such as translocations, insertions, inversions, amplifications, and marker chromosome formations. Here, examples are given for all these kinds of chromosomal aberrations, detected as constitutional rearrangements in clinical cases. Application perspectives of the probe set in tumors as well as in evolutionary cytogenetic studies are given.
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Affiliation(s)
- Maria Bucksch
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
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15
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Louis S, Benedek K, Mowat M, Klein G, Mai S. Elongated mouse chromosomes suitable for enhanced molecular cytogenetics. Cytotechnology 2011; 44:143-9. [PMID: 19003236 DOI: 10.1007/s10616-004-2978-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2004] [Accepted: 09/07/2004] [Indexed: 11/26/2022] Open
Abstract
Characterization of genetic disorders in humans and animal models requires identification of chromosomal aberrations. However, identifying fine deletions or insertion in metaphase chromosomes has been always a challenge due to limitations of resolution. In this study we developed a rapid method for chromosome elongation using two different intercalating agents: ethidium bromide and 5-bromo-2'-deoxyuridine (BrdU), together with a short-term mitotic block using colcemid. About 70% of the chromosomes from cells that underwent this elongation procedure reached three times longer than those prepared from control cells. FISH experiments using elongated chromosomes revealed a duplicated region of chromosome 11 that was not visible in cells prepared with conventional methods.
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Affiliation(s)
- Sherif Louis
- Manitoba Institute of Cell Biology, Cancer Care Manitoba, University of Manitoba, 675 McDermot Avenue, Winnipeg, MB, R3E 0V9, Canada
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16
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The progress on genetic analysis of nasopharyngeal carcinoma. Comp Funct Genomics 2010:57513. [PMID: 18288251 PMCID: PMC2233780 DOI: 10.1155/2007/57513] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Accepted: 12/09/2007] [Indexed: 12/14/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a rare malignancy in most parts of the world, but is one of the most common cancers in Southeast Asia. Both genetic and environmental factors contribute to the tumorigenesis of NPC, most notably the consumption of certain salted food items and Epstein-Barr virus infection. This review will focus on the current progress of the genetic analysis of NPC (genetic susceptibilities and somatic alterations). We will review the current advances in genomic technologies and their shaping of the future direction of NPC research.
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17
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Li Z, Zhang Q, Mao JH, Weise A, Mrasek K, Fan X, Zhang X, Liehr T, Lu KH, Balmain A, Cai WW. An HDAC1-binding domain within FATS bridges p21 turnover to radiation-induced tumorigenesis. Oncogene 2010; 29:2659-71. [DOI: 10.1038/onc.2010.19] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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18
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Vielfarben-Fluoreszenz-in-situ-Hybridisierung. MED GENET-BERLIN 2008. [DOI: 10.1007/s11825-008-0133-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Zusammenfassung
Die molekulare Zytogenetik ist ein wesentliches Instrument der Diagnostik und Forschung an menschlichen Chromosomen. Die Fluoreszenz-in-situ-Hybridisierung (FISH) ist hierbei die maßgebliche Technik. Seit Mitte der 1990er Jahre wurde eine Vielzahl verschiedener Vielfarben-FISH-Sondensets für unterschiedliche Fragestellungen etabliert und verfügbar gemacht. Im vorliegenden Beitrag wird diese Entwicklung aufgezeigt und dargestellt. Die der Vielfarben-FISH zugrunde liegenden Prinzipien, deren vielfältigen Spielarten und Anwendungen werden zusammengefasst. Schließlich wird eine Prognose bezüglich der Bedeutung der molekularen Zytogenetik im künftigen Zusammenspiel mit den Chiptechnologien getroffen.
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19
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Zhou X, Yu T, Cole SW, Wong DTW. Advancement in characterization of genomic alterations for improved diagnosis, treatment and prognostics in cancer. Expert Rev Mol Diagn 2007; 6:39-50. [PMID: 16359266 DOI: 10.1586/14737159.6.1.39] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Most human cancers are characterized by genetic instabilities. These instabilities manifest themselves as a series of genetic alterations, including discrete mutations and chromosomal aberrations. With the human genome deciphered, high-throughput technologies are rapidly advancing the field to generate genome-wide gene expression and mutation profiles that are highly correlative of biologic and disease phenotypes. While recent advancement in comprehensive genomic characterization presents an unprecedented opportunity for advancing the treatment of cancer, there are still many challenges that need to be overcome before we can fully utilize genomic markers and targets for cancer prediction, diagnostics, treatment and prognostics. This review describes recent advances in comprehensive genomic characterization at the DNA level, and considers some of the challenges that remain for defining the precise genomic portrait of tumors. Potential solutions that may help overcome these challenges are also offered.
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Affiliation(s)
- Xiaofeng Zhou
- Dental Research Institute, School of Dentistry & Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, USA.
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20
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Liehr T, Starke H, Heller A, Kosyakova N, Mrasek K, Gross M, Karst C, Steinhaeuser U, Hunstig F, Fickelscher I, Kuechler A, Trifonov V, Romanenko SA, Weise A. Multicolor fluorescence in situ hybridization (FISH) applied to FISH-banding. Cytogenet Genome Res 2006; 114:240-4. [PMID: 16954660 DOI: 10.1159/000094207] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Accepted: 09/13/2005] [Indexed: 11/19/2022] Open
Abstract
During the last decade not only multicolor fluorescence in situ hybridization (FISH) using whole chromosome paints as probes, but also numerous chromosome banding techniques based on FISH have been developed for the human and for the murine genome. This review focuses on such FISH-banding techniques, which were recently defined as 'any kind of FISH technique, which provide the possibility to characterize simultaneously several chromosomal subregions smaller than a chromosome arm. FISH-banding methods fitting that definition may have quite different characteristics, but share the ability to produce a DNA-specific chromosomal banding'. While the standard chromosome banding techniques like GTG lead to a protein-related black and white banding pattern, FISH-banding techniques are DNA-specific, more colorful and, thus, more informative. For some, even high-resolution FISH-banding techniques the development is complete and they can be used for whole genome hybridizations in one step. Other FISH-banding methods are only available for selected chromosomes and/or are still under development. FISH-banding methods have successfully been applied in research in evolution- and radiation-biology, as well as in studies on the nuclear architecture. Moreover, their suitability for diagnostic purposes has been proven in prenatal, postnatal and tumor cytogenetics, indicating that they are an important tool with the potential to partly replace the conventional banding techniques in the future.
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Affiliation(s)
- T Liehr
- Institute of Human Genetics and Anthropology, Friedrich Schiller University, Jena, Germany.
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21
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Liehr T, Gross M, Karst C, Glaser M, Mrasek K, Starke H, Weise A, Mkrtchyan H, Kuechler A. FISH banding in tumor cytogenetics. ACTA ACUST UNITED AC 2006; 164:88-9. [PMID: 16364770 DOI: 10.1016/j.cancergencyto.2005.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2005] [Accepted: 06/03/2005] [Indexed: 11/16/2022]
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22
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Trifonov V, Karst C, Claussen U, Mrasek K, Michel S, Avner P, Liehr T. Microdissection-derived murine mcb probes from somatic cell hybrids. J Histochem Cytochem 2005; 53:791-2. [PMID: 15928329 DOI: 10.1369/jhc.4b6598.2005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The multicolor-banding (mcb) technique is a fluorescence in situ hybridization (FISH)-banding approach, which is based on region-specific microdissection libraries producing changing fluorescence intensity ratios along the chromosomes. The latter are used to assign different pseudocolors to specific chromosomal regions. Here we present the first three available mcb-probe sets for the Mus musculus chromosomes 3, 6, and 18. In the present work, the creation of the microdissection libraries was done for the first time on mouse/human somatic cell hybrids. During creation of the mcb-probes, the latter enabled an unambiguous identification of the, otherwise in GTG-banding, hardly distinguishable murine chromosomes.
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Affiliation(s)
- Vladimir Trifonov
- Institut für Human Genetics and Anthropology, Postfach, D-07740 Jena, Germany
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23
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Filichev VV, Christensen UB, Pedersen EB, Babu BR, Wengel J. Locked nucleic acids and intercalating nucleic acids in the design of easily denaturing nucleic acids: thermal stability studies. Chembiochem 2005; 5:1673-9. [PMID: 15532065 DOI: 10.1002/cbic.200400222] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Intercalating nucleic acids (INA(R)s) with insertions of (R)-1-O-(1-pyrenylmethyl)glycerol were hybridized with locked nucleic acids (LNAs). INA/LNA duplexes were found to be less stable than the corresponding DNA/LNA duplexes when the INA monomer was inserted as a bulge close to the LNA monomers in the opposite strand. This property was used to make "quenched" complements that possess LNA in hairpins and in duplexes and are consequently more accessible for targeting native DNA. The duplex between a fully modified 13-mer LNA sequence and a complementary INA with six pyrene residues inserted after every second base as a bulge was found to be very unstable (Tm=30.1 degrees C) in comparison with the unmodified double-stranded DNA (Tm=48.7 degrees C) and the corresponding duplexes of LNA/DNA (Tm=81.6 degrees C) and INA/DNA (Tm=66.4 degrees C). A thermal melting experiment of a mixture of an LNA hairpin, with five LNA nucleotides in the stem, and its complementary DNA sequence gave a transition with an extremely low increase in optical density (hyperchromicity). When two INA monomers were inserted into the stem of the LNA hairpin, the same experiment resulted in a significant hyperchromicity comparable with the one obtained for the corresponding DNA/DNA duplex.
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Affiliation(s)
- Vyacheslav V Filichev
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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24
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Seidel J, Heller A, Senger G, Starke H, Chudoba I, Kelbova C, Tönnies H, Neitzel H, Haase C, Beensen V, Zintl F, Claussen U, Liehr T. A multiple translocation event in a patient with hexadactyly, facial dysmorphism, mental retardation and behaviour disorder characterised comprehensively by molecular cytogenetics. Case report and review of the literature. Eur J Pediatr 2003; 162:582-8. [PMID: 12819962 DOI: 10.1007/s00431-003-1254-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2002] [Revised: 04/14/2003] [Accepted: 04/22/2003] [Indexed: 11/30/2022]
Abstract
UNLABELLED We report a 13-year-old female patient with multiple congenital abnormalities (microcephaly, facial dysmorphism, anteverted dysplastic ears and postaxial hexadactyly), mental retardation, and adipose-gigantism. Ultrasonography revealed no signs of a heart defect or renal abnormalities. She showed no speech development and suffered from a behavioural disorder. CNS abnormalities were excluded by cerebral MRI. Initial cytogenetic studies by Giemsa banding revealed an aberrant karyotype involving three chromosomes, t(2;4;11). By high resolution banding and multicolour fluoresence in-situ hybridisation (M-FISH, MCB), chromosome 1 was also found to be involved in the complex chromosomal aberrations, confirming the karyotype 46,XX,t(2;11;4).ish t(1;4;2;11)(q43;q21.1;p12-p13.1;p14.1). To the best of our knowledge no patient has been previously described with such a complex translocation involving 4 chromosomes. This case demonstrates that conventional chromosome banding techniques such as Giemsa banding are not always sufficient to characterise complex chromosomal abnormalities. Only by the additional utilisation of molecular cytogenetic techniques could the complexity of the present chromosomal rearrangements and the origin of the involved chromosomal material be detected. Further molecular genetic studies will be performed to clarify the chromosomal breakpoints potentially responsible for the observed clinical symptoms. CONCLUSION This report demonstrates that multicolour-fluorescence in-situ hybridisation studies should be performed in patients with congenital abnormalities and suspected aberrant karyotypes in addition to conventional Giemsa banding.
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Affiliation(s)
- Jörg Seidel
- Department of Paediatrics, Friedrich-Schiller University, Kochstrasse 2, 07740 Jena, Germany.
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26
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Kuechler A, Weise A, Michel S, Schaeferhenrich A, Pool-Zobel BL, Claussen U, Liehr T. Precise breakpoint characterization of the colon adenocarcinoma cell line HT-29 clone 19A by means of 24-color fluorescence in situ hybridization and multicolor banding. Genes Chromosomes Cancer 2003; 36:207-10. [PMID: 12508250 DOI: 10.1002/gcc.10163] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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