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Pettersson M, Grochowski CM, Wincent J, Eisfeldt J, Breman AM, Cheung SW, Krepischi ACV, Rosenberg C, Lupski JR, Ottosson J, Lovmar L, Gacic J, Lundberg ES, Nilsson D, Carvalho CMB, Lindstrand A. Cytogenetically visible inversions are formed by multiple molecular mechanisms. Hum Mutat 2020; 41:1979-1998. [PMID: 32906200 PMCID: PMC7702065 DOI: 10.1002/humu.24106] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 08/10/2020] [Accepted: 08/28/2020] [Indexed: 01/25/2023]
Abstract
Cytogenetically detected inversions are generally assumed to be copy number and phenotypically neutral events. While nonallelic homologous recombination is thought to play a major role, recent data suggest the involvement of other molecular mechanisms in inversion formation. Using a combination of short-read whole-genome sequencing (WGS), 10X Genomics Chromium WGS, droplet digital polymerase chain reaction and array comparative genomic hybridization we investigated the genomic structure of 18 large unique cytogenetically detected chromosomal inversions and achieved nucleotide resolution of at least one chromosomal inversion junction for 13/18 (72%). Surprisingly, we observed that seemingly copy number neutral inversions can be accompanied by a copy-number gain of up to 350 kb and local genomic complexities (3/18, 17%). In the resolved inversions, the mutational signatures are consistent with nonhomologous end-joining (8/13, 62%) or microhomology-mediated break-induced replication (5/13, 38%). Our study indicates that short-read 30x coverage WGS can detect a substantial fraction of chromosomal inversions. Moreover, replication-based mechanisms are responsible for approximately 38% of those events leading to a significant proportion of inversions that are actually accompanied by additional copy-number variation potentially contributing to the overall phenotypic presentation of those patients.
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Affiliation(s)
- Maria Pettersson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | | | - Josephine Wincent
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Amy M Breman
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Sau W Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ana C V Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Texas Children's Hospital, Houston, Texas, USA
| | - Jesper Ottosson
- Department of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Lovisa Lovmar
- Department of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jelena Gacic
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Elisabeth S Lundberg
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Pacific Northwest Research Institute, Seattle, Washington, USA
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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Ghorbel M, Baklouti-Gargouri S, ElGhazel H, Zribi N, Ben Abdallah F, Cherif M, Fakhfakh F, Saad A, Ammar-Keskes L. Pericentric inversion of chromosom 12 [Inv (12) (p12q12)] associated with idiopathic azoospermia in one infertile Tunisian man. Biochem Biophys Res Commun 2013; 432:472-4. [PMID: 23399567 DOI: 10.1016/j.bbrc.2013.01.110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 01/29/2013] [Indexed: 10/27/2022]
Abstract
Chromosome aberrations are found in 2-7% of couples with fertility problems and pericentric inversions are structural chromosomal abnormalities, potentially associated with infertility or multiple miscarriages. In this study, we report the first case of pericentric inversion of chromosome 12 associated with non-obstructive azoospermia. A karyogram revealed pericentric inversion of chromosome 12 with breakpoints at 12p12 and 12q12. Testicular histopathology confirmed the Sertoli cell-only syndrome.
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Affiliation(s)
- Myriam Ghorbel
- Laboratory of Human Molecular Genetics, Faculty of Medicine, Sfax, Tunisia.
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3
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Chromosomal defects in infertile men with poor semen quality. J Assist Reprod Genet 2012; 29:451-6. [PMID: 22406877 DOI: 10.1007/s10815-012-9737-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 02/22/2012] [Indexed: 10/28/2022] Open
Abstract
PURPOSE To assess the incidence and the type of chromosomal aberrations in males with infertility we reviewed cytogenetic results in 76 Tunisian infertile men (54 nonobstructive azoospermia and 22 oligo-asthenospermia). METHODS Karyotyping was performed on peripheral blood lymphocytes according to the standard methods. Molecular diagnosis of classical and partial Y-chromosomal microdeletions was performed by amplifying Y-specific STSs markers. RESULTS Various numerical and structural chromosome abnormalities were identified in 15 patients (19.48%). The occurrence of chromosomal abnormality in the azoospermics and severe oligo-asthnospermic was 21.7% and 13.5%, respectively. The most common was Klinefelter syndrome, accounting for 10 of the 15 cytogenetic defects. The total frequency of Y chromosomal microdeletions was 17.1%, with respective frequencies in azoospermic and severe oligospermic groups, 11.1% and 31.8%. The most frequent of Y chromosomal deletions were the partial ones (11.1% in azoospermic and 27.2% in oligospermic). CONCLUSION The occurrence of chromosomal abnormalities among infertile males strongly suggests the need for routine genetic testing and counseling prior to the employment of assisted reproduction techniques.
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Kim YO, Baek HJ, Woo YJ, Choi YY, Chung TW. Moyamoya syndrome in a child with trisomy 12p syndrome. Pediatr Neurol 2006; 35:442-5. [PMID: 17138018 DOI: 10.1016/j.pediatrneurol.2006.06.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2005] [Revised: 06/09/2006] [Accepted: 06/29/2006] [Indexed: 11/26/2022]
Abstract
A female, 2 years and 7 months of age, was admitted to the hospital with stupor and nystagmus following projectile vomiting. She had been prenatally diagnosed with trisomy 12p with a familial pericentric inversion of chromosome 12 originating from her mother. She manifested developmental delay and some dysmorphic features of the face and limbs compatible with the clinical features of trisomy 12p. Four-vessel cerebral angiography revealed severe stenosis and occlusion of the supraclinoid portion of the right and left internal carotid arteries with numerous collateral vessels in the vicinity of the occlusion. These features are consistent with moyamoya syndrome. This report presents the first case of moyamoya syndrome with trisomy 12p with a familial pericentric inversion of chromosome 12.
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Affiliation(s)
- Young Ok Kim
- Department of Pediatrics, Chonnam National University Hospital, Gwangju, Korea.
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Grosso S, Pucci L, Farnetani M, Di Bartolo RM, Galimberti D, Mostardini R, Anichini C, Balestri M, Morgese G, Balestri P. Epilepsy and electroencephalographic findings in pericentric inversion of chromosome 12. J Child Neurol 2004; 19:604-8. [PMID: 15605470 DOI: 10.1177/088307380401900807] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Epilepsy, together with mental retardation, represents a common manifestation of chromosomal aberrations. Specific electroencephalographic (EEG) and epileptic patterns have been described in several chromosomal disorders, such as Angelman's syndrome, Miller-Dieker syndrome, Wolf-Hirschhorn syndrome, and ring 20 syndrome. A peculiar electroclinical pattern has also been identified in trisomy 12p syndrome. We report three patients with a pericentric inversion of chromosome 12, with breakpoints localized to p11-q13 and affected by epilepsy or EEG anomalies. Two suffered from epilepsy, which, in the clinical course, was mainly characterized by complex partial seizures with a semiology related to the temporal lobe. In one patient, myoclonic absences, head drop, and massive jerky attacks were also present. In both patients, generalized 3 Hz bursts were registered, together with multifocal and focal paroxysmal activity, which were most prominent in the temporoparietal and temporal areas, respectively. In the other patient, who had no epilepsy, EEG showed bioccipital paroxysmal activity. In all patients, the clinical picture was characterized by the presence of moderate mental retardation and behavioral disorders. The incidence of epilepsy or EEG anomalies among patients with a pericentric inversion of chromosome 12 remains to be ascertained. However, the present study confirms that chromosome 12 anomalies can be associated with epilepsy. Although myoclonic absence-like episodes can occasionally be part of the epileptic phenotype, the electroclinical pattern in pericentric inversion of chromosome 12 seems to be more polymorphic when compared with that observed in trisomy 12p syndrome.
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Lagier-Tourenne C, Ginglinger E, Alembik Y, De Saint Martin A, Peter MO, Dulucq P, Jonveaux P, Jeandidier E. Two cousins with partial trisomy 12q and monosomy 12p recombinants of a familial pericentric inversion of the chromosome 12. Am J Med Genet A 2004; 125A:77-85. [PMID: 14755471 DOI: 10.1002/ajmg.a.20450] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Partial trisomy 12q and monosomy 12p lead to multiple malformation syndromes. Instead of trisomy 12q that has been reported as a clinically identifiable syndrome, monosomy 12p is characterized by a wide phenotypic spectrum. We report two cousins suffering from severe mental retardation, seizures, and dysmorphic features related to a trisomy 12q24.3-->qter and a monosomy 12p13-->pter resulting from a familial pericentric inversion of chromosome 12. In an attempt to improve the clinical delineation of these two syndromes, we compared our two patients with previous reports of these aneusomies. This review emphasizes the high frequency of familial translocations, including a breakpoint at 12q24 involved in trisomy 12q whereas monosomy 12p occurs most frequently de novo. Despite the poor specificity of the signs, this comparison allowed us to determine the clinical features present in more than 20% of patients with trisomy 12q or monosomy 12p. We particularly emphasize some consistent leading features of monosomy 12p, including microcephaly, dental, cardio-vascular, extremity, and sensorial abnormalities, initially not reported as recurrent in this syndrome.
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Uehara S, Tanigawara S, Takeyama Y, Okamura K, Yajima A. A family with pericentric inversion of chromosome 12. THE JAPANESE JOURNAL OF HUMAN GENETICS 1994; 39:201-4. [PMID: 8025298 DOI: 10.1007/bf01915957] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A heterozygous pericentric inversion of chromosome 12 (inv(12)) was prenatally diagnosed. The breakpoints were localized to p12.3 and q14, resulting in more than one-third of the total length of the chromosome being inverted. The inversions was transmitted from the father whose phenotype was completely normal. The newborn also showed normal phenotype and grew without any clinical problems. The parents had no history of infertility. Based on these facts, it is indicated that pericentric inv(12)(p12.3q14) does not affect phenotype.
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Affiliation(s)
- S Uehara
- Department of Obstetrics and Gynecology, Tohoku University School of Medicine, Sendai, Japan
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Abstract
A BrdU-requiring fragile site, fra(12)(q24.2), on human chromosome 12 of some individuals is reported. This fragile site is inherited in a Mendelian codominant fashion and does not seem to be associated with any physical or mental abnormality in carriers. It was mostly observed as a chromatid gap: no acentric fragments, triradials or deleted chromosomes were found. The fra(12)(q24.2) was expressed in 34%-48% of metaphases in lymphocyte cultures from carriers when BrdU and FdU were added 6.5 h before harvest, while the expression ranged between 5% and 20% when the cultures were treated with BrdU alone. The fra(12)(q24.2) represents the second BrdU-requiring rare fragile site described on human chromosomes.
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Affiliation(s)
- I Voiculescu
- Institut für Humangenetik und Anthropologie Universität, Freiburg i.Br., Federal Republic of Germany
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