1
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Grigelioniene G, Suzuki HI, Taylan F, Mirzamohammadi F, Borochowitz ZU, Ayturk UM, Tzur S, Horemuzova E, Lindstrand A, Weis MA, Grigelionis G, Hammarsjö A, Marsk E, Nordgren A, Nordenskjöld M, Eyre DR, Warman ML, Nishimura G, Sharp PA, Kobayashi T. Gain-of-function mutation of microRNA-140 in human skeletal dysplasia. Nat Med 2019; 25:583-590. [PMID: 30804514 PMCID: PMC6622181 DOI: 10.1038/s41591-019-0353-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/11/2019] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression. Heterozygous loss-of-function point mutations of miRNA genes are associated with several human congenital disorders1-5, but neomorphic (gain-of-new-function) mutations in miRNAs due to nucleotide substitutions have not been reported. Here we describe a neomorphic seed region mutation in the chondrocyte-specific, super-enhancer-associated MIR140 gene encoding microRNA-140 (miR-140) in a novel autosomal dominant human skeletal dysplasia. Mice with the corresponding single nucleotide substitution show skeletal abnormalities similar to those of the patients but distinct from those of miR-140-null mice6. This mutant miRNA gene yields abundant mutant miR-140-5p expression without miRNA-processing defects. In chondrocytes, the mutation causes widespread derepression of wild-type miR-140-5p targets and repression of mutant miR-140-5p targets, indicating that the mutation produces both loss-of-function and gain-of-function effects. Furthermore, the mutant miR-140-5p seed competes with the conserved RNA-binding protein Ybx1 for overlapping binding sites. This finding may explain the potent target repression and robust in vivo effect by this mutant miRNA even in the absence of evolutionary selection of miRNA-target RNA interactions, which contributes to the strong regulatory effects of conserved miRNAs7,8. Our study presents the first case of a pathogenic gain-of-function miRNA mutation and provides molecular insight into neomorphic actions of emerging and/or mutant miRNAs.
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Affiliation(s)
- Giedre Grigelioniene
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Hiroshi I Suzuki
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Fatemeh Mirzamohammadi
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Zvi U Borochowitz
- Rappaport Faculty of Medicine, Technion-Israeli Institute of Technology, Medical Genetics Clinics, Assuta Medical Center, Haifa, Israel
| | - Ugur M Ayturk
- Orthopaedic Research Labs, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA, USA
| | - Shay Tzur
- Laboratory of Molecular Medicine, Rambam Health Care Campus, Haifa, Israel.,Genomic Research Department, Emedgene Technologies, Tel Aviv, Israel
| | - Eva Horemuzova
- Department for Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Pediatric Endocrinology Unit, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Mary Ann Weis
- Department of Orthopedics and Sports Medicine, University of Washington, Seattle, WA, USA
| | - Gintautas Grigelionis
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Hammarsjö
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Elin Marsk
- Department of Otorhinolaryngology, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - David R Eyre
- Department of Orthopedics and Sports Medicine, University of Washington, Seattle, WA, USA
| | - Matthew L Warman
- Orthopaedic Research Labs, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA, USA
| | - Gen Nishimura
- Center for Intractable Diseases, Saitama Medical University Hospital, Saitama, Japan
| | - Phillip A Sharp
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tatsuya Kobayashi
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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2
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Nilsson D, Pettersson M, Gustavsson P, Förster A, Hofmeister W, Wincent J, Zachariadis V, Anderlid BM, Nordgren A, Mäkitie O, Wirta V, Käller M, Vezzi F, Lupski JR, Nordenskjöld M, Lundberg ES, Carvalho CMB, Lindstrand A. Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation. Hum Mutat 2017; 38:180-192. [PMID: 27862604 PMCID: PMC5225243 DOI: 10.1002/humu.23146] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/01/2016] [Indexed: 11/07/2022]
Abstract
Most balanced translocations are thought to result mechanistically from nonhomologous end joining or, in rare cases of recurrent events, by nonallelic homologous recombination. Here, we use low-coverage mate pair whole-genome sequencing to fine map rearrangement breakpoint junctions in both phenotypically normal and affected translocation carriers. In total, 46 junctions from 22 carriers of balanced translocations were characterized. Genes were disrupted in 48% of the breakpoints; recessive genes in four normal carriers and known dominant intellectual disability genes in three affected carriers. Finally, seven candidate disease genes were disrupted in five carriers with neurocognitive disabilities (SVOPL, SUSD1, TOX, NCALD, SLC4A10) and one XX-male carrier with Tourette syndrome (LYPD6, GPC5). Breakpoint junction analyses revealed microhomology and small templated insertions in a substantive fraction of the analyzed translocations (17.4%; n = 4); an observation that was substantiated by reanalysis of 37 previously published translocation junctions. Microhomology associated with templated insertions is a characteristic seen in the breakpoint junctions of rearrangements mediated by error-prone replication-based repair mechanisms. Our data implicate that a mechanism involving template switching might contribute to the formation of at least 15% of the interchromosomal translocation events.
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Affiliation(s)
- Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Peter Gustavsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Alisa Förster
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Wolfgang Hofmeister
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Josephine Wincent
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Vasilios Zachariadis
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Outi Mäkitie
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
- Children's Hospital, Helsinki University Central Hospital and University of Helsinki, 00290 Helsinki, Finland
- Folkhälsan Institute of Genetics, 00290 Helsinki, Finland
| | - Valtteri Wirta
- SciLifeLab, School of Biotechnology, KTH Royal Institute of Technology, 171 71 Stockholm, Sweden
| | - Max Käller
- SciLifeLab, School of Biotechnology, KTH Royal Institute of Technology, 171 71 Stockholm, Sweden
| | - Francesco Vezzi
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, 171 21 Stockholm, Sweden
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, 77030 Houston TX, USA
- Texas Children’s Hospital, 77030 Houston TX, USA
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Elisabeth Syk Lundberg
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Claudia M. B. Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, 77030 Houston TX, USA
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
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3
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Hofmeister W, Nilsson D, Topa A, Anderlid BM, Darki F, Matsson H, Tapia Páez I, Klingberg T, Samuelsson L, Wirta V, Vezzi F, Kere J, Nordenskjöld M, Syk Lundberg E, Lindstrand A. CTNND2-a candidate gene for reading problems and mild intellectual disability. J Med Genet 2014; 52:111-22. [PMID: 25473103 DOI: 10.1136/jmedgenet-2014-102757] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Cytogenetically visible chromosomal translocations are highly informative as they can pinpoint strong effect genes even in complex genetic disorders. METHODS AND RESULTS Here, we report a mother and daughter, both with borderline intelligence and learning problems within the dyslexia spectrum, and two apparently balanced reciprocal translocations: t(1;8)(p22;q24) and t(5;18)(p15;q11). By low coverage mate-pair whole-genome sequencing, we were able to pinpoint the genomic breakpoints to 2 kb intervals. By direct sequencing, we then located the chromosome 5p breakpoint to intron 9 of CTNND2. An additional case with a 163 kb microdeletion exclusively involving CTNND2 was identified with genome-wide array comparative genomic hybridisation. This microdeletion at 5p15.2 is also present in mosaic state in the patient's mother but absent from the healthy siblings. We then investigated the effect of CTNND2 polymorphisms on normal variability and identified a polymorphism (rs2561622) with significant effect on phonological ability and white matter volume in the left frontal lobe, close to cortical regions previously associated with phonological processing. Finally, given the potential role of CTNND2 in neuron motility, we used morpholino knockdown in zebrafish embryos to assess its effects on neuronal migration in vivo. Analysis of the zebrafish forebrain revealed a subpopulation of neurons misplaced between the diencephalon and telencephalon. CONCLUSIONS Taken together, our human genetic and in vivo data suggest that defective migration of subpopulations of neuronal cells due to haploinsufficiency of CTNND2 contribute to the cognitive dysfunction in our patients.
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Affiliation(s)
- Wolfgang Hofmeister
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Alexandra Topa
- Department of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Fahimeh Darki
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Hans Matsson
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Isabel Tapia Páez
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Torkel Klingberg
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Lena Samuelsson
- Department of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Valtteri Wirta
- SciLifeLab, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Francesco Vezzi
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden Molecular Neurology Research Program, University of Helsinki, and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Elisabeth Syk Lundberg
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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4
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Moysés-Oliveira M, Mancini TI, Takeno SS, Rodrigues ADS, Bachega TASS, Bertola D, Melaragno MI. Congenital adrenal hyperplasia, ovarian failure and Ehlers-Danlos syndrome due to a 6p deletion. Sex Dev 2014; 8:139-45. [PMID: 24970489 DOI: 10.1159/000363779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2014] [Indexed: 11/19/2022] Open
Abstract
Cryptic deletions in balanced de novo translocations represent a frequent cause of abnormal phenotypes, including Mendelian diseases. In this study, we describe a patient with multiple congenital abnormalities, such as late-onset congenital adrenal hyperplasia (CAH), primary ovarian failure and Ehlers-Danlos syndrome (EDS), who carries a de novo t(6;14)(p21;q32) translocation. Genomic array analysis identified a cryptic 1.1-Mb heterozygous deletion, adjacent to the breakpoint on chromosome 6, extending from 6p21.33 to 6p21.32 and affecting 85 genes, including CYP21A2,TNXB and MSH5. Multiplex ligation-dependent probe amplification analysis of the 6p21.3 region was performed in the patient and her family and revealed a 30-kb deletion in the patient's normal chromosome 6, inherited from her mother, resulting in homozygous loss of genes CYP21A1P and C4B. CYP21A2 sequencing showed that its promoter region was not affected by the 30-kb deletion, suggesting that the deletion of other regulatory sequences in the normal chromosome 6 caused a loss of function of the CYP21A2 gene. EDS and primary ovarian failure phenotypes could be explained by the loss of genes TNXB and MSH5, a finding that may contribute to the characterization of disease-causing genes. The detection of this de novo microdeletion drastically reduced the estimated recurrence risk for CAH in the family.
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Affiliation(s)
- Mariana Moysés-Oliveira
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
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5
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Mucciolo M, Magini P, Marozza A, Mongelli P, Mencarelli MA, Hayek G, Tavalazzi F, Mari F, Seri M, Renieri A, Graziano C. 9q31.1q31.3 deletion in two patients with similar clinical features: a newly recognized microdeletion syndrome? Am J Med Genet A 2013; 164A:685-90. [PMID: 24376033 DOI: 10.1002/ajmg.a.36361] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 10/12/2013] [Indexed: 11/07/2022]
Abstract
Interstitial deletions of the long arm of chromosome 9 are rare and most patients have been detected by conventional cytogenetic techniques. Disparities in size and localization are large and no consistent region of overlap has been delineated. We report two similar de novo deletions of 6.3 Mb involving the 9q31.1q31.3 region, identified in two monozygotic twins and one unrelated patient through array-CGH analysis. By cloning the deletion breakpoints, we could show that these deletions are not mediated by segmental duplications. The patients displayed a distinct clinical phenotype characterized by mild intellectual disability, short stature with high body mass index, thick hair, arched eyebrows, flat profile with broad chin and mild prognathism, broad, and slightly overhanging tip of the nose, short neck with cervical gibbus. The twin patients developed a metabolic syndrome (type 2 diabetes, hypercholesterolemia, vascular hypertension) during the third decade of life. Although long-term follow-up and collection of additional patients will be needed to obtain a better definition of the phenotype, our findings characterize a previously undescribed syndromic disorder associated with haploinsufficiency of the chromosome 9q31.1q31.3 region.
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Affiliation(s)
- M Mucciolo
- U.O.C. Genetica Medica, Policlinico S. Maria alle Scotte, Siena, Italy
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6
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Simons A, Sikkema-Raddatz B, de Leeuw N, Konrad NC, Hastings RJ, Schoumans J. Genome-wide arrays in routine diagnostics of hematological malignancies. Hum Mutat 2012; 33:941-8. [PMID: 22488943 DOI: 10.1002/humu.22057] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Accepted: 02/03/2012] [Indexed: 11/10/2022]
Abstract
Over the last three decades, cytogenetic analysis of malignancies has become an integral part of disease evaluation and prediction of prognosis or responsiveness to therapy. In most diagnostic laboratories, conventional karyotyping, in conjunction with targeted fluorescence in situ hybridization analysis, is routinely performed to detect recurrent aberrations with prognostic implications. However, the genetic complexity of cancer cells requires a sensitive genome-wide analysis, enabling the detection of small genomic changes in a mixed cell population, as well as of regions of homozygosity. The advent of comprehensive high-resolution genomic tools, such as molecular karyotyping using comparative genomic hybridization or single-nucleotide polymorphism microarrays, has overcome many of the limitations of traditional cytogenetic techniques and has been used to study complex genomic lesions in, for example, leukemia. The clinical impact of the genomic copy-number and copy-neutral alterations identified by microarray technologies is growing rapidly and genome-wide array analysis is evolving into a diagnostic tool, to better identify high-risk patients and predict patients' outcomes from their genomic profiles. Here, we review the added clinical value of an array-based genome-wide screen in leukemia, and discuss the technical challenges and an interpretation workflow in applying arrays in the acquired cytogenetic diagnostic setting.
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Affiliation(s)
- Annet Simons
- Laboratory of Tumor Genetics, Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands
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7
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Phylipsen M, Traeger-Synodinos J, van der Kraan M, van Delft P, Bakker G, Geerts M, Kanavakis E, Stamoulakatou A, Karagiorga M, Giordano PC, Harteveld CL. A novel α0-thalassemia deletion in a Greek patient with HbH disease and β-thalassemia trait. Eur J Haematol 2012; 88:356-62. [DOI: 10.1111/j.1600-0609.2012.01748.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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8
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Phylipsen M, Chaibunruang A, Vogelaar IP, Balak JRA, Schaap RAC, Ariyurek Y, Fucharoen S, den Dunnen JT, Giordano PC, Bakker E, Harteveld CL. Fine-tiling array CGH to improve diagnostics for α- and β-thalassemia rearrangements. Hum Mutat 2011; 33:272-80. [PMID: 21922597 DOI: 10.1002/humu.21612] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 08/26/2011] [Indexed: 12/21/2022]
Abstract
Implementation of multiplex ligation-dependent probe amplification (MLPA) for thalassemia causing deletions has lead to the detection of new rearrangements. Knowledge of the exact breakpoint sequences should give more insight into the molecular mechanisms underlying these rearrangements, and would facilitate the design of gap-PCRs. We have designed a custom fine-tiling array with oligonucleotides covering the complete globin gene clusters. We hybridized 27 DNA samples containing newly identified deletions and nine positive controls. We designed specific primers to amplify relatively short fragments containing the breakpoint sequence and analyzed these by direct sequencing. Results from nine positive controls showed that array comparative genomic hybridization (aCGH) is suitable to detect small and large rearrangements. We were able to locate all breakpoints to a region of approximately 2 kb. We designed breakpoint primers for 22 cases and amplification was successful in 19 cases. For 12 of these, the exact locations of the breakpoints were determined. Seven of these deletions have not been reported before. aCGH is a valuable tool for high-resolution breakpoint characterization. The combination of MLPA and aCGH has lead to relatively cheap and easy to perform PCR assays, which might be of use for laboratories as an alternative for MLPA in populations where only a limited number of specific deletions occur with high frequency.
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Affiliation(s)
- Marion Phylipsen
- Hemoglobinopathies Laboratory, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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