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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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Kariminejad A, Bozorgmehr B, Alizadeh H, Ghaderi-Sohi S, Toksoy G, Uyguner ZO, Kayserili H. Skull defects, alopecia, hypertelorism, and notched alae nasi caused by homozygousALX4gene mutation. Am J Med Genet A 2014; 164A:1322-7. [DOI: 10.1002/ajmg.a.36008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 04/03/2013] [Indexed: 01/22/2023]
Affiliation(s)
| | - Bita Bozorgmehr
- Kariminejad-Najmabadi Pathology & Genetics Center; Tehran Iran
| | - Houman Alizadeh
- Tehran University of Medical Sciences, Children's Medical Center Hospital; Tehran Iran
| | | | - Güven Toksoy
- Medical Genetics Department, Istanbul Medical Faculty; Istanbul University; Istanbul Turkey
| | - Zehra Oya Uyguner
- Medical Genetics Department, Istanbul Medical Faculty; Istanbul University; Istanbul Turkey
| | - Hülya Kayserili
- Medical Genetics Department, Istanbul Medical Faculty; Istanbul University; Istanbul Turkey
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Bertola DR, Rodrigues MG, Quaio CRDC, Kim CA, Passos-Bueno MR. Vertical transmission of a frontonasal phenotype caused by a novel ALX4 mutation. Am J Med Genet A 2013; 161A:600-4. [PMID: 23401352 DOI: 10.1002/ajmg.a.35762] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 10/16/2012] [Indexed: 11/06/2022]
Abstract
Frontonasal dysplasias (FND) comprise a spectrum of disorders caused by abnormal median facial development. Its etiology is still poorly understood but recently frontonasal dysplasia phenotypes were linked to loss-of-function mutations in the ALX homeobox gene family, which comprises the ALX1, ALX3, and ALX4 genes. All ALX-related frontonasal phenotypes till date had been compatible with an autosomal recessive mode of inheritance. In contrast, heterozygous loss-of-function mutations in ALX4 had been only associated with isolated symmetrical parietal ossification defects at the intersection of the sagittal and lambdoid sutures, known as enlarged parietal foramina. We report a family with vertical transmission from mother to son of mild frontonasal dysplasia phenotype caused by a novel ALX4 gene mutation (c.1080-1089_delGACCCGGTGCinsCTAAGATCTCAACAGAGATGGCAACT, p.Asp326fsX21).This is the first report of a frontonasal phenotype related to a heterozygous mutation in ALX4. This mutation is predicted to cause the loss of the aristaless domain in the C-terminal region of the protein and preserves the homeodomain. We speculate that a different mechanism, a dominant-negative effect, is responsible for the distinct phenotype in this family.
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Gajecka M, Saadeh R, Mackay KL, Glotzbach CD, Spodar K, Chitayat D, Shaffer LG. Clinical and molecular cytogenetic characterization of four patients with unbalanced translocation der(1)t(1;22)(p36;q13). Am J Med Genet A 2008; 146A:2777-84. [DOI: 10.1002/ajmg.a.32427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Pramparo T, de Gregori M, Gimelli S, Ciccone R, Frondizi D, Liehr T, Pellacani S, Masi G, Brovedani P, Zuffardi O, Guerrini R. A 7 Mb duplication at 22q13 in a girl with bipolar disorder and hippocampal malformation. Am J Med Genet A 2008; 146A:1754-60. [DOI: 10.1002/ajmg.a.32326] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Mavrogiannis LA, Taylor IB, Davies SJ, Ramos FJ, Olivares JL, Wilkie AOM. Enlarged parietal foramina caused by mutations in the homeobox genes ALX4 and MSX2: from genotype to phenotype. Eur J Hum Genet 2006; 14:151-8. [PMID: 16319823 PMCID: PMC1477589 DOI: 10.1038/sj.ejhg.5201526] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Heterozygous mutations of the homeobox genes ALX4 and MSX2 cause skull defects termed enlarged parietal foramina (PFM) and cranium bifidum (CB); a single MSX2 mutation has been documented in a unique craniosynostosis (CRS) family. However, the relative mutational contribution of these genes to PFM/CB and CRS is not known and information on genotype-phenotype correlations is incomplete. We analysed ALX4 and MSX2 in 11 new unrelated cases or families with PFM/CB, 181 cases of CRS, and a single family segregating a submicroscopic deletion of 11p11.2, including ALX4. We explored the correlations between skull defect size and age, gene, and mutation type, and reviewed additional phenotypic manifestations. Four PFM cases had mutations in either ALX4 or MSX2; including previous families, we have identified six ALX4 and six MSX2 mutations, accounting for 11/13 familial, but only 1/6 sporadic cases. The deletion family confirms the delineation of a mental retardation locus to within 1.1 Mb region of 11p11.2. Overall, no significant size difference was found between ALX4- and MSX2-related skull defects, but the ALX4 mutation p.R218Q tends to result in persistent CB and is associated with anatomical abnormalities of the posterior fossa. We conclude that PFM caused by mutations in ALX4 and MSX2 have a similar prevalence and are usually clinically indistinguishable. Mutation screening has a high pickup rate in PFM, especially in familial cases, but is not indicated in CRS.
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Affiliation(s)
- Lampros A Mavrogiannis
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Indira B Taylor
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Sally J Davies
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Feliciano J Ramos
- Sección Genética, Departamento Pediatría, Facultad de Medicina, Hospital Clínico Universitario, Universidad de Zaragoza, Zaragoza, Spain
| | - José L Olivares
- Departamento Pediatría, Facultad de Medicina, Hospital Clínico Universitario, Universidad de Zaragoza, Zaragoza, Spain
| | - Andrew OM Wilkie
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Correspondence: Professor AOM Wilkie, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK. Tel: +44 1865 222619; Fax: +44 1865 222500; E-mail:
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