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Mosley TJ, Johnston HR, Cutler DJ, Zwick ME, Mulle JG. Sex-specific recombination patterns predict parent of origin for recurrent genomic disorders. BMC Med Genomics 2021; 14:154. [PMID: 34107974 PMCID: PMC8190997 DOI: 10.1186/s12920-021-00999-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 06/02/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Structural rearrangements of the genome, which generally occur during meiosis and result in large-scale (> 1 kb) copy number variants (CNV; deletions or duplications ≥ 1 kb), underlie genomic disorders. Recurrent pathogenic CNVs harbor similar breakpoints in multiple unrelated individuals and are primarily formed via non-allelic homologous recombination (NAHR). Several pathogenic NAHR-mediated recurrent CNV loci demonstrate biases for parental origin of de novo CNVs. However, the mechanism underlying these biases is not well understood. METHODS We performed a systematic, comprehensive literature search to curate parent of origin data for multiple pathogenic CNV loci. Using a regression framework, we assessed the relationship between parental CNV origin and the male to female recombination rate ratio. RESULTS We demonstrate significant association between sex-specific differences in meiotic recombination and parental origin biases at these loci (p = 1.07 × 10-14). CONCLUSIONS Our results suggest that parental origin of CNVs is largely influenced by sex-specific recombination rates and highlight the need to consider these differences when investigating mechanisms that cause structural variation.
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Affiliation(s)
- Trenell J Mosley
- Graduate Program in Genetics and Molecular Biology, Laney Graduate School, Emory University, 201 Dowman Drive, Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
| | - H Richard Johnston
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
- Emory Integrated Computational Core, Emory University, 101 Woodruff Circle, Atlanta, GA, 30322, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University School of Medicine, 2015 Uppergate Drive, Atlanta, GA, 30322, USA
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA.
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA.
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Osborne LR, Mervis CB. 7q11.23 deletion and duplication. Curr Opin Genet Dev 2021; 68:41-48. [DOI: 10.1016/j.gde.2021.01.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/14/2021] [Accepted: 01/29/2021] [Indexed: 01/24/2023]
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Qaiser F, Yin Y, Mervis CB, Morris CA, Klein-Tasman BP, Tam E, Osborne LR, Yuen RKC. Rare and low frequency genomic variants impacting neuronal functions modify the Dup7q11.23 phenotype. Orphanet J Rare Dis 2021; 16:6. [PMID: 33407644 PMCID: PMC7788915 DOI: 10.1186/s13023-020-01648-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/14/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND 7q11.23 duplication (Dup7) is one of the most frequent recurrent copy number variants (CNVs) in individuals with autism spectrum disorder (ASD), but based on gold-standard assessments, only 19% of Dup7 carriers have ASD, suggesting that additional genetic factors are necessary to manifest the ASD phenotype. To assess the contribution of additional genetic variants to the Dup7 phenotype, we conducted whole-genome sequencing analysis of 20 Dup7 carriers: nine with ASD (Dup7-ASD) and 11 without ASD (Dup7-non-ASD). RESULTS We identified three rare variants of potential clinical relevance for ASD: a 1q21.1 microdeletion (Dup7-non-ASD) and two deletions which disrupted IMMP2L (one Dup7-ASD, one Dup7-non-ASD). There were no significant differences in gene-set or pathway variant burden between the Dup7-ASD and Dup7-non-ASD groups. However, overall intellectual ability negatively correlated with the number of rare loss-of-function variants present in nervous system development and membrane component pathways, and adaptive behaviour standard scores negatively correlated with the number of low-frequency likely-damaging missense variants found in genes expressed in the prenatal human brain. ASD severity positively correlated with the number of low frequency loss-of-function variants impacting genes expressed at low levels in the brain, and genes with a low level of intolerance. CONCLUSIONS Our study suggests that in the presence of the same pathogenic Dup7 variant, rare and low frequency genetic variants act additively to contribute to components of the overall Dup7 phenotype.
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Affiliation(s)
- Farah Qaiser
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
- Genetics & Genome Biology Program, The Hospital for Sick Children, 686 Bay St., Toronto, ON M5G 0A4 Canada
| | - Yue Yin
- Genetics & Genome Biology Program, The Hospital for Sick Children, 686 Bay St., Toronto, ON M5G 0A4 Canada
| | - Carolyn B. Mervis
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, KY USA
| | - Colleen A. Morris
- Department of Pediatrics, UNLV School of Medicine, Las Vegas, NV USA
| | | | - Elaine Tam
- Department of Medicine, University of Toronto, Toronto, ON Canada
| | - Lucy R. Osborne
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
- Department of Medicine, University of Toronto, Toronto, ON Canada
| | - Ryan K. C. Yuen
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
- Genetics & Genome Biology Program, The Hospital for Sick Children, 686 Bay St., Toronto, ON M5G 0A4 Canada
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Tinker RJ, Burghel GJ, Garg S, Steggall M, Cuvertino S, Banka S. Haploinsufficiency of ATP6V0C possibly underlies 16p13.3 deletions that cause microcephaly, seizures, and neurodevelopmental disorder. Am J Med Genet A 2020; 185:196-202. [PMID: 33090716 DOI: 10.1002/ajmg.a.61905] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/15/2020] [Accepted: 09/19/2020] [Indexed: 12/11/2022]
Abstract
We recently contributed to the description of eight individuals with a novel condition caused by 16p13.3 microdeletions encompassing TBC1D24, ATP6V0C, and PDPK1 and resulting in epilepsy, microcephaly and neurodevelopmental problems. The phenotypic spectrum, the minimum overlapping region and the underlying disease mechanism for this disorder remain to be clarified. Here we report a 3.5-year-old male, with microcephaly, autism spectrum disorder and a de novo 16p13.3 microdeletion. We performed detailed in silico analysis to show that the minimum overlapping region for the condition is ~80Kb encompassing five protein coding genes. Analysis of loss of function constraint metrics, transcript-aware evaluation of the population variants, GeVIR scores, analysis of reported pathogenic point variants, detailed review of the known functions of gene products and their animal models showed that the haploinsufficiency of ATP6V0C likely underlies the phenotype of this condition. Protein-protein interaction network, gene phenology and analysis of topologically associating domain showed that it was unlikely that the disorder has an epistatic or regulatory basis. 16p13.3 deletions encompassing ATP6V0C cause a neurodevelopmental disorder. Our results broaden the phenotypic spectrum of this disorder and clarify the likely underlying disease mechanism for the condition.
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Affiliation(s)
- Rory J Tinker
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Foundation NHS Trust, Manchester, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Foundation NHS Trust, Manchester, UK
| | - Shruti Garg
- Division of Neuroscience & Experimental Psychology, School of Biological Sciences, University of Manchester, Manchester, UK
- Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Greater Manchester Mental Health NHS Trust, Manchester, UK
- Department of Child and Adolescent Psychiatry, Royal Manchester Children's Hospital, Manchester, UK
| | - Maggie Steggall
- Department of Paediatric Medicine, Royal Manchester Children's Hospital, Manchester, UK
| | - Sara Cuvertino
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Foundation NHS Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
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Codina-Sola M, Costa-Roger M, Pérez-García D, Flores R, Palacios-Verdú MG, Cusco I, Pérez-Jurado LA. Genetic factors contributing to autism spectrum disorder in Williams-Beuren syndrome. J Med Genet 2019; 56:801-808. [PMID: 31413120 PMCID: PMC6929708 DOI: 10.1136/jmedgenet-2019-106080] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 07/11/2019] [Accepted: 07/16/2019] [Indexed: 01/10/2023]
Abstract
BACKGROUND The hallmark of the neurobehavioural phenotype of Williams-Beuren syndrome (WBS) is increased sociability and relatively preserved language skills, often described as opposite to autism spectrum disorders (ASD). However, the prevalence of ASD in WBS is 6-10 times higher than in the general population. We have investigated the genetic factors that could contribute to the ASD phenotype in individuals with WBS. METHODS We studied four males and four females with WBS and a confirmed diagnosis of ASD by the Autism Diagnostic Interview-Revised. We performed a detailed molecular characterisation of the deletion and searched for genomic variants using exome sequencing. RESULTS A de novo deletion of 1.55 Mb (6 cases) or 1.83 Mb (2 cases) at 7q11.23 was detected, being in 7/8 patients of paternal origin. No common breakpoint, deletion mechanism or size was found. Two cases were hemizygous for the rare T allele at rs12539160 in MLXIPL, previously associated with ASD. Inherited rare variants in ASD-related or functionally constrained genes and a de novo nonsense mutation in the UBR5 gene were identified in six cases, with higher burden in females compared with males (p=0.016). CONCLUSIONS The increased susceptibility to ASD in patients with WBS might be due to additive effects of the common WBS deletion, inherited and de novo rare sequence variants in ASD-related genes elsewhere in the genome, with higher burden of deleterious mutations required for females, and possible hypomorphic variants in the hemizygous allele or cis-acting mechanisms on imprinting.
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Affiliation(s)
- Marta Codina-Sola
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat Pompeu Fabra Departament de Ciences Experimentals i de la Salut, Barcelona, Spain
- Clinical and Molecular Genetics Area, Vall Hebrón Hospital Research Institute (VHIR), Hospital Vall d'Hebron, Barcelona, Spain
| | - Mar Costa-Roger
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat Pompeu Fabra Departament de Ciences Experimentals i de la Salut, Barcelona, Spain
| | - Debora Pérez-García
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat Pompeu Fabra Departament de Ciences Experimentals i de la Salut, Barcelona, Spain
| | - Raquel Flores
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat Pompeu Fabra Departament de Ciences Experimentals i de la Salut, Barcelona, Spain
| | - Maria Gabriela Palacios-Verdú
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat Pompeu Fabra Departament de Ciences Experimentals i de la Salut, Barcelona, Spain
- Fundacio Dexeus Salut de la Dona, Barcelona, Spain
| | - Ivon Cusco
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat Pompeu Fabra Departament de Ciences Experimentals i de la Salut, Barcelona, Spain
- Clinical and Molecular Genetics Area, Vall Hebrón Hospital Research Institute (VHIR), Hospital Vall d'Hebron, Barcelona, Spain
| | - Luis Alberto Pérez-Jurado
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat Pompeu Fabra Departament de Ciences Experimentals i de la Salut, Barcelona, Spain
- SA Clinical Genetics, Women's and Children's Hospital, South Australian Health and Medical Research Institute (SAHMRI) and University of Adelaide, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
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