1
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Zhang L, Chang M, Liu C, Xu Y, Feng Q, Yin S, Wu W. A case of de novo -α 3.7 thalassaemia and the utility of CATSA for detecting de novo mutations in thalassaemia. Br J Haematol 2024; 205:360-363. [PMID: 38757312 DOI: 10.1111/bjh.19507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
Affiliation(s)
- Lei Zhang
- Medical Genetics Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
| | - Ming Chang
- Department of Hematology, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Chao Liu
- Medical Genetics Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
| | - Yong Xu
- Medical Genetics Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
| | - Qing Feng
- Medical Genetics Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
| | - Shanshan Yin
- Medical Genetics Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
| | - Weiqing Wu
- Medical Genetics Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
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2
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Klussmeier A, Putke K, Klasberg S, Kohler M, Sauter J, Schefzyk D, Schöfl G, Massalski C, Schäfer G, Schmidt AH, Roers A, Lange V. High population frequencies of MICA copy number variations originate from independent recombination events. Front Immunol 2023; 14:1297589. [PMID: 38035108 PMCID: PMC10684724 DOI: 10.3389/fimmu.2023.1297589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
MICA is a stress-induced ligand of the NKG2D receptor that stimulates NK and T cell responses and was identified as a key determinant of anti-tumor immunity. The MICA gene is located inside the MHC complex and is in strong linkage disequilibrium with HLA-B. While an HLA-B*48-linked MICA deletion-haplotype was previously described in Asian populations, little is known about other MICA copy number variations. Here, we report the genotyping of more than two million individuals revealing high frequencies of MICA duplications (1%) and MICA deletions (0.4%). Their prevalence differs between ethnic groups and can rise to 2.8% (Croatia) and 9.2% (Mexico), respectively. Targeted sequencing of more than 70 samples indicates that these copy number variations originate from independent nonallelic homologous recombination events between segmental duplications upstream of MICA and MICB. Overall, our data warrant further investigation of disease associations and consideration of MICA copy number data in oncological study protocols.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Axel Roers
- Institute for Immunology, Medical Faculty Carl Gustav Carus, University of Technology (TU) Dresden, Dresden, Germany
- Institute for Immunology, University Hospital Heidelberg, Heidelberg, Germany
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3
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NGS4THAL, a one-stop molecular diagnosis and carrier screening tool for thalassemia and other hemoglobinopathies by next-generation sequencing. J Mol Diagn 2022; 24:1089-1099. [PMID: 35868510 DOI: 10.1016/j.jmoldx.2022.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 04/03/2022] [Accepted: 06/21/2022] [Indexed: 11/21/2022] Open
Abstract
Thalassemia is one of the most common genetic diseases and a major health threat worldwide. Accurate, efficient and scalable analysis of next-generation sequencing (NGS) data is much needed for its molecular diagnosis and carrier screening. We developed NGS4THAL, a bioinformatics analysis pipeline analyzing next generation sequencing (NGS) data to detect pathogenic variants for thalassemia and other hemoglobinopathies. NGS4THAL realigns ambiguously mapped NGS reads derived from the homologous hemoglobin gene clusters for accurate detection of point mutations and small insertion/deletions (InDels). It uses a combination of complementary structural variant (SV) detection tools and an inhouse database of control data containing specific SVs to achieve accurate detection of the complex SV types. Detected variants are matched with those in HbVar database, allowing recognition of known pathogenic variants, including disease modifiers. Tested on simulation data, NGS4THAL achieved high sensitivity and specificity. For targeted NGS sequencing data from samples with laboratory-confirmed pathogenic hemoglobin variants, it achieved 100% detection accuracy. Application of NGS4THAL on whole genome sequencing data from unrelated studies revealed thalassemia mutation carrier rates for Hong Kong Chinese and Northern Vietnamese that were consistent with previous reports. NGS4THAL is a highly accurate and efficient molecular diagnosis tool for thalassemia and other hemoglobinopathies based on tailored analysis of NGS data and is potentially scalable for population carrier screening.
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4
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Montefiori LE, Bendig S, Gu Z, Chen X, Pölönen P, Ma X, Murison A, Zeng A, Garcia-Prat L, Dickerson K, Iacobucci I, Abdelhamed S, Hiltenbrand R, Mead PE, Mehr CM, Xu B, Cheng Z, Chang TC, Westover T, Ma J, Stengel A, Kimura S, Qu C, Valentine MB, Rashkovan M, Luger S, Litzow MR, Rowe JM, den Boer ML, Wang V, Yin J, Kornblau SM, Hunger SP, Loh ML, Pui CH, Yang W, Crews KR, Roberts KG, Yang JJ, Relling MV, Evans WE, Stock W, Paietta EM, Ferrando AA, Zhang J, Kern W, Haferlach T, Wu G, Dick JE, Klco JM, Haferlach C, Mullighan CG. Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia. Cancer Discov 2021; 11:2846-2867. [PMID: 34103329 PMCID: PMC8563395 DOI: 10.1158/2159-8290.cd-21-0145] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/27/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022]
Abstract
Lineage-ambiguous leukemias are high-risk malignancies of poorly understood genetic basis. Here, we describe a distinct subgroup of acute leukemia with expression of myeloid, T lymphoid, and stem cell markers driven by aberrant allele-specific deregulation of BCL11B, a master transcription factor responsible for thymic T-lineage commitment and specification. Mechanistically, this deregulation was driven by chromosomal rearrangements that juxtapose BCL11B to superenhancers active in hematopoietic progenitors, or focal amplifications that generate a superenhancer from a noncoding element distal to BCL11B. Chromatin conformation analyses demonstrated long-range interactions of rearranged enhancers with the expressed BCL11B allele and association of BCL11B with activated hematopoietic progenitor cell cis-regulatory elements, suggesting BCL11B is aberrantly co-opted into a gene regulatory network that drives transformation by maintaining a progenitor state. These data support a role for ectopic BCL11B expression in primitive hematopoietic cells mediated by enhancer hijacking as an oncogenic driver of human lineage-ambiguous leukemia. SIGNIFICANCE: Lineage-ambiguous leukemias pose significant diagnostic and therapeutic challenges due to a poorly understood molecular and cellular basis. We identify oncogenic deregulation of BCL11B driven by diverse structural alterations, including de novo superenhancer generation, as the driving feature of a subset of lineage-ambiguous leukemias that transcend current diagnostic boundaries.This article is highlighted in the In This Issue feature, p. 2659.
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Affiliation(s)
- Lindsey E Montefiori
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Zhaohui Gu
- Department of Computational and Quantitative Medicine, City of Hope Comprehensive Cancer Center, Duarte, California
- Department of Systems Biology, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Petri Pölönen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Alex Murison
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Andy Zeng
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Laura Garcia-Prat
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Kirsten Dickerson
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ryan Hiltenbrand
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Paul E Mead
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Cyrus M Mehr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Zhongshan Cheng
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Shunsuke Kimura
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Chunxu Qu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Marcus B Valentine
- Cytogenetics Core Facility, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Marissa Rashkovan
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Selina Luger
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mark R Litzow
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Jacob M Rowe
- Department of Hematology, Shaare Zedek Medical Center, Jerusalem, Israel
| | | | - Victoria Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jun Yin
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, Minnesota
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen P Hunger
- Department of Pediatrics, Children's Hospital of Philadelphia, and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kristine R Crews
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Wendy Stock
- University of Chicago Comprehensive Cancer Center, Chicago, Illinois
| | | | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, New York
- Department of Pediatrics, Columbia University, New York, New York
- Department of Pathology and Cell Biology, Columbia University, New York, New York
- Department of Systems Biology, Columbia University, New York, New York
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | | | - Gang Wu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John E Dick
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | | | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
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5
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Ndila CM, Nyirongo V, Macharia AW, Jeffreys AE, Rowlands K, Hubbart C, Busby GBJ, Band G, Harding RM, Rockett KA, Williams TN. Haplotype heterogeneity and low linkage disequilibrium reduce reliable prediction of genotypes for the ‑α 3.7I form of α-thalassaemia using genome-wide microarray data. Wellcome Open Res 2021; 5:287. [PMID: 34632085 PMCID: PMC8474104 DOI: 10.12688/wellcomeopenres.16320.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2021] [Indexed: 12/26/2022] Open
Abstract
Background: The -α
3.7I-thalassaemia deletion is very common throughout Africa because it protects against malaria. When undertaking studies to investigate human genetic adaptations to malaria or other diseases, it is important to account for any confounding effects of α-thalassaemia to rule out spurious associations. Methods: In this study, we have used direct α-thalassaemia genotyping to understand why GWAS data from a large malaria association study in Kilifi Kenya did not identify the α-thalassaemia signal. We then explored the potential use of a number of new approaches to using GWAS data for imputing α-thalassaemia as an alternative to direct genotyping by PCR. Results: We found very low linkage-disequilibrium of the directly typed data with the GWAS SNP markers around α-thalassaemia and across the haemoglobin-alpha (
HBA) gene region, which along with a complex haplotype structure, could explain the lack of an association signal from the GWAS SNP data. Some indirect typing methods gave results that were in broad agreement with those derived from direct genotyping and could identify an association signal, but none were sufficiently accurate to allow correct interpretation compared with direct typing, leading to confusing or erroneous results. Conclusions: We conclude that going forwards, direct typing methods such as PCR will still be required to account for α-thalassaemia in GWAS studies.
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Affiliation(s)
- Carolyne M Ndila
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, PO BOX 230-80108, Kenya
| | - Vysaul Nyirongo
- United Nation Statistics Division, United Nations, New York, New York, 10017, USA
| | - Alexander W Macharia
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, PO BOX 230-80108, Kenya
| | - Anna E Jeffreys
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK
| | - Kate Rowlands
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK
| | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK
| | - George B J Busby
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK.,Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, Oxfordshire, OX3 7LF, UK
| | - Gavin Band
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK.,Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Rosalind M Harding
- Departments of Zoology and Statistics, University of Oxford, Oxford, Oxfordshire, OX1 3SZ, UK
| | - Kirk A Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK.,Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Thomas N Williams
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, PO BOX 230-80108, Kenya.,Department of Infectious Diseases, Imperial College Faculty of Medicine, London, W2 1NY, UK
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6
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Hollox EJ, Zuccherato LW, Tucci S. Genome structural variation in human evolution. Trends Genet 2021; 38:45-58. [PMID: 34284881 DOI: 10.1016/j.tig.2021.06.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 01/01/2023]
Abstract
Structural variation (SV) is a large difference (typically >100 bp) in the genomic structure of two genomes and includes both copy number variation and variation that does not change copy number of a genomic region, such as an inversion. Improved reference genomes, combined with widespread genome sequencing using short-read sequencing technology, and increasingly using long-read sequencing, have reignited interest in SV. Recent large-scale studies and functional focused analyses have highlighted the role of SV in human evolution. In this review, we highlight human-specific SVs involved in changes in the brain, population-specific SVs that affect response to the environment, including adaptation to diet and infectious diseases, and summarise the contribution of archaic hominin admixture to present-day human SV.
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Affiliation(s)
- Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, UK.
| | - Luciana W Zuccherato
- Núcleo de Ensino e Pesquisa, Instituto Mário Penna, Belo Horizonte, Brazil; Departmento de Bioquímica e Imunologia, Universidade de Minas Gerais, Belo Horizonte, Brazil
| | - Serena Tucci
- Department of Anthropology, Yale University, New Haven, CT, USA
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7
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Ndila CM, Nyirongo V, Macharia AW, Jeffreys AE, Rowlands K, Hubbart C, Busby GBJ, Band G, Harding RM, Rockett KA, Williams TN. Haplotype heterogeneity and low linkage disequilibrium reduce reliable prediction of genotypes for the ‑α3.7I form of α-thalassaemia using genome-wide microarray data. Wellcome Open Res 2020; 5:287. [DOI: 10.12688/wellcomeopenres.16320.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2020] [Indexed: 11/20/2022] Open
Abstract
Background: The -α3.7I-thalassaemia deletion is very common throughout Africa because it protects against malaria. When undertaking studies to investigate human genetic adaptations to malaria or other diseases, it is important to account for any confounding effects of α-thalassaemia to rule out spurious associations. Methods: In this study we have used direct α-thalassaemia genotyping to understand why GWAS data from a large malaria association study in Kilifi Kenya did not identify the α-thalassaemia signal. We then explored the potential use of a number of new approaches to using GWAS data for imputing α-thalassaemia as an alternative to direct genotyping by PCR. Results: We found very low linkage-disequilibrium of the directly typed data with the GWAS SNP markers around α-thalassaemia and across the haemoglobin-alpha (HBA) gene region, which along with a complex haplotype structure, could explain the lack of an association signal from the GWAS SNP data. Some indirect typing methods gave results that were in broad agreement with those derived from direct genotyping and could identify an association signal, but none were sufficiently accurate to allow correct interpretation compared with direct typing, leading to confusing or erroneous results. Conclusions: We conclude that going forwards, direct typing methods such as PCR will still be required to account for α-thalassaemia in GWAS studies.
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8
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Pang D, Shang X, Cai D, Zhu F, Cheng Y, Zhong J, Yi S, Zhang Q, Xu X. Thalassaemia intermedia caused by coinheritance of a β‐thalassaemia mutation and a
de novo
duplication of α‐globin genes in the paternal allele. Br J Haematol 2019; 186:620-624. [DOI: 10.1111/bjh.15958] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 03/05/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Dejian Pang
- Department of Medical Genetics School of Basic Medical Sciences Southern Medical UniversityGuangzhou Guangdong China
| | - Xuan Shang
- Department of Medical Genetics School of Basic Medical Sciences Southern Medical UniversityGuangzhou Guangdong China
- Guangdong Genetics Testing Engineering Research CentreGuangzhou Guangdong China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application Guangzhou GuangdongChina
| | - Decheng Cai
- Department of Medical Genetics School of Basic Medical Sciences Southern Medical UniversityGuangzhou Guangdong China
| | - Fei Zhu
- Department of Medical Genetics School of Basic Medical Sciences Southern Medical UniversityGuangzhou Guangdong China
| | - Yi Cheng
- Department of Medical Genetics School of Basic Medical Sciences Southern Medical UniversityGuangzhou Guangdong China
| | - Jianmei Zhong
- Department of Medical Genetics School of Basic Medical Sciences Southern Medical UniversityGuangzhou Guangdong China
| | - Sheng Yi
- Prenatal Diagnostic Centre Guangxi Zhuang Autonomous Region Women and Children Care Hospital Nanning Guangxi China
| | - Qianqian Zhang
- Department of Medical Genetics School of Basic Medical Sciences Southern Medical UniversityGuangzhou Guangdong China
| | - Xiangmin Xu
- Department of Medical Genetics School of Basic Medical Sciences Southern Medical UniversityGuangzhou Guangdong China
- Guangdong Genetics Testing Engineering Research CentreGuangzhou Guangdong China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application Guangzhou GuangdongChina
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9
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Piazza A, Heyer WD. Multi-Invasion-Induced Rearrangements as a Pathway for Physiological and Pathological Recombination. Bioessays 2018; 40:e1700249. [PMID: 29578583 PMCID: PMC6072258 DOI: 10.1002/bies.201700249] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/08/2018] [Indexed: 01/24/2023]
Abstract
Cells mitigate the detrimental consequences of DNA damage on genome stability by attempting high fidelity repair. Homologous recombination templates DNA double-strand break (DSB) repair on an identical or near identical donor sequence in a process that can in principle access the entire genome. Other physiological processes, such as homolog recognition and pairing during meiosis, also harness the HR machinery using programmed DSBs to physically link homologs and generate crossovers. A consequence of the homology search process by a long nucleoprotein filament is the formation of multi-invasions (MI), a joint molecule in which the damaged ssDNA has invaded more than one donor molecule. Processing of MI joint molecules can compromise the integrity of both donor sites and lead to their rearrangement. Here, two mechanisms for the generation of rearrangements as a pathological consequence of MI processing are detailed and the potential relevance for non-allelic homologous recombination discussed. Finally, it is proposed that MI-induced crossover formation may be a feature of physiological recombination.
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Affiliation(s)
- Aurèle Piazza
- Department of Microbiology and Molecular Genetics, One Shields Avenue, University of California, Davis, CA, 95616, USA
- Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, One Shields Avenue, University of California, Davis, CA, 95616, USA
- Department of Molecular and Cellular Biology, One Shields Avenue, University of California, Davis, CA, 95616, USA
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10
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Farashi S, Harteveld CL. Molecular basis of α-thalassemia. Blood Cells Mol Dis 2017; 70:43-53. [PMID: 29032940 DOI: 10.1016/j.bcmd.2017.09.004] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 09/14/2017] [Accepted: 09/14/2017] [Indexed: 02/05/2023]
Abstract
α-Thalassemia is an inherited, autosomal recessive, disorder characterized by a microcytic hypochromic anemia. It is one of the most common monogenic gene disorders in the world population. The clinical severity varies from almost asymptomatic, to mild microcytic hypochromic, and to a lethal hemolytic condition, called Hb Bart's Hydrops Foetalis Syndrome. The molecular basis are usually deletions and less frequently, point mutations affecting the expression of one or more of the duplicated α-genes. The clinical variation and increase in disease severity is directly related to the decreased expression of one, two, three or four copies of the α-globin genes. Deletions and point mutations in the α-globin genes and their regulatory elements have been studied extensively in carriers and patients and these studies have given insight into the α-globin genes are regulated. By looking at naturally occurring deletions and point mutations, our knowledge of globin-gene regulation and expression will continue to increase and will lead to new targets of therapy.
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Affiliation(s)
- Samaneh Farashi
- Dept. of Clinical Genetics, Hemoglobinopathy Expert Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Cornelis L Harteveld
- Dept. of Clinical Genetics, Hemoglobinopathy Expert Center, Leiden University Medical Center, Leiden, The Netherlands.
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11
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Soler AM, Schelotto M, de Oliveira Mota N, Dorta Ferreira R, Sonati MDF, da Luz JA. The -(α)(5.2) Deletion Detected in a Uruguayan Family: First Case Report in the Americas. Hemoglobin 2017; 40:289-92. [PMID: 27492768 DOI: 10.1080/03630269.2016.1200072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In Uruguay, α-thalassemia (α-thal) mutations were introduced predominantly by Mediterranean European immigrant populations and by slave trade of African populations. A patient with anemia with hypochromia and microcytosis, refractory to iron treatment and with normal hemoglobin (Hb) electrophoresis was analyzed for α-thal mutations by multiplex gap-polymerase chain reaction (gap-PCR), automated sequencing and multiplex ligation-dependent probe amplification (MLPA) analyses. Agarose gel electrophoresis of the multiplex gap-PCR showed a band of unexpected size (approximately 700 bp) in the samples from the proband and mother. Automated sequencing of the amplified fragment showed the presence of the -(α)(5.2) deletion (NG_000006.1: g.32867_38062del5196) [an α-thal-1 deletion of 5196 nucleotides (nts)]. The MLPA analysis of the proband's sample also showed the presence of the -(α)(5.2) deletion in heterozygous state. We report here the presence of the -(α)(5.2) deletion, for the first time in the Americas, in a Uruguayan family with Italian ancestry, detected with a previously described multiplex gap-PCR.
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Affiliation(s)
- Ana María Soler
- a Laboratorio De Genética Molecular Humana , Centro Universitario Regional (CENUR) Litoral Norte-Sede Salto, Universidad De La República , Salto , Uruguay
| | - Magdalena Schelotto
- b Servicio De Hemato-Oncología Pediátrica, Centro Hospitalario Pereira Rosell , Montevideo , Uruguay
| | - Natalia de Oliveira Mota
- c Departamento De Patología Clinica , Faculdade De Ciências Médicas, Universidade De Campinas , São Paulo , Brazil
| | - Roberta Dorta Ferreira
- c Departamento De Patología Clinica , Faculdade De Ciências Médicas, Universidade De Campinas , São Paulo , Brazil
| | - Maria de Fatima Sonati
- c Departamento De Patología Clinica , Faculdade De Ciências Médicas, Universidade De Campinas , São Paulo , Brazil
| | - Julio Abayubá da Luz
- a Laboratorio De Genética Molecular Humana , Centro Universitario Regional (CENUR) Litoral Norte-Sede Salto, Universidad De La República , Salto , Uruguay
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12
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Prunier J, Caron S, MacKay J. CNVs into the wild: screening the genomes of conifer trees (Picea spp.) reveals fewer gene copy number variations in hybrids and links to adaptation. BMC Genomics 2017; 18:97. [PMID: 28100184 PMCID: PMC5241962 DOI: 10.1186/s12864-016-3458-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/22/2016] [Indexed: 12/31/2022] Open
Abstract
Background Copy number variations (CNVs) have been linked to different phenotypes in human, including many diseases. A genome-scale understanding of CNVs is available in a few plants but none are wild species, leaving a knowledge gap regarding their genome biology and evolutionary role. We developed a reliable CNV detection method for species lacking contiguous reference genome. We selected multiple probes within 14,078 gene sequences and developed comparative genome hybridization on arrays. Gene CNVs were assessed in three full-sib families from species with 20 Gb genomes, i.e., white and black spruce, and interior spruce - a natural hybrid. Results We discovered hundreds of gene CNVs in each species, 3612 in total, which were enriched in functions related to stress and defense responses and narrow expression profiles, indicating a potential role in adaptation. The number of shared CNVs was in accordance with the degree of relatedness between individuals and species. The genetically mapped subset of these genes showed a wide distribution across the genome, implying numerous structural variations. The hybrid family presented significantly fewer CNVs, suggesting that the admixture of two species within one genome reduces the occurrence of CNVs. Conclusions The approach we developed is of particular interest in non-model species lacking a reference genome. Our findings point to a role for CNVs in adaptation. Their reduced abundance in the hybrid may limit genetic variability and evolvability of hybrids. We propose that CNVs make a qualitatively distinct contribution to adaptation which could be important for short term change. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3458-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julien Prunier
- Institute for System and Integrative Biology (IBIS), Université Laval, Quebec, QC, G1V 0A6, Canada. .,Centre for Forest Research, Université Laval, Quebec, QC, G1V 0A6, Canada.
| | - Sébastien Caron
- Institute for System and Integrative Biology (IBIS), Université Laval, Quebec, QC, G1V 0A6, Canada
| | - John MacKay
- Centre for Forest Research, Université Laval, Quebec, QC, G1V 0A6, Canada.,Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
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13
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Xin Y, Zhou J, Ding Q, Chen C, Wu X, Wang X, Wang H, Jiang X. A pericentric inversion of chromosome X disruptingF8and resulting in haemophilia A. J Clin Pathol 2017; 70:656-661. [DOI: 10.1136/jclinpath-2016-204050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 11/04/2022]
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14
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Carvalho CMB, Lupski JR. Mechanisms underlying structural variant formation in genomic disorders. Nat Rev Genet 2016; 17:224-38. [PMID: 26924765 DOI: 10.1038/nrg.2015.25] [Citation(s) in RCA: 414] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With the recent burst of technological developments in genomics, and the clinical implementation of genome-wide assays, our understanding of the molecular basis of genomic disorders, specifically the contribution of structural variation to disease burden, is evolving quickly. Ongoing studies have revealed a ubiquitous role for genome architecture in the formation of structural variants at a given locus, both in DNA recombination-based processes and in replication-based processes. These reports showcase the influence of repeat sequences on genomic stability and structural variant complexity and also highlight the tremendous plasticity and dynamic nature of our genome in evolution, health and disease susceptibility.
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Affiliation(s)
- Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Centro de Pesquisas René Rachou - FIOCRUZ, Belo Horizonte, MG 30190-002, Brazil
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Texas Children's Hospital, Houston, Texas 77030, USA
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15
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Abstract
During meiosis, numerous DNA double-strand breaks (DSBs) are formed as part of the normal developmental program. This seemingly destructive behavior is necessary for successful meiosis, since repair of the DSBs through homologous recombination (HR) helps to produce physical links between the homologous chromosomes essential for correct chromosome segregation later in meiosis. However, DSB formation at such a massive scale also introduces opportunities to generate gross chromosomal rearrangements. In this review, we explore ways in which meiotic DSBs can result in such genomic alterations.
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16
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Xie XM, Wu MY, Li DZ. Evidence of Selection for theα-Globin Gene Deletions and Triplications in a Southern Chinese Population. Hemoglobin 2015; 39:442-4. [DOI: 10.3109/03630269.2015.1072551] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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17
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Andersson DI, Jerlström-Hultqvist J, Näsvall J. Evolution of new functions de novo and from preexisting genes. Cold Spring Harb Perspect Biol 2015; 7:7/6/a017996. [PMID: 26032716 DOI: 10.1101/cshperspect.a017996] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
How the enormous structural and functional diversity of new genes and proteins was generated (estimated to be 10(10)-10(12) different proteins in all organisms on earth [Choi I-G, Kim S-H. 2006. Evolution of protein structural classes and protein sequence families. Proc Natl Acad Sci 103: 14056-14061] is a central biological question that has a long and rich history. Extensive work during the last 80 years have shown that new genes that play important roles in lineage-specific phenotypes and adaptation can originate through a multitude of different mechanisms, including duplication, lateral gene transfer, gene fusion/fission, and de novo origination. In this review, we focus on two main processes as generators of new functions: evolution of new genes by duplication and divergence of pre-existing genes and de novo gene origination in which a whole protein-coding gene evolves from a noncoding sequence.
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Affiliation(s)
- Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jon Jerlström-Hultqvist
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Joakim Näsvall
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
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18
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Ido Y, Yoshitomi T, Ohkura K, Yamamoto T, Shinohara Y. Utility of syntenic relationships of VDAC1 pseudogenes for not only an understanding of the phylogenetic divergence history of rodents, but also ascertaining possible pseudogene candidates as genuine pseudogenes. Genomics 2014; 104:128-33. [PMID: 24858958 DOI: 10.1016/j.ygeno.2014.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 05/06/2014] [Accepted: 05/14/2014] [Indexed: 11/20/2022]
Abstract
Rodent and human genomes were screened to identify pseudogenes of the type 1 voltage-dependent anion channel (VDAC1) in mitochondria. In addition to the 16 pseudogenes of rat VDAC1 identified in our recent study, 15 and 13 sequences were identified as pseudogenes of VDAC1 in mouse and human genome, respectively; and 4, 2, and 1 sequences, showing lower similarities with the VDAC1 sequence, were identified as "possible pseudogene candidates" in rat, mouse, and human, respectively. No syntenic combination was observed between rodent and human pseudogenes, but 2 and 1 possible pseudogene candidates of VDAC1 of rat and mouse, respectively, were found to have syntenic counterparts in mouse and rat genome, respectively; and these syntenic counterparts were genuine VDAC1 pseudogenes. Therefore, syntenic combinations of pseudogenes of VDAC1 were useful not only for a better understanding of the phylogenetic divergence history of rodents but also for ascertaining possible pseudogene candidates as genuine pseudogenes.
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Affiliation(s)
- Yusuke Ido
- Institute for Genome Research, University of Tokushima, Kuramoto-cho-3, Tokushima 770-8503, Japan; Faculty of Pharmaceutical Sciences, University of Tokushima, Shomachi-1, Tokushima 770-8505, Japan
| | - Tatsuki Yoshitomi
- Institute for Genome Research, University of Tokushima, Kuramoto-cho-3, Tokushima 770-8503, Japan; Faculty of Pharmaceutical Sciences, University of Tokushima, Shomachi-1, Tokushima 770-8505, Japan
| | - Kazuto Ohkura
- Faculty of Pharmaceutical Science, Suzuka University of Medical Science, Minamitamagaki-cho, Suzuka 513-8670, Japan
| | - Takenori Yamamoto
- Institute for Genome Research, University of Tokushima, Kuramoto-cho-3, Tokushima 770-8503, Japan; Faculty of Pharmaceutical Sciences, University of Tokushima, Shomachi-1, Tokushima 770-8505, Japan
| | - Yasuo Shinohara
- Institute for Genome Research, University of Tokushima, Kuramoto-cho-3, Tokushima 770-8503, Japan; Faculty of Pharmaceutical Sciences, University of Tokushima, Shomachi-1, Tokushima 770-8505, Japan.
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19
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Tandem duplication PCR: an ultrasensitive assay for the detection of internal tandem duplications of the FLT3 gene. ACTA ACUST UNITED AC 2014; 22:149-55. [PMID: 23846441 DOI: 10.1097/pdm.0b013e31828308a1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Internal tandem duplication (ITD) mutations of the FLT3 gene have been associated with a poor prognosis in acute myeloid leukemia. Detection of ITD-positive minor clones at the initial diagnosis and during the minimal residual disease stage may be essential. We previously designed a delta-PCR strategy to improve the sensitivity to 0.1% ITD-positive leukemia cells and showed that minor mutants with an allele burden of <1% can be clinically significant. In this study, we report on tandem duplication PCR (TD-PCR), a modified inverse PCR assay, and demonstrate a limit of detection of a few molecules of ITD mutants. The TD-PCR was initially designed to confirm ITD mutation of an amplicon, which was undetectable by capillary electrophoresis and was incidentally isolated by a molecular fraction collecting tool. Subsequently, TD-PCR detected ITD mutation in 2 of 77 patients previously reported as negative for ITD mutation by a standard PCR assay. TD-PCR can also potentially be applied to monitor minimal residual disease with high analytic sensitivity in a portion of ITD-positive acute myeloid leukemia patients. Further studies using TD-PCR to detect ITD mutants at diagnosis may clarify the clinical significance of those ITD mutants with extremely low allele burden.
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20
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Baudat F, Imai Y, de Massy B. Meiotic recombination in mammals: localization and regulation. Nat Rev Genet 2013; 14:794-806. [PMID: 24136506 DOI: 10.1038/nrg3573] [Citation(s) in RCA: 390] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
During meiosis, a programmed induction of DNA double-strand breaks (DSBs) leads to the exchange of genetic material between homologous chromosomes. These exchanges increase genome diversity and are essential for proper chromosome segregation at the first meiotic division. Recent findings have highlighted an unexpected molecular control of the distribution of meiotic DSBs in mammals by a rapidly evolving gene, PR domain-containing 9 (PRDM9), and genome-wide analyses have facilitated the characterization of meiotic DSB sites at unprecedented resolution. In addition, the identification of new players in DSB repair processes has allowed the delineation of recombination pathways that have two major outcomes, crossovers and non-crossovers, which have distinct mechanistic roles and consequences for genome evolution.
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Affiliation(s)
- Frédéric Baudat
- Institute of Human Genetics, Unité Propre de Recherche 1142, Centre National de la Recherche Scientifique, 141 rue de la Cardonille, 34396 Montpellier, France
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21
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Katju V, Bergthorsson U. Copy-number changes in evolution: rates, fitness effects and adaptive significance. Front Genet 2013; 4:273. [PMID: 24368910 PMCID: PMC3857721 DOI: 10.3389/fgene.2013.00273] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 11/18/2013] [Indexed: 11/13/2022] Open
Abstract
Gene copy-number differences due to gene duplications and deletions are rampant in natural populations and play a crucial role in the evolution of genome complexity. Per-locus analyses of gene duplication rates in the pre-genomic era revealed that gene duplication rates are much higher than the per nucleotide substitution rate. Analyses of gene duplication and deletion rates in mutation accumulation lines of model organisms have revealed that these high rates of copy-number mutations occur at a genome-wide scale. Furthermore, comparisons of the spontaneous duplication and deletion rates to copy-number polymorphism data and bioinformatic-based estimates of duplication rates from sequenced genomes suggest that the vast majority of gene duplications are detrimental and removed by natural selection. The rate at which new gene copies appear in populations greatly influences their evolutionary dynamics and standing gene copy-number variation in populations. The opportunity for mutations that result in the maintenance of duplicate copies, either through neofunctionalization or subfunctionalization, also depends on the equilibrium frequency of additional gene copies in the population, and hence on the spontaneous gene duplication (and loss) rate. The duplication rate may therefore have profound effects on the role of adaptation in the evolution of duplicated genes as well as important consequences for the evolutionary potential of organisms. We further discuss the broad ramifications of this standing gene copy-number variation on fitness and adaptive potential from a population-genetic and genome-wide perspective.
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Affiliation(s)
- Vaishali Katju
- Department of Biology, University of New Mexico Albuquerque, NM, USA
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22
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Bengesser K, Vogt J, Mussotter T, Mautner VF, Messiaen L, Cooper DN, Kehrer-Sawatzki H. Analysis of crossover breakpoints yields new insights into the nature of the gene conversion events associated with large NF1 deletions mediated by nonallelic homologous recombination. Hum Mutat 2013; 35:215-26. [PMID: 24186807 DOI: 10.1002/humu.22473] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 10/18/2013] [Indexed: 12/31/2022]
Abstract
Large NF1 deletions are mediated by nonallelic homologous recombination (NAHR). An in-depth analysis of gene conversion operating in the breakpoint-flanking regions of large NF1 deletions was performed to investigate whether the rate of discontinuous gene conversion during NAHR with crossover is increased, as has been previously noted in NAHR-mediated rearrangements. All 20 germline type-1 NF1 deletions analyzed were mediated by NAHR associated with continuous gene conversion within the breakpoint-flanking regions. Continuous gene conversion was also observed in 31/32 type-2 NF1 deletions investigated. In contrast to the meiotic type-1 NF1 deletions, type-2 NF1 deletions are predominantly of post-zygotic origin. Our findings therefore imply that the mitotic as well as the meiotic NAHR intermediates of large NF1 deletions are processed by long-patch mismatch repair (MMR), thereby ensuring gene conversion tract continuity instead of the discontinuous gene conversion that is characteristic of short-patch repair. However, the single type-2 NF1 deletion not exhibiting continuous gene conversion was processed without MMR, yielding two different deletion-bearing chromosomes, which were distinguishable in terms of their breakpoint positions. Our findings indicate that MMR failure during NAHR, followed by post-meiotic/mitotic segregation, has the potential to give rise to somatic mosaicism in human genomic rearrangements by generating breakpoint heterogeneity.
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23
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Zhang J, Zuo T, Peterson T. Generation of tandem direct duplications by reversed-ends transposition of maize ac elements. PLoS Genet 2013; 9:e1003691. [PMID: 23966872 PMCID: PMC3744419 DOI: 10.1371/journal.pgen.1003691] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 06/18/2013] [Indexed: 11/19/2022] Open
Abstract
Tandem direct duplications are a common feature of the genomes of eukaryotes ranging from yeast to human, where they comprise a significant fraction of copy number variations. The prevailing model for the formation of tandem direct duplications is non-allelic homologous recombination (NAHR). Here we report the isolation of a series of duplications and reciprocal deletions isolated de novo from a maize allele containing two Class II Ac/Ds transposons. The duplication/deletion structures suggest that they were generated by alternative transposition reactions involving the termini of two nearby transposable elements. The deletion/duplication breakpoint junctions contain 8 bp target site duplications characteristic of Ac/Ds transposition events, confirming their formation directly by an alternative transposition mechanism. Tandem direct duplications and reciprocal deletions were generated at a relatively high frequency (~0.5 to 1%) in the materials examined here in which transposons are positioned nearby each other in appropriate orientation; frequencies would likely be much lower in other genotypes. To test whether this mechanism may have contributed to maize genome evolution, we analyzed sequences flanking Ac/Ds and other hAT family transposons and identified three small tandem direct duplications with the structural features predicted by the alternative transposition mechanism. Together these results show that some class II transposons are capable of directly inducing tandem sequence duplications, and that this activity has contributed to the evolution of the maize genome.
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Affiliation(s)
- Jianbo Zhang
- Department of Genetics, Development and Cell Biology, Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | - Tao Zuo
- Department of Genetics, Development and Cell Biology, Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | - Thomas Peterson
- Department of Genetics, Development and Cell Biology, Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
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24
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Yap ZM, Sun KM, Teo CR, Tan AS, Chong SS. Evidence of differential selection for the −α3.7and −α4.2single-α-globin gene deletions within the same population. Eur J Haematol 2013; 90:210-3. [DOI: 10.1111/ejh.12058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2012] [Indexed: 11/27/2022]
Affiliation(s)
- Zhi Min Yap
- University College London Medical School; University College London; London; UK
| | - Kar Mun Sun
- School of Biological Sciences; Nanyang Technological University of Singapore; Singapore
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25
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Abstract
The globin gene disorders including the thalassemias are among the most common human genetic diseases with more than 300,000 severely affected individuals born throughout the world every year. Because of the easy accessibility of purified, highly specialized, mature erythroid cells from peripheral blood, the hemoglobinopathies were among the first tractable human molecular diseases. From the 1970s onward, the analysis of the large repertoire of mutations underlying these conditions has elucidated many of the principles by which mutations occur and cause human genetic diseases. This work will summarize our current knowledge of the α-thalassemias, illustrating how detailed analysis of this group of diseases has contributed to our understanding of the general molecular mechanisms underlying many orphan and common diseases.
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Affiliation(s)
- Douglas R Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK.
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26
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Sun Z, Liu P, Jia X, Withers MA, Jin L, Lupski JR, Zhang F. Replicative mechanisms of CNV formation preferentially occur as intrachromosomal events: evidence from Potocki-Lupski duplication syndrome. Hum Mol Genet 2012; 22:749-56. [PMID: 23161748 DOI: 10.1093/hmg/dds482] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Copy number variations (CNVs) in the human genome contribute significantly to disease. De novo CNV mutations arise via genomic rearrangements, which can occur in 'trans', i.e. via interchromosomal events, or in 'cis', i.e. via intrachromosomal events. However, what molecular mechanisms occur between chromosomes versus between or within chromatids has not been systematically investigated. We hypothesized that distinct CNV mutational mechanisms, based on their intrinsic properties, may occur in a biased intrachromosomal versus interchromosomal manner. Here, we studied 62 genomic duplications observed in association with sporadic Potocki-Lupski syndrome (PTLS), in which multiple mutational mechanisms appear to be operative. Intriguingly, more interchromosomal than intrachromosomal events were identified in recurrent PTLS duplications mediated by non-allelic homologous recombination, whereas the reciprocal distribution was found for replicative mechanisms and non-homologous end-joining, likely reflecting the differences in spacial proximity of homologous chromosomes during different mutational processes.
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Affiliation(s)
- Zhe Sun
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
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27
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Vogt J, Mussotter T, Bengesser K, Claes K, Högel J, Chuzhanova N, Fu C, van den Ende J, Mautner VF, Cooper DN, Messiaen L, Kehrer-Sawatzki H. Identification of recurrent type-2 NF1 microdeletions reveals a mitotic nonallelic homologous recombination hotspot underlying a human genomic disorder. Hum Mutat 2012; 33:1599-609. [PMID: 22837079 DOI: 10.1002/humu.22171] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 07/11/2012] [Indexed: 01/08/2023]
Abstract
Nonallelic homologous recombination (NAHR) is one of the major mechanisms underlying copy number variation in the human genome. Although several disease-associated meiotic NAHR breakpoints have been analyzed in great detail, hotspots for mitotic NAHR are not well characterized. Type-2 NF1 microdeletions, which are predominantly of postzygotic origin, constitute a highly informative model with which to investigate the features of mitotic NAHR. Here, a custom-designed MLPA- and PCR-based approach was used to identify 23 novel NAHR-mediated type-2 NF1 deletions. Breakpoint analysis of these 23 type-2 deletions, together with 17 NAHR-mediated type-2 deletions identified previously, revealed that the breakpoints are nonuniformly distributed within the paralogous SUZ12 and SUZ12P sequences. Further, the analysis of this large group of type-2 deletions revealed breakpoint recurrence within short segments (ranging in size from 57 to 253-bp) as well as the existence of a novel NAHR hotspot of 1.9-kb (termed PRS4). This hotspot harbored 20% (8/40) of the type-2 deletion breakpoints and contains the 253-bp recurrent breakpoint region BR6 in which four independent type-2 deletion breakpoints were identified. Our findings indicate that a combination of an open chromatin conformation and short non-B DNA-forming repeats may predispose to recurrent mitotic NAHR events between SUZ12 and its pseudogene.
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Affiliation(s)
- Julia Vogt
- Institute of Human Genetics, University of Ulm, Ulm, Germany
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28
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Simmons AD, Carvalho CMB, Lupski JR. What have studies of genomic disorders taught us about our genome? Methods Mol Biol 2012; 838:1-27. [PMID: 22228005 DOI: 10.1007/978-1-61779-507-7_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The elucidation of genomic disorders began with molecular technologies that enabled detection of genomic changes which were (a) smaller than those resolved by traditional cytogenetics (less than 5 Mb) and (b) larger than what could be determined by conventional gel electrophoresis. Methods such as pulsed field gel electrophoresis (PFGE) and fluorescent in situ hybridization (FISH) could resolve such changes but were limited to locus-specific studies. The study of genomic disorders has rapidly advanced with the development of array-based techniques. These enabled examination of the entire human genome at a higher level of resolution, thus allowing elucidation of the basis of many new disorders, mechanisms that result in genomic changes that can result in copy number variation (CNV), and most importantly, a deeper understanding of the characteristics, features, and plasticity of our genome. In this chapter, we focus on the structural and architectural features of the genome, which can potentially result in genomic instability, delineate how mechanisms, such as NAHR, NHEJ, and FoSTeS/MMBIR lead to disease-causing rearrangements, and briefly describe the relationship between the leading methods presently used in studying genomic disorders. We end with a discussion on our new understanding about our genome including: the contribution of new mutation CNV to disease, the abundance of mosaicism, the extent of subtelomeric rearrangements, the frequency of de novo rearrangements associated with sporadic birth defects, the occurrence of balanced and unbalanced translocations, the increasing discovery of insertional translocations, the exploration of complex rearrangements and exonic CNVs. In the postgenomic era, our understanding of the genome has advanced very rapidly as the level of technical resolution has become higher. This leads to a greater understanding of the effects of rearrangements present both in healthy subjects and individuals with clinically relevant phenotypes.
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29
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Malhotra D, Sebat J. CNVs: harbingers of a rare variant revolution in psychiatric genetics. Cell 2012; 148:1223-41. [PMID: 22424231 PMCID: PMC3351385 DOI: 10.1016/j.cell.2012.02.039] [Citation(s) in RCA: 593] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Indexed: 12/21/2022]
Abstract
The genetic bases of neuropsychiatric disorders are beginning to yield to scientific inquiry. Genome-wide studies of copy number variation (CNV) have given rise to a new understanding of disease etiology, bringing rare variants to the forefront. A proportion of risk for schizophrenia, bipolar disorder, and autism can be explained by rare mutations. Such alleles arise by de novo mutation in the individual or in recent ancestry. Alleles can have specific effects on behavioral and neuroanatomical traits; however, expressivity is variable, particularly for neuropsychiatric phenotypes. Knowledge from CNV studies reflects the nature of rare alleles in general and will serve as a guide as we move forward into a new era of whole-genome sequencing.
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Affiliation(s)
- Dheeraj Malhotra
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA 1020103, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 1020103, USA
| | - Jonathan Sebat
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA 1020103, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 1020103, USA
- Department of Cellular Molecular and Molecular Medicine, University of California, San Diego, La Jolla, CA 1020103, USA
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 1020103, USA
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30
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Abstract
Structural variation (SV) encompasses diverse types of genomic variants including deletions, duplications, inversions, transpositions, translocations, and complex rearrangements, and is now recognized to be an abundant class of genetic variation in mammals. Different individuals, or strains, of a given species can differ by thousands of variants. However, despite a large number of studies over the past decade and impressive progress on many fronts, there remain significant gaps in our knowledge, particularly in species other than human. Arguably the most relevant among these are genetically tractable models such as mouse, rat, and dog. The emergence of efficient and affordable DNA sequencing technologies presents an opportunity to make rapid progress toward understanding the nature, origin, and function of SV in these, and other, domesticated species. Here, we summarize the current state of knowledge of SV in mammals, with a focus on the similarities and differences between domesticated species and human. We then present methods to identify SV breakpoints from next-generation sequence (NGS) data by paired-end mapping, split-read mapping, and local assembly, and discuss challenges that arise when interpreting these data in lineages with complex breeding histories and incomplete reference genomes. We further describe technical modifications that allow for identification of variants involving repetitive DNA elements such as transposons and segmental duplications. Finally, we explore a few of the key biological insights that can be gained by applying NGS methods to model organisms.
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Affiliation(s)
- Ira M Hall
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
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31
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Quinlan AR, Hall IM. Characterizing complex structural variation in germline and somatic genomes. Trends Genet 2011; 28:43-53. [PMID: 22094265 DOI: 10.1016/j.tig.2011.10.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 10/02/2011] [Accepted: 10/03/2011] [Indexed: 10/15/2022]
Abstract
Genome structural variation (SV) is a major source of genetic diversity in mammals and a hallmark of cancer. Although SV is typically defined by its canonical forms (duplication, deletion, insertion, inversion and translocation), recent breakpoint mapping studies have revealed a surprising number of 'complex' variants that evade simple classification. Complex SVs are defined by clustered breakpoints that arose through a single mutation but cannot be explained by one simple end-joining or recombination event. Some complex variants exhibit profoundly complicated rearrangements between distinct loci from multiple chromosomes, whereas others involve more subtle alterations at a single locus. These diverse and unpredictable features present a challenge for SV mapping experiments. Here, we review current knowledge of complex SV in mammals, and outline techniques for identifying and characterizing complex variants using next-generation DNA sequencing.
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Affiliation(s)
- Aaron R Quinlan
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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Hedrick PW. Selection and mutation for α Thalassemia in nonmalarial and malarial environments. Ann Hum Genet 2011; 75:468-74. [PMID: 21534938 DOI: 10.1111/j.1469-1809.2011.00653.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
α thalassemia is the result of the loss of one or both copies of the two human α globin genes. α thalassemia appears to be the most common monogenic disease in the world and is in high frequency where malaria is, or has been, endemic. In nonmalarial environments, α thalassemia is rare and its frequency can be explained by a balance of deletional mutation and purifying selection. In malarial environments, the loss of one or two copies of the four α globin genes in normal diploid genotypes confers resistance (lower mortality) to malaria. Fitness estimates from data from Kenyan and Papua New Guinea populations are used to predict the increase in the --α haplotype (with one deleted gene). The frequency of double deletions (-- haplotypes) is higher in some Asian populations than that of single deletions. In this case, heterozygotes with normal αα haplotypes are expected to have the highest fitness. Overall, this population genetic examination provides an evolutionary framework for understanding the worldwide frequency of α thalassemia and the deletions that cause it in both nonmalarial and malarial environments.
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Affiliation(s)
- Philip W Hedrick
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA.
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33
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High spontaneous rate of gene duplication in Caenorhabditis elegans. Curr Biol 2011; 21:306-10. [PMID: 21295484 DOI: 10.1016/j.cub.2011.01.026] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2010] [Revised: 11/30/2010] [Accepted: 01/10/2011] [Indexed: 12/30/2022]
Abstract
Gene and genome duplications are the primary source of new genes and novel functions and have played a pivotal role in the evolution of genomic and organismal complexity. The spontaneous rate of gene duplication is a critical parameter for understanding the evolutionary dynamics of gene duplicates; yet few direct empirical estimates exist and differ widely. The presence of a large population of recently derived gene duplicates in sequenced genomes suggests a high rate of spontaneous origin, also evidenced by population genomic studies reporting rampant copy-number polymorphism at the intraspecific level. An analysis of long-term mutation accumulation lines of Caenorhabditis elegans for gene copy-number changes with array comparative genomic hybridization yields the first direct estimate of the genome-wide rate of gene duplication in a multicellular eukaryote. The gene duplication rate in C. elegans is quite high, on the order of 10(-7) duplications/gene/generation. This rate is two orders of magnitude greater than the spontaneous rate of point mutation per nucleotide site in this species and also greatly exceeds an earlier estimate derived from the frequency distribution of extant gene duplicates in the sequenced C. elegans genome.
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Roehl AC, Vogt J, Mussotter T, Zickler AN, Spöti H, Högel J, Chuzhanova NA, Wimmer K, Kluwe L, Mautner VF, Cooper DN, Kehrer-Sawatzki H. Intrachromosomal mitotic nonallelic homologous recombination is the major molecular mechanism underlying type-2 NF1 deletions. Hum Mutat 2011; 31:1163-73. [PMID: 20725927 DOI: 10.1002/humu.21340] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Nonallelic homologous recombination (NAHR) is responsible for the recurrent rearrangements that give rise to genomic disorders. Although meiotic NAHR has been investigated in multiple contexts, much less is known about mitotic NAHR despite its importance for tumorigenesis. Because type-2 NF1 microdeletions frequently result from mitotic NAHR, they represent a good model in which to investigate the features of mitotic NAHR. We have used microsatellite analysis and SNP arrays to distinguish between the various alternative recombinational possibilities, thereby ascertaining that 17 of 18 type-2 NF1 deletions, with breakpoints in the SUZ12 gene and its highly homologous pseudogene, originated via intrachromosomal recombination. This high proportion of intrachromosomal NAHR causing somatic type-2 NF1 deletions contrasts with the interchromosomal origin of germline type-1 NF1 microdeletions, whose breakpoints are located within the NF1-REPs (low-copy repeats located adjacent to the SUZ12 sequences). Further, meiotic NAHR causing type-1 NF1 deletions occurs within recombination hotspots characterized by high GC-content and DNA duplex stability, whereas the type-2 breakpoints associated with the mitotic NAHR events investigated here do not cluster within hotspots and are located within regions of significantly lower GC-content and DNA stability. Our findings therefore point to fundamental mechanistic differences between the determinants of mitotic and meiotic NAHR.
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Fu W, Zhang F, Wang Y, Gu X, Jin L. Identification of copy number variation hotspots in human populations. Am J Hum Genet 2010; 87:494-504. [PMID: 20920665 DOI: 10.1016/j.ajhg.2010.09.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 08/09/2010] [Accepted: 09/15/2010] [Indexed: 01/22/2023] Open
Abstract
Copy number variants (CNVs) in the human genome contribute to both Mendelian and complex traits as well as to genomic plasticity in evolution. The investigation of mutational rates of CNVs is critical to understanding genomic instability and the etiology of the copy number variation (CNV)-related traits. However, the evaluation of the CNV mutation rate at the genome level poses an insurmountable practical challenge that requires large samples and accurate typing. In this study, we show that an approximate estimation of the CNV mutation rate could be achieved by using the phylogeny information of flanking SNPs. This allows a genome-wide comparison of mutation rates between CNVs with the use of vast, readily available data of SNP genotyping. A total of 4187 CNV regions (CNVRs) previously identified in HapMap populations were investigated in this study. We showed that the mutation rates for the majority of these CNVRs are at the order of 10⁻⁵ per generation, consistent with experimental observations at individual loci. Notably, the mutation rates of 104 (2.5%) CNVRs were estimated at the order of 10⁻³ per generation; therefore, they were identified as potential hotspots. Additional analyses revealed that genome architecture at CNV loci has a potential role in inciting mutational hotspots in the human genome. Interestingly, 49 (47%) CNV hotspots include human genes, some of which are known to be functional CNV loci (e.g., CNVs of C4 and β-defensin causing autoimmune diseases and CNVs of HYDIN with implication in control of cerebral cortex size), implicating the important role of CNV in human health and evolution, especially in common and complex diseases.
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Molina O, Anton E, Vidal F, Blanco J. Sperm rates of 7q11.23, 15q11q13 and 22q11.2 deletions and duplications: a FISH approach. Hum Genet 2010; 129:35-44. [PMID: 20931230 DOI: 10.1007/s00439-010-0894-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Accepted: 09/23/2010] [Indexed: 11/30/2022]
Abstract
Genomic disorders are human diseases caused by meiotic chromosomal rearrangements of unstable regions flanked by Low Copy Repeats (LCRs). LCRs act as substrates for Non-Allelic Homologous Recombination (NAHR) leading to deletions and duplications. The aim of this study was to assess the basal frequency of deletions and duplications of the 7q11.23, 15q11-q13 and 22q11.2 regions in spermatozoa from control donors to check differences in the susceptibility to generate anomalies and to assess the contribution of intra- and inter-chromatid NAHR events. Semen samples from ten control donors were processed by FISH. A customized combination of probes was used to discriminate among normal, deleted and duplicated sperm genotypes. A minimum of 10,000 sperm were assessed per sample and region. There were no differences in the mean frequency of deletions and duplications (del + dup) among the 7q11.23, 15q11-q13 and 22q11.2 regions (frequency ± SEM, 0.37 ± 0.02; 0.46 ± 0.07 and 0.27 ± 0.07%, respectively) (P = 0.122). Nevertheless, hierarchical cluster analysis reveals interindividual differences suggesting that particular haplotypes could be the main source of variability in NAHR rates. The mean frequency of deletions was not different from the mean frequency of duplications in the 7q11.23 (P = 0.202) and 15q11-q13 (P = 0.609) regions, indicating a predominant inter-chromatid NAHR. By contrast, in the 22q11.2 region the frequency of deletions slightly exceed duplications (P = 0.032), although at the individual level any donor showed differences. Altogether, our results support the inter-chromatid NAHR as the predominant mechanism involved in the generation of sperm deletions and duplications.
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MESH Headings
- Adult
- Chromatids/genetics
- Chromosome Aberrations
- Chromosomes, Human, Pair 15/genetics
- Chromosomes, Human, Pair 22/genetics
- Chromosomes, Human, Pair 7/genetics
- DNA Sequence, Unstable/genetics
- Gene Deletion
- Gene Duplication
- Haplotypes/genetics
- Humans
- In Situ Hybridization, Fluorescence
- Male
- Middle Aged
- Recombination, Genetic
- Segmental Duplications, Genomic/genetics
- Spermatozoa
- Tissue Donors
- Young Adult
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Affiliation(s)
- Oscar Molina
- Unitat de Biologia Cel·lular, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Bellaterra (Cerdanyola del Vallès), Spain
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Higgs DR, Gibbons RJ. The molecular basis of α-thalassemia: a model for understanding human molecular genetics. Hematol Oncol Clin North Am 2010; 24:1033-54. [PMID: 21075279 DOI: 10.1016/j.hoc.2010.08.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Down-regulation of α-globin synthesis causes α-thalassemia with underproduction of fetal (HbF, α(2)γ(2)) and adult (HbA, α(2)β(2)) hemoglobin. This article focuses on the human α-globin cluster, which has been characterized in great depth over the past 30 years. In particular the authors describe how the α genes are normally switched on during erythropoiesis and switched off as hematopoietic stem cells commit to nonerythroid lineages. In addition, the principles by which α-globin expression may be perturbed by natural mutations that cause α-thalassemia are reviewed.
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Affiliation(s)
- Douglas R Higgs
- John Radcliffe Hospital, MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford, UK.
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38
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Dynamics and processes of copy number instability in human gamma-globin genes. Proc Natl Acad Sci U S A 2010; 107:8304-9. [PMID: 20404158 DOI: 10.1073/pnas.1003634107] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Copy number variation in the human genome is prevalent but relatively little is known about the dynamics of DNA rearrangement. We therefore used the duplicated gamma-globin genes as a simple system to explore de novo copy number changes. Rearrangements that changed gene number were seen in both germline and somatic DNA, and mainly arose by unequal sister chromatid exchange between homologous sequences, with evidence from recurrent mosaic rearrangements that many, if not all, of these events in sperm arise before meiosis. Unequal exchange frequencies are apparently controlled primarily by the degree of sequence identity shared by the duplicate genes, leading to substantial variation between haplotypes in copy number instability. Additional, more complex rearrangements generated by mechanisms not involving homologous recombination, and in some cases showing DNA transfer between chromosomes, were also detected but were rare. Sequence changes were also seen in gamma-globin DNA molecules, with strong evidence that some were genuine de novo base substitutions. They were present in sperm at a frequency far higher than predicted from current estimates of germline mutation rates, raising interesting questions about base mutation dynamics in the male germline.
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39
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Genome destabilization by homologous recombination in the germ line. Nat Rev Mol Cell Biol 2010; 11:182-95. [PMID: 20164840 DOI: 10.1038/nrm2849] [Citation(s) in RCA: 159] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Meiotic recombination, which promotes proper homologous chromosome segregation at the first meiotic division, normally occurs between allelic sequences on homologues. However, recombination can also take place between non-allelic DNA segments that share high sequence identity. Such non-allelic homologous recombination (NAHR) can markedly alter genome architecture during gametogenesis by generating chromosomal rearrangements. Indeed, NAHR-mediated deletions, duplications, inversions and other alterations have been implicated in numerous human genetic disorders. Studies in yeast have provided insights into the molecular mechanisms of meiotic NAHR as well as the cellular strategies that limit it.
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40
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Genetic recombination as a major cause of mutagenesis in the human globin gene clusters. Clin Biochem 2009; 42:1839-50. [DOI: 10.1016/j.clinbiochem.2009.07.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 06/23/2009] [Accepted: 07/01/2009] [Indexed: 11/18/2022]
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41
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Hastings PJ, Lupski JR, Rosenberg SM, Ira G. Mechanisms of change in gene copy number. Nat Rev Genet 2009. [PMID: 19597530 DOI: 10.1038/nrg2593.mechanisms] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Deletions and duplications of chromosomal segments (copy number variants, CNVs) are a major source of variation between individual humans and are an underlying factor in human evolution and in many diseases, including mental illness, developmental disorders and cancer. CNVs form at a faster rate than other types of mutation, and seem to do so by similar mechanisms in bacteria, yeast and humans. Here we review current models of the mechanisms that cause copy number variation. Non-homologous end-joining mechanisms are well known, but recent models focus on perturbation of DNA replication and replication of non-contiguous DNA segments. For example, cellular stress might induce repair of broken replication forks to switch from high-fidelity homologous recombination to non-homologous repair, thus promoting copy number change.
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Affiliation(s)
- P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.
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42
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Hastings PJ, Lupski JR, Rosenberg SM, Ira G. Mechanisms of change in gene copy number. Nat Rev Genet 2009; 10:551-64. [PMID: 19597530 DOI: 10.1038/nrg2593] [Citation(s) in RCA: 846] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Deletions and duplications of chromosomal segments (copy number variants, CNVs) are a major source of variation between individual humans and are an underlying factor in human evolution and in many diseases, including mental illness, developmental disorders and cancer. CNVs form at a faster rate than other types of mutation, and seem to do so by similar mechanisms in bacteria, yeast and humans. Here we review current models of the mechanisms that cause copy number variation. Non-homologous end-joining mechanisms are well known, but recent models focus on perturbation of DNA replication and replication of non-contiguous DNA segments. For example, cellular stress might induce repair of broken replication forks to switch from high-fidelity homologous recombination to non-homologous repair, thus promoting copy number change.
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Affiliation(s)
- P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.
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43
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Abstract
Despite the long recognised effects of chromosomal structural abnormalities and completion of the Human Genome Project, much of the structural variation in the genome has gone unrecognised until recently. Deletions and duplications of DNA strands of between a few hundred bp and several million bp-collectively referred to as copy number variants-are now known to be widespread. Since 2007, rigorous and adequately powered genome-wide association studies based on single nucleotide polymorphisms have yielded replicated associations to several common diseases. Some copy number variants explain rare, previously uncharacterised disorders, and they are now expected to explain some of the genetic contribution to common diseases. We review efforts to map copy number variants and discuss present and future prospects for assessment of their relation to human health and disease.
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Affiliation(s)
- Louise V Wain
- Department of Health Sciences and Department of Genetics, University of Leicester, Leicester, UK
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44
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Moradkhani K, Préhu C, Old J, Henderson S, Balamitsa V, Luo HY, Poon MC, Chui DHK, Wajcman H, Patrinos GP. Mutations in the paralogous human alpha-globin genes yielding identical hemoglobin variants. Ann Hematol 2009; 88:535-43. [PMID: 18923834 PMCID: PMC2690850 DOI: 10.1007/s00277-008-0624-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Accepted: 09/25/2008] [Indexed: 11/25/2022]
Abstract
The human alpha-globin genes are paralogues, sharing a high degree of DNA sequence similarity and producing an identical alpha-globin chain. Over half of the alpha-globin structural variants reported to date are only characterized at the amino acid level. It is likely that a fraction of these variants, with phenotypes differing from one observation to another, may be due to the same mutation but on a different alpha-globin gene. There have been very few previous examples of hemoglobin variants that can be found at both HBA1 and HBA2 genes. Here, we report the results of a systematic multicenter study in a large multiethnic population to identify such variants and to analyze their differences from a functional and evolutionary perspective. We identified 14 different Hb variants resulting from identical mutations on either one of the two human alpha-globin paralogue genes. We also showed that the average percentage of hemoglobin variants due to a HBA2 gene mutation (alpha2) is higher than the percentage of hemoglobin variants due to the same HBA1 gene mutation (alpha1) and that the alpha2/alpha1 ratio varied between variants. These alpha-globin chain variants have most likely occurred via recurrent mutations, gene conversion events, or both. Based on these data, we propose a nomenclature for hemoglobin variants that fall into this category.
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Affiliation(s)
- Kamran Moradkhani
- Biochimie Génétique, AP-HP, Hôpital Henri Mondor, 94010 Créteil, France
- INSERM, U841, 94010 Créteil, France
| | - Claude Préhu
- Biochimie Génétique, AP-HP, Hôpital Henri Mondor, 94010 Créteil, France
- INSERM, U841, 94010 Créteil, France
| | - John Old
- National Haemoglobinopathy Reference Laboratory, Oxford Haemophilia Centre, Churchill Hospital, Oxford, UK
| | - Shirley Henderson
- National Haemoglobinopathy Reference Laboratory, Oxford Haemophilia Centre, Churchill Hospital, Oxford, UK
| | - Vera Balamitsa
- Unit for Prevention of Thalassemia, Trikala General Hospital, Trikala, Greece
| | - Hong-Yuan Luo
- Departments of Medicine, Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA USA
| | - Man-Chiu Poon
- Departments of Medicine and Pediatrics, University of Calgary and Calgary Health Region, Calgary, AB Canada
| | - David H. K. Chui
- Departments of Medicine, Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA USA
| | - Henri Wajcman
- Biochimie Génétique, AP-HP, Hôpital Henri Mondor, 94010 Créteil, France
- INSERM, U841, 94010 Créteil, France
| | - George P. Patrinos
- MGC-Department of Cell Biology and Genetics, Erasmus University Medical Center, Faculty of Medicine and Health Sciences, P. O. Box 2040, 3000 CA Rotterdam, the Netherlands
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45
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Novara F, Beri S, Bernardo ME, Bellazzi R, Malovini A, Ciccone R, Cometa AM, Locatelli F, Giorda R, Zuffardi O. Different molecular mechanisms causing 9p21 deletions in acute lymphoblastic leukemia of childhood. Hum Genet 2009; 126:511-20. [PMID: 19484265 PMCID: PMC2762534 DOI: 10.1007/s00439-009-0689-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Accepted: 05/19/2009] [Indexed: 12/03/2022]
Abstract
Deletion of chromosome 9p21 is a crucial event for the development of several cancers including acute lymphoblastic leukemia (ALL). Double strand breaks (DSBs) triggering 9p21 deletions in ALL have been reported to occur at a few defined sites by illegitimate action of the V(D)J recombination activating protein complex. We have cloned 23 breakpoint junctions for a total of 46 breakpoints in 17 childhood ALL (9 B- and 8 T-lineages) showing different size deletions at one or both homologous chromosomes 9 to investigate which particular sequences make the region susceptible to interstitial deletion. We found that half of 9p21 deletion breakpoints were mediated by ectopic V(D)J recombination mechanisms whereas the remaining half were associated to repeated sequences, including some with potential for non-B DNA structure formation. Other mechanisms, such as microhomology-mediated repair, that are common in other cancers, play only a very minor role in ALL. Nucleotide insertions at breakpoint junctions and microinversions flanking the breakpoints have been detected at 20/23 and 2/23 breakpoint junctions, respectively, both in the presence of recombination signal sequence (RSS)-like sequences and of other unspecific sequences. The majority of breakpoints were unique except for two cases, both T-ALL, showing identical deletions. Four of the 46 breakpoints coincide with those reported in other cases, thus confirming the presence of recurrent deletion hotspots. Among the six cases with heterozygous 9p deletions, we found that the remaining CDKN2A and CDKN2B alleles were hypermethylated at CpG islands.
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Affiliation(s)
- Francesca Novara
- Biologia Generale e Genetica Medica, Università degli Studi di Pavia, Via Forlanini, 14, 27100 Pavia, Italy
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46
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Abstract
It is now becoming generally accepted that a significant amount of human genetic variation is due to structural changes of the genome rather than to base-pair changes in the DNA. As for base-pair changes, knowledge of gene and genome function has been informed by structural alterations that convey clinical phenotypes. Genomic disorders are a class of human conditions that result from structural changes of the human genome that convey traits or susceptibility to traits. The path to the delineation of genomic disorders is intertwined with the evolving technologies that have enabled the resolution of human genome analyses to continue increasing. Similarly, the ability to perform high-resolution human genome analysis has fueled the current and future clinical implementation of such discoveries in the evolving field of genome medicine.
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Affiliation(s)
- James R Lupski
- Departments of Molecular and Human Genetics, and Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, TX 77030, USA.
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47
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Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution. Proc Natl Acad Sci U S A 2009; 106:7079-82. [PMID: 19357307 DOI: 10.1073/pnas.0900523106] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) are approximately 30 nucleotide noncoding RNAs that may be involved in transposon silencing in mammalian germline cells. Most piRNA sequences are found in a small number of genomic regions referred to as clusters, which range from 1 to hundreds of kilobases. We studied the evolution of 140 rodent piRNA clusters, 103 of which do not overlap protein-coding genes. Phylogenetic analysis revealed that 14 clusters were acquired after rat-mouse divergence and another 44 after rodent-primate divergence. Most clusters originated in a process analogous to the duplication of protein-coding genes by ectopic recombination, via insertions of long sequences that were mediated by flanking chromosome-specific repetitive elements (REs). Source sequences for such insertions are often located on the same chromosomes and also harbor clusters. The rate of piRNA cluster expansion is higher than that of any known gene family and, in contrast to other large gene families, there was not a single cluster loss. These observations suggest that piRNA cluster expansion is driven by positive selection, perhaps caused by the need to silence the ever-expanding repertoire of mammalian transposons.
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48
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Allelic recombination between distinct genomic locations generates copy number diversity in human beta-defensins. Proc Natl Acad Sci U S A 2009; 106:853-8. [PMID: 19131514 DOI: 10.1073/pnas.0809073106] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Beta-defensins are small secreted antimicrobial and signaling peptides involved in the innate immune response of vertebrates. In humans, a cluster of at least 7 of these genes shows extensive copy number variation, with a diploid copy number commonly ranging between 2 and 7. Using a genetic mapping approach, we show that this cluster is at not 1 but 2 distinct genomic loci approximately 5 Mb apart on chromosome band 8p23.1, contradicting the most recent genome assembly. We also demonstrate that the predominant mechanism of change in beta-defensin copy number is simple allelic recombination occurring in the interval between the 2 distinct genomic loci for these genes. In 416 meiotic transmissions, we observe 3 events creating a haplotype copy number not found in the parent, equivalent to a germ-line rate of copy number change of approximately 0.7% per gamete. This places it among the fastest-changing copy number variants currently known.
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49
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Hollox EJ, Barber JCK, Brookes AJ, Armour JAL. Defensins and the dynamic genome: what we can learn from structural variation at human chromosome band 8p23.1. Genome Res 2009; 18:1686-97. [PMID: 18974263 DOI: 10.1101/gr.080945.108] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Over the past four years, genome-wide studies have uncovered numerous examples of structural variation in the human genome. This includes structural variation that changes copy number, such as deletion and duplication, and structural variation that does not change copy number, such as orientation and positional polymorphism. One region that contains all these types of variation spans the chromosome band 8p23.1. This region has been studied in some depth, and the focus of this review is to examine our current understanding of the variation of this region. We also consider whether this region is a good model for other structurally variable regions in the genome and what the implications of this variation are for clinical studies. Finally, we discuss the bioinformatics challenges raised, discuss the evolution of the region, and suggest some future priorities for structural variation research.
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Affiliation(s)
- Edward J Hollox
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom.
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50
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Abstract
Copy number variation (CNV) is a source of genetic diversity in humans. Numerous CNVs are being identified with various genome analysis platforms, including array comparative genomic hybridization (aCGH), single nucleotide polymorphism (SNP) genotyping platforms, and next-generation sequencing. CNV formation occurs by both recombination-based and replication-based mechanisms and de novo locus-specific mutation rates appear much higher for CNVs than for SNPs. By various molecular mechanisms, including gene dosage, gene disruption, gene fusion, position effects, etc., CNVs can cause Mendelian or sporadic traits, or be associated with complex diseases. However, CNV can also represent benign polymorphic variants. CNVs, especially gene duplication and exon shuffling, can be a predominant mechanism driving gene and genome evolution.
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Affiliation(s)
- Feng Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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