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Abstract
For over a century, mice have been used to model human disease, leading to many fundamental discoveries about mammalian biology and the development of new therapies. Mouse genetics research has been further catalysed by a plethora of genomic resources developed in the last 20 years, including the genome sequence of C57BL/6J and more recently the first draft reference genomes for 16 additional laboratory strains. Collectively, the comparison of these genomes highlights the extreme diversity that exists at loci associated with the immune system, pathogen response, and key sensory functions, which form the foundation for dissecting phenotypic traits in vivo. We review the current status of the mouse genome across the diversity of the mouse lineage and discuss the value of mice to understanding human disease.
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Affiliation(s)
- Jingtao Lilue
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
- Instituto Gulbenkian de Ciência, Oeiras, Lisbon, Portugal
| | - Anu Shivalikanjli
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
| | | | - Thomas M. Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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Immuno-PET identifies the myeloid compartment as a key contributor to the outcome of the antitumor response under PD-1 blockade. Proc Natl Acad Sci U S A 2019; 116:16971-16980. [PMID: 31375632 DOI: 10.1073/pnas.1905005116] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Immunotherapy using checkpoint-blocking antibodies against PD-1 has produced impressive results in a wide range of cancers. However, the response remains heterogeneous among patients. We used noninvasive immuno-positron emission tomography (PET), using 89Zr-labeled PEGylated single-domain antibody fragments (nanobodies or VHHs), to explore the dynamics and distribution of intratumoral CD8+ T cells and CD11b+ myeloid cells in response to anti-PD-1 treatment in the MC38 colorectal mouse adenocarcinoma model. Responding and nonresponding tumors showed consistent differences in the distribution of CD8+ and CD11b+ cells. Anti-PD-1 treatment mobilized CD8+ T cells from the tumor periphery to a more central location. Only those tumors fully infiltrated by CD8+ T cells went on to complete resolution. All tumors contained CD11b+ myeloid cells from the outset of treatment, with later recruitment of additional CD11b+ cells. As tumors grew, the distribution of intratumoral CD11b+ cells became more heterogeneous. Shrinkage of tumors in responders correlated with an increase in the CD11b+ population in the center of the tumors. The changes in distribution of CD8+ and CD11b+ cells, as assessed by PET, served as biomarkers to gauge the efficacy of anti-PD-1 treatment. Single-cell RNA sequencing of RNA from intratumoral CD45+ cells showed that CD11b+ cells in responders and nonresponders were markedly different. The responders exhibited a dominant population of macrophages with an M1-like signature, while the CD45+ population in the nonresponders displayed an M2-like transcriptional signature. Thus, by using immuno-PET and single-cell RNA sequencing, we show that anti-PD-1 treatment not only affects interactions of CD8+ T cells with the tumor but also impacts the intratumoral myeloid compartment.
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Watanabe H, Takeda R, Hirota K, Kondoh G. Lipid raft dynamics linked to sperm competency for fertilization in mice. Genes Cells 2017; 22:493-500. [PMID: 28425215 DOI: 10.1111/gtc.12491] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 03/18/2017] [Indexed: 12/13/2022]
Abstract
It is well known that mammalian sperm acquires fertilization ability after several maturation processes, particularly within the female reproductive tract. In a previous study, we found that both glycosylphosphatidylinositol (GPI)-anchored protein (GPI-AP) release and lipid raft movement occur during the sperm maturation process. In several genetic studies, release of GPI-AP is a crucial step for sperm fertilization ability in the mouse. Here, we show that lipid raft movement is also fundamental for sperm to be competent for fertilization by comparing the sperm maturation process of two mouse inbred strains, C57BL/6 and BALB/c. We found that ganglioside GM1 movement was exclusively reduced in BALB/c compared with C57BL/6 among other examined sperm maturation parameters, such as GPI-AP release, sperm migration to the oviduct, cholesterol efflux, protein tyrosine phosphorylation and acrosome reaction, and was strongly linked to sperm fertility phenotype. The relationship between GM1 movement and in vitro fertilization ability was confirmed in other mouse strains, suggesting that lipid raft movement is one of the important steps for completing the sperm maturation process.
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Affiliation(s)
- Hitomi Watanabe
- Laboratory of Integrative Biological Science and Animal Experiments for Regeneration, Institute for Frontier Life and Medical Sciences and Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Rie Takeda
- Laboratory of Integrative Biological Science and Animal Experiments for Regeneration, Institute for Frontier Life and Medical Sciences and Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Keiji Hirota
- Laboratory of Integrative Biological Science and Animal Experiments for Regeneration, Institute for Frontier Life and Medical Sciences and Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Gen Kondoh
- Laboratory of Integrative Biological Science and Animal Experiments for Regeneration, Institute for Frontier Life and Medical Sciences and Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
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Wang H, Wang C, Yang K, Liu J, Zhang Y, Wang Y, Xu X, Michal JJ, Jiang Z, Liu B. Genome Wide Distributions and Functional Characterization of Copy Number Variations between Chinese and Western Pigs. PLoS One 2015; 10:e0131522. [PMID: 26154170 PMCID: PMC4496047 DOI: 10.1371/journal.pone.0131522] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 06/03/2015] [Indexed: 01/02/2023] Open
Abstract
Copy number variations (CNVs) refer to large insertions, deletions and duplications in the genomic structure ranging from one thousand to several million bases in size. Since the development of next generation sequencing technology, several methods have been well built for detection of copy number variations with high credibility and accuracy. Evidence has shown that CNV occurring in gene region could lead to phenotypic changes due to the alteration in gene structure and dosage. However, it still remains unexplored whether CNVs underlie the phenotypic differences between Chinese and Western domestic pigs. Based on the read-depth methods, we investigated copy number variations using 49 individuals derived from both Chinese and Western pig breeds. A total of 3,131 copy number variation regions (CNVRs) were identified with an average size of 13.4 Kb in all individuals during domestication, harboring 1,363 genes. Among them, 129 and 147 CNVRs were Chinese and Western pig specific, respectively. Gene functional enrichments revealed that these CNVRs contribute to strong disease resistance and high prolificacy in Chinese domestic pigs, but strong muscle tissue development in Western domestic pigs. This finding is strongly consistent with the morphologic characteristics of Chinese and Western pigs, indicating that these group-specific CNVRs might have been preserved by artificial selection for the favored phenotypes during independent domestication of Chinese and Western pigs. In this study, we built high-resolution CNV maps in several domestic pig breeds and discovered the group specific CNVs by comparing Chinese and Western pigs, which could provide new insight into genomic variations during pigs’ independent domestication, and facilitate further functional studies of CNV-associated genes.
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Affiliation(s)
- Hongyang Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, PR China
| | - Chao Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, PR China
| | - Kui Yang
- Modern Educational & Technology Centre of Huazhong Agricultural University, Wuhan, PR China
| | - Jing Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, PR China
| | - Yu Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, PR China
| | - Yanan Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, PR China
| | - Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, PR China
| | - Jennifer J. Michal
- Department of Animal Sciences, Washington State University, Pullman, WA, United States of America
| | - Zhihua Jiang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China
- Department of Animal Sciences, Washington State University, Pullman, WA, United States of America
| | - Bang Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, PR China
- * E-mail:
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Zhang M, Tsimelzon A, Chang CH, Fan C, Wolff A, Perou CM, Hilsenbeck SG, Rosen JM. Intratumoral heterogeneity in a Trp53-null mouse model of human breast cancer. Cancer Discov 2015; 5:520-33. [PMID: 25735774 DOI: 10.1158/2159-8290.cd-14-1101] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 02/20/2015] [Indexed: 12/24/2022]
Abstract
UNLABELLED Intratumoral heterogeneity correlates with clinical outcome and reflects the cellular complexity and dynamics within a tumor. Such heterogeneity is thought to contribute to radio- and chemoresistance because many treatments may target only certain tumor cell subpopulations. A better understanding of the functional interactions between various subpopulations of cells, therefore, may help in the development of effective cancer treatments. We identified a unique subpopulation of tumor cells expressing mesenchymal-like markers in a Trp53-null mouse model of basal-like breast cancer using fluorescence-activated cell sorting and microarray analysis. Both in vitro and in vivo experiments revealed the existence of cross-talk between these "mesenchymal-like" cells and tumor-initiating cells. Knockdown of genes encoding ligands upregulated in the mesenchymal cells and their corresponding receptors in the tumor-initiating cells resulted in reduced tumorigenicity and increased tumor latency. These studies illustrate the non-cell-autonomous properties and importance of cooperativity between tumor subpopulations. SIGNIFICANCE Intratumoral heterogeneity has been considered one important factor in assessing a patient's initial response to treatment and selecting drug regimens to effectively increase tumor response rate. Elucidating the functional interactions between various subpopulations of tumor cells will help provide important new insights in understanding treatment response and tumor progression.
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Affiliation(s)
- Mei Zhang
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.
| | - Anna Tsimelzon
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Chi-Hsuan Chang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Andrew Wolff
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina. Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina. Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Susan G Hilsenbeck
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Jeffrey M Rosen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas.
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Abstract
We constructed a 400K WG tiling oligoarray for the horse and applied it for the discovery of copy number variations (CNVs) in 38 normal horses of 16 diverse breeds, and the Przewalski horse. Probes on the array represented 18,763 autosomal and X-linked genes, and intergenic, sub-telomeric and chrY sequences. We identified 258 CNV regions (CNVRs) across all autosomes, chrX and chrUn, but not in chrY. CNVs comprised 1.3% of the horse genome with chr12 being most enriched. American Miniature horses had the highest and American Quarter Horses the lowest number of CNVs in relation to Thoroughbred reference. The Przewalski horse was similar to native ponies and draft breeds. The majority of CNVRs involved genes, while 20% were located in intergenic regions. Similar to previous studies in horses and other mammals, molecular functions of CNV-associated genes were predominantly in sensory perception, immunity and reproduction. The findings were integrated with previous studies to generate a composite genome-wide dataset of 1476 CNVRs. Of these, 301 CNVRs were shared between studies, while 1174 were novel and require further validation. Integrated data revealed that to date, 41 out of over 400 breeds of the domestic horse have been analyzed for CNVs, of which 11 new breeds were added in this study. Finally, the composite CNV dataset was applied in a pilot study for the discovery of CNVs in 6 horses with XY disorders of sexual development. A homozygous deletion involving AKR1C gene cluster in chr29 in two affected horses was considered possibly causative because of the known role of AKR1C genes in testicular androgen synthesis and sexual development. While the findings improve and integrate the knowledge of CNVs in horses, they also show that for effective discovery of variants of biomedical importance, more breeds and individuals need to be analyzed using comparable methodological approaches. Genomes of individuals in a species vary in many ways, one of which is DNA copy number variation (CNV). This includes deletions, duplications, and complex rearrangements typically larger than 50 base-pairs. CNVs are part of normal genetic variation contributing to phenotypic diversity but can also be pathogenic and associated with diseases and disorders. In order to distinguish between the two, detailed knowledge about CNVs in the species of interest is needed. Here we studied the genomes of 38 normal horses of 16 diverse breeds, and identified 258 CNV regions. We integrated our findings with previously published horse CNVs and generated a composite dataset of ∼1400 CNVRs. Despite this large number, our analysis shows that CNV research in horses needs further improvement because the current data are based on 10% of horse breeds and that most CNVRs are study-specific and require validation. Finally, we analyzed CNVs in horses with disorders of sexual development and found in two male pseudo-hermaphrodites a large deletion disrupting a group of genes involved in sex hormone metabolism and sexual differentiation. The findings underline the possible role of CNVs in complex disorders such as development and reproduction.
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Molin AM, Berglund J, Webster MT, Lindblad-Toh K. Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array. BMC Genomics 2014; 15:210. [PMID: 24640994 PMCID: PMC4234435 DOI: 10.1186/1471-2164-15-210] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 03/13/2014] [Indexed: 12/23/2022] Open
Abstract
Background Substantial contribution to phenotypic diversity is accounted for by copy number variants (CNV). In human, as well as other species, the effect of CNVs range from benign to directly disease-causing which motivates the continued investigations of CNVs. Previous canine genome-wide screenings for CNVs have been performed using high-resolution comparative genomic hybridisation arrays which have contributed with a detailed catalogue of CNVs. Here, we present the first CNV investigation in dogs based on the recently reported CanineHD 170 K genotyping array. The hitherto largest dataset in canine CNV discovery was assessed, 351 dogs from 30 different breeds, enabling identification of novel CNVs and a thorough characterisation of breed-specific CNVs. Results A stringent procedure identified 72 CNV regions with the smallest size of 38 kb and of the 72 CNV regions, 38 overlapped 148 annotated genes. A total of 29 novel CNV regions were found containing 44 genes. Furthermore, 15 breed specific CNV regions were identified of which 14 were novel and some of them overlapped putative disease susceptibility genes. In addition, the human ortholog of 23 canine copy number variable genes identified herein has been previously suggested to be dosage-sensitive in human. Conclusions The present study evaluated the performance of the CanineHD in detecting CNVs and extends the current catalogue of canine CNV regions with several dozens of novel CNV regions. These novel CNV regions, which harbour candidate genes that possibly contribute to phenotypic variation in dogs or to disease-susceptibility, are a rich resource for future investigations.
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Affiliation(s)
- Anna-Maja Molin
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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Yu P, Wang CH, Xu Q, Feng Y, Yuan XP, Yu HY, Wang YP, Tang SX, Wei XH. Genome-wide copy number variations in Oryza sativa L. BMC Genomics 2013; 14:649. [PMID: 24059626 PMCID: PMC3856455 DOI: 10.1186/1471-2164-14-649] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 09/16/2013] [Indexed: 01/16/2023] Open
Abstract
Background Copy number variation (CNV) can lead to intra-specific genome variations. It is not only part of normal genetic variation, but also is the source of phenotypic differences. Rice (Oryza sativa L.) is a model organism with a well-annotated genome, but investigation of CNVs in rice lags behind its mammalian counterparts. Results We comprehensively assayed CNVs using high-density array comparative genomic hybridization in a panel of 20 Asian cultivated rice comprising six indica, three aus, two rayada, two aromatic, three tropical japonica, and four temperate japonica varieties. We used a stringent criterion to identify a total of 2886 high-confidence copy number variable regions (CNVRs), which span 10.28 Mb (or 2.69%) of the rice genome, overlapping 1321 genes. These genes were significantly enriched for specific biological functions involved in cell death, protein phosphorylation, and defense response. Transposable elements (TEs) and other repetitive sequences were identified in the majority of CNVRs. Chromosome 11 showed the greatest enrichment for CNVs. Of subspecies-specific CNVRs, 55.75% and 61.96% were observed in only one cultivar of ssp. indica and ssp. japonica, respectively. Some CNVs with high frequency differences among groups resided in genes underlying rice adaptation. Conclusions Higher recombination rates and the presence of homologous gene clusters are probably predispositions for generation of the higher number of CNVs on chromosome 11 by non-allelic homologous recombination events. The subspecies-specific variants are enriched for rare alleles, which suggests that CNVs are relatively recent events that have arisen within breeding populations. A number of the CNVs identified in this study are candidates for generation of group-specific phenotypes.
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Affiliation(s)
- Ping Yu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
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Raish M, Khurshid M, Ansari MA, Chaturvedi PK, Bae SM, Kim JH, Park EK, Park DC, Ahn WS. Analysis of molecular cytogenetic alterations in uterine leiomyosarcoma by array-based comparative genomic hybridization. J Cancer Res Clin Oncol 2012; 138:1173-86. [DOI: 10.1007/s00432-012-1182-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 02/20/2012] [Indexed: 10/28/2022]
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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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Gene duplication of endothelin 3 is closely correlated with the hyperpigmentation of the internal organs (Fibromelanosis) in silky chickens. Genetics 2011; 190:627-38. [PMID: 22135351 DOI: 10.1534/genetics.111.136705] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
During early development in vertebrates, pluripotent cells are generated from the neural crest and migrate according to their presumptive fate. In birds and mammals, one of the progeny cells, melanoblasts, generally migrate through a dorsolateral route of the trunk region and differentiate to melanocytes. However, Silky is an exceptional chicken in which numerous melanoblasts travel via a ventral pathway and disperse into internal organs. Finally, these ectopic melanocytes induce heavy dermal and visceral melanization known as Fibromelanosis (Fm). To identify the genetic basis of this phenotype, we confirmed the mode of inheritance of Fm as autosomal dominant and then performed linkage analysis with microsatellite markers and sequence-tagged site markers. Using 85 backcross progeny from crossing Black Minorca chickens (BM-C) with F(1) individuals between White Silky (WS) and BM-C Fm was located on 10.2-11.7 Mb of chicken chromosome 20. In addition, we noticed a DNA marker that all Silky chickens and the F(1) individuals showed heterozygous genotyping patterns, suggesting gene duplication in the Fm region. By quantitative real-time PCR assay, Silky line-specific gene duplication was detected as an ~130-kb interval. It contained five genes including endothelin 3 (EDN3), which encoded a potent mitogen for melanoblasts/melanocytes. EDN3 with another three of these duplicated genes in Silky chickens expressed almost twofold of those in BM-C. Present results strongly suggest that the increase of the expression levels resulting from the gene duplication in the Fm region is the trigger of hypermelanization in internal organs of Silky chickens.
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Holcomb IN, Trask BJ. Comparative genomic hybridization to detect variation in the copy number of large DNA segments. Cold Spring Harb Protoc 2011; 2011:1323-1333. [PMID: 22046040 DOI: 10.1101/pdb.top066589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Array comparative genomic hybridization (CGH) is an excellent tool to scan the genome for copy number variations (CNVs) when used conscientiously. This article is intended to provide an understanding of the basic principles of array CGH and the different options available to the user to design their array CGH experiments. Specifically, the six subsections discuss the different array platforms available, test and reference DNA preparation, reference DNA choice, the basics of hybridization, data processing, and our current understanding of CNVs in the human genome.
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Samarakoon U, Gonzales JM, Patel JJ, Tan A, Checkley L, Ferdig MT. The landscape of inherited and de novo copy number variants in a Plasmodium falciparum genetic cross. BMC Genomics 2011; 12:457. [PMID: 21936954 PMCID: PMC3191341 DOI: 10.1186/1471-2164-12-457] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 09/22/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy number is a major source of genome variation with important evolutionary implications. Consequently, it is essential to determine copy number variant (CNV) behavior, distributions and frequencies across genomes to understand their origins in both evolutionary and generational time frames. We use comparative genomic hybridization (CGH) microarray and the resolution provided by a segregating population of cloned progeny lines of the malaria parasite, Plasmodium falciparum, to identify and analyze the inheritance of 170 genome-wide CNVs. RESULTS We describe CNVs in progeny clones derived from both Mendelian (i.e. inherited) and non-Mendelian mechanisms. Forty-five CNVs were present in the parent lines and segregated in the progeny population. Furthermore, extensive variation that did not conform to strict Mendelian inheritance patterns was observed. 124 CNVs were called in one or more progeny but in neither parent: we observed CNVs in more than one progeny clone that were not identified in either parent, located more frequently in the telomeric-subtelomeric regions of chromosomes and singleton de novo CNVs distributed evenly throughout the genome. Linkage analysis of CNVs revealed dynamic copy number fluctuations and suggested mechanisms that could have generated them. Five of 12 previously identified expression quantitative trait loci (eQTL) hotspots coincide with CNVs, demonstrating the potential for broad influence of CNV on the transcriptional program and phenotypic variation. CONCLUSIONS CNVs are a significant source of segregating and de novo genome variation involving hundreds of genes. Examination of progeny genome segments provides a framework to assess the extent and possible origins of CNVs. This segregating genetic system reveals the breadth, distribution and dynamics of CNVs in a surprisingly plastic parasite genome, providing a new perspective on the sources of diversity in parasite populations.
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Affiliation(s)
- Upeka Samarakoon
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
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14
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Lee EC, Fitzgerald M, Bannerman B, Donelan J, Bano K, Terkelsen J, Bradley DP, Subakan O, Silva MD, Liu R, Pickard M, Li Z, Tayber O, Li P, Hales P, Carsillo M, Neppalli VT, Berger AJ, Kupperman E, Manfredi M, Bolen JB, Van Ness B, Janz S. Antitumor activity of the investigational proteasome inhibitor MLN9708 in mouse models of B-cell and plasma cell malignancies. Clin Cancer Res 2011; 17:7313-23. [PMID: 21903769 DOI: 10.1158/1078-0432.ccr-11-0636] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The clinical success of the first-in-class proteasome inhibitor bortezomib (VELCADE) has validated the proteasome as a therapeutic target for treating human cancers. MLN9708 is an investigational proteasome inhibitor that, compared with bortezomib, has improved pharmacokinetics, pharmacodynamics, and antitumor activity in preclinical studies. Here, we focused on evaluating the in vivo activity of MLN2238 (the biologically active form of MLN9708) in a variety of mouse models of hematologic malignancies, including tumor xenograft models derived from a human lymphoma cell line and primary human lymphoma tissue, and genetically engineered mouse (GEM) models of plasma cell malignancies (PCM). EXPERIMENTAL DESIGN Both cell line-derived OCI-Ly10 and primary human lymphoma-derived PHTX22L xenograft models of diffuse large B-cell lymphoma were used to evaluate the pharmacodynamics and antitumor effects of MLN2238 and bortezomib. The iMyc(Cα)/Bcl-X(L) GEM model was used to assess their effects on de novo PCM and overall survival. The newly developed DP54-Luc-disseminated model of iMyc(Cα)/Bcl-X(L) was used to determine antitumor activity and effects on osteolytic bone disease. RESULTS MLN2238 has an improved pharmacodynamic profile and antitumor activity compared with bortezomib in both OCI-Ly10 and PHTX22L models. Although both MLN2238 and bortezomib prolonged overall survival, reduced splenomegaly, and attenuated IgG2a levels in the iMyc(Cα)/Bcl-X(L) GEM model, only MLN2238 alleviated osteolytic bone disease in the DP54-Luc model. CONCLUSIONS Our results clearly showed the antitumor activity of MLN2238 in a variety of mouse models of B-cell lymphoma and PCM, supporting its clinical development. MLN9708 is being evaluated in multiple phase I and I/II trials.
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Affiliation(s)
- Edmund C Lee
- Millennium Pharmaceuticals, Inc., Cambridge, Massachusetts, USA.
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Flatscher-Bader T, Foldi CJ, Chong S, Whitelaw E, Moser RJ, Burne THJ, Eyles DW, McGrath JJ. Increased de novo copy number variants in the offspring of older males. Transl Psychiatry 2011; 1:e34. [PMID: 22832608 PMCID: PMC3309504 DOI: 10.1038/tp.2011.30] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The offspring of older fathers have an increased risk of neurodevelopmental disorders, such as schizophrenia and autism. In light of the evidence implicating copy number variants (CNVs) with schizophrenia and autism, we used a mouse model to explore the hypothesis that the offspring of older males have an increased risk of de novo CNVs. C57BL/6J sires that were 3- and 12-16-months old were mated with 3-month-old dams to create control offspring and offspring of old sires, respectively. Applying genome-wide microarray screening technology, 7 distinct CNVs were identified in a set of 12 offspring and their parents. Competitive quantitative PCR confirmed these CNVs in the original set and also established their frequency in an independent set of 77 offspring and their parents. On the basis of the combined samples, six de novo CNVs were detected in the offspring of older sires, whereas none were detected in the control group. Two of the CNVs were associated with behavioral and/or neuroanatomical phenotypic features. One of the de novo CNVs involved Auts2 (autism susceptibility candidate 2), and other CNVs included genes linked to schizophrenia, autism and brain development. This is the first experimental demonstration that the offspring of older males have an increased risk of de novo CNVs. Our results support the hypothesis that the offspring of older fathers have an increased risk of neurodevelopmental disorders such as schizophrenia and autism by generation of de novo CNVs in the male germline.
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Affiliation(s)
- T Flatscher-Bader
- Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia,The Queensland Institute of Medical Research, Herston, QLD, Australia
| | - C J Foldi
- Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia
| | - S Chong
- The Queensland Institute of Medical Research, Herston, QLD, Australia
| | - E Whitelaw
- The Queensland Institute of Medical Research, Herston, QLD, Australia
| | | | - T H J Burne
- Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia,Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD, Australia
| | - D W Eyles
- Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia,Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD, Australia
| | - J J McGrath
- Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia,Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD, Australia,Discipline of Psychiatry, The University of Queensland, St Lucia, QLD, Australia,Queensland Brain Institute, The University of Queensland, St Lucia, Queensland 4072, Australia. E-mail:
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16
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Bai Z, Yuan Y, Yue G, Li J. Molecular cloning and copy number variation of a ferritin subunit (Fth1) and its association with growth in freshwater pearl mussel Hyriopsis cumingii. PLoS One 2011; 6:e22886. [PMID: 21818403 PMCID: PMC3144951 DOI: 10.1371/journal.pone.0022886] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 07/06/2011] [Indexed: 11/24/2022] Open
Abstract
Iron is one of the most important minor elements in the shells of bivalves. This study was designed to investigate the involvement of ferritin, the principal protein for iron storage, in shell growth. A novel ferritin subunit (Fth1) cDNA from the freshwater pearl mussel (Hyriopsis cumingii) was isolated and characterized. The complete cDNA contained 822 bp, with an open reading frame (ORF) of 525 bp, a 153 bp 5′ untranslated region (UTR) and a 144 bp 3′ UTR. The complete genomic DNA was 4125 bp, containing four exons and three introns. The ORF encoded a protein of 174 amino acids without a signal sequence. The deduced ferritin contained a highly conserved motif for the ferroxidase center comprising seven residues of a typical vertebrate heavy-chain ferritin. It contained one conserved iron associated residue (Try27) and iron-binding region signature 1 residues. The mRNA contained a 27 bp iron-responsive element with a typical stem-loop structure in the 5′-UTR position. Copy number variants (CNVs) of Fth1 in two populations (PY and JH) were detected using quantitative real-time PCR. Associations between CNVs and growth were also analyzed. The results showed that the copy number of the ferritin gene of in the diploid genome ranged from two to 12 in PY, and from two to six in JH. The copy number variation in PY was higher than that in JH. In terms of shell length, mussels with four copies of the ferritin gene grew faster than those with three copies (P<0.05), suggesting that CNVs in the ferritin gene are associated with growth in shell length and might be a useful molecular marker in selective breeding of H. cumingii.
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Affiliation(s)
- Zhiyi Bai
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Yiming Yuan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Genhua Yue
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Jiale Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai Ocean University, Shanghai, China
- E-Institute of Shanghai Universities, Shanghai Ocean University, Shanghai, China
- * E-mail:
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17
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Wang X, Nahashon S, Feaster TK, Bohannon-Stewart A, Adefope N. An initial map of chromosomal segmental copy number variations in the chicken. BMC Genomics 2010; 11:351. [PMID: 20525236 PMCID: PMC2996973 DOI: 10.1186/1471-2164-11-351] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 06/03/2010] [Indexed: 02/02/2023] Open
Abstract
Background Chromosomal segmental copy number variation (CNV) has been recently recognized as a very important source of genetic variability. Some CNV loci involve genes or conserved regulatory elements. Compelling evidence indicates that CNVs impact genome functions. The chicken is a very important farm animal species which has also served as a model for biological and biomedical research for hundreds of years. A map of CNVs in chickens could facilitate the identification of chromosomal regions that segregate for important agricultural and disease phenotypes. Results Ninety six CNVs were identified in three lines of chickens (Cornish Rock broiler, Leghorn and Rhode Island Red) using whole genome tiling array. These CNVs encompass 16 Mb (1.3%) of the chicken genome. Twenty six CNVs were found in two or more animals. Whereas most small sized CNVs reside in none coding sequences, larger CNV regions involve genes (for example prolactin receptor, aldose reductase and zinc finger proteins). These results suggest that chicken CNVs potentially affect agricultural or disease related traits. Conclusion An initial map of CNVs for the chicken has been described. Although chicken genome is approximately one third the size of a typical mammalian genome, the pattern of chicken CNVs is similar to that of mammals. The number of CNVs detected per individual was also similar to that found in dogs, mice, rats and macaques. A map of chicken CNVs provides new information on genetic variations for the understanding of important agricultural traits and disease.
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Affiliation(s)
- Xiaofei Wang
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA.
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18
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Fadista J, Thomsen B, Holm LE, Bendixen C. Copy number variation in the bovine genome. BMC Genomics 2010; 11:284. [PMID: 20459598 PMCID: PMC2902221 DOI: 10.1186/1471-2164-11-284] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Accepted: 05/06/2010] [Indexed: 12/12/2022] Open
Abstract
Background Copy number variations (CNVs), which represent a significant source of genetic diversity in mammals, have been shown to be associated with phenotypes of clinical relevance and to be causative of disease. Notwithstanding, little is known about the extent to which CNV contributes to genetic variation in cattle. Results We designed and used a set of NimbleGen CGH arrays that tile across the assayable portion of the cattle genome with approximately 6.3 million probes, at a median probe spacing of 301 bp. This study reports the highest resolution map of copy number variation in the cattle genome, with 304 CNV regions (CNVRs) being identified among the genomes of 20 bovine samples from 4 dairy and beef breeds. The CNVRs identified covered 0.68% (22 Mb) of the genome, and ranged in size from 1.7 to 2,031 kb (median size 16.7 kb). About 20% of the CNVs co-localized with segmental duplications, while 30% encompass genes, of which the majority is involved in environmental response. About 10% of the human orthologous of these genes are associated with human disease susceptibility and, hence, may have important phenotypic consequences. Conclusions Together, this analysis provides a useful resource for assessment of the impact of CNVs regarding variation in bovine health and production traits.
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Affiliation(s)
- João Fadista
- Group of Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Blichers Allé 20, DK-8830 Tjele, Denmark
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19
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Abstract
The zebrafish system has been established as a useful model for the study of carcinogenesis. The cytogenetic characterization of the genome is vital for furthering our understanding of the progression of the disease. Establishing a basic description of the zebrafish chromosomal karyotype and markers for each specific chromosome permitted the first cytogenetic characterization of the reference genome and the genome of cancer models. As the field of cancer cytogenetics is highly dependent on technology, each advance in technique and methodology has resulted in a corresponding wave of discoveries. We have witnessed great improvement in the resolution of the assays allowing for more detailed characterization of cytogenetic abnormalities, including the efficient and accurate identification of DNA copy number alterations of specific chromosomal regions. Herein, we will discuss major advancements in the field of cytogenetics, along with examples of how these technologies have been utilized in studies to characterize zebrafish cancer disease models. Finally, we will discuss the current state of the field and how microarray technology are being implemented to scan the whole genome at high resolution for DNA copy number alterations observed in various cancer types throughout the progression of the disease.
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Affiliation(s)
- Samuel M Peterson
- School of Health Sciences, Purdue University, West Lafayette, Indiana, USA
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20
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Liu GE, Hou Y, Zhu B, Cardone MF, Jiang L, Cellamare A, Mitra A, Alexander LJ, Coutinho LL, Dell'Aquila ME, Gasbarre LC, Lacalandra G, Li RW, Matukumalli LK, Nonneman D, Regitano LCDA, Smith TPL, Song J, Sonstegard TS, Van Tassell CP, Ventura M, Eichler EE, McDaneld TG, Keele JW. Analysis of copy number variations among diverse cattle breeds. Genome Res 2010; 20:693-703. [PMID: 20212021 DOI: 10.1101/gr.105403.110] [Citation(s) in RCA: 223] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here, we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, three Bos indicus, and three composite breeds for beef, dairy, or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 megabases or approximately 1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions, such as immunity, lactation, reproduction, and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research.
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Affiliation(s)
- George E Liu
- USDA-ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland 20705, USA
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21
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Scavetta RJ, Tautz D. Copy number changes of CNV regions in intersubspecific crosses of the house mouse. Mol Biol Evol 2010; 27:1845-56. [PMID: 20200126 DOI: 10.1093/molbev/msq064] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Copy number variation (CNV) contributes significantly to natural genetic variation within and between populations. However, the mutational mechanisms leading to CNV, as well as the processes that control the size of CNV regions, are so far not well understood. Here, we have analyzed a gene family that forms CNV regions on the X and the Y chromosomes in Mus musculus. These CNV regions show copy number differences in two subspecies, M. musculus domesticus and M. musculus musculus. Assessment of copy numbers at these loci for individuals caught in a natural hybrid zone showed copy number increases and a large variance among individuals. Crosses of natural hybrid animals among each other produced even more extreme variants with major differences in copy number in the offspring from the same parents. To assess the inheritance pattern of the loci further, we have produced F1 and backcross hybrid animals from these subspecies. We found that copy number expansions can already be traced in F1 offspring and they became stronger in the backcross individuals. Specific analysis of hybrid male offspring indicated that neither meiotic recombination nor interchromosomal exchange was required for creating these changes because the X and Y chromosomes have no homologues in males. This suggests that intrachromosomal exchanges can drive CNV and that this can occur at an elevated frequency in interspecific crosses, even within an individual. Accordingly, we find copy number mosaicism in individuals, that is, DNA from different tissues of the same individual can have different copy numbers for the loci studied. A preliminary survey of autosomal loci suggests that these can also be subject to change in hybrids. Hence, we conclude that the effects we see are not only restricted to some specific loci but may also be caused by a general induction of replication-coupled repair processes.
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Affiliation(s)
- Rick J Scavetta
- Max-Planck Institut für Evolutionsbiologie, Abteilung Evolutionsgenetik, Plön, Germany
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22
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Kaszynski RH, Akatsuka S, Hiratsuka T, Jin G, Ozeki M, Okuno T, Nakamura T, Manabe T, Takakuwa T, Hiai H, Toyokuni S, Tamaki K, Tsuruyama T. A quantitative trait locus responsible for inducing B-cell lymphoblastic lymphoma is a hotspot for microsatellite instability. Cancer Sci 2010; 101:800-5. [PMID: 20353532 PMCID: PMC11159001 DOI: 10.1111/j.1349-7006.2009.01437.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Revised: 11/02/2009] [Accepted: 11/04/2009] [Indexed: 01/16/2023] Open
Abstract
While the molecular mechanisms underlying microsatellite instability (MSI) have been exhaustively investigated, identifying the patterns of MSI distribution within diverse cancer genomes has remained an elusive issue. In the present study, we conducted genome-wide MSI screening in B-cell lymphoblastic lymphomas (B-LBL) which spontaneously develop in the SL/Kh strain of mice. Tumor samples harvested from 16 mice were investigated using a framework map consisting of 150 microsatellite markers spaced at increments of roughly 0.5-3.0 centimorgans, spanning the entirety of mouse chromosomes (mus musculus chromosomes [MMU]) 3-6. MMU3 contains a quantitative trait locus (QTL), Bomb1 (bone marrow pre-B1), known to induce an aberrant expansion of pre-B cells in bone marrow prior to the onset of B-LBL in SL/Kh mice. The remaining chromosomes were selected on the basis of those most closely resembling MMU3 in terms of total estimated length (maximum variance 10 Mb). MSI was confirmed at 2
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Affiliation(s)
- Richard H Kaszynski
- Department of Forensic Medicine and Molecular Pathology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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23
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Jeon JP, Shim SM, Jung JS, Nam HY, Lee HJ, Oh BS, Kim K, Kim HL, Han BG. A comprehensive profile of DNA copy number variations in a Korean population: identification of copy number invariant regions among Koreans. Exp Mol Med 2010; 41:618-28. [PMID: 19478558 DOI: 10.3858/emm.2009.41.9.068] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
To examine copy number variations among the Korean population, we compared individual genomes with the Korean reference genome assembly using the publicly available Korean HapMap SNP 50 k chip data from 90 individuals. Korean individuals exhibited 123 copy number variation regions (CNVRs) covering 27.2 mb, equivalent to 1.0% of the genome in the copy number variation (CNV) analysis using the combined criteria of P value (P<0.01) and standard deviation of copy numbers (SD>or= 0.25) among study subjects. In contrast, when compared to the Affymetrix reference genome assembly from multiple ethnic groups, considerably more CNVRs (n=643) were detected in larger proportions (5.0%) of the genome covering 135.1 mb even by more stringent criteria (P<0.001 and SD>or=0.25), reflecting ethnic diversity of structural variations between Korean and other populations. Some CNVRs were validated by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method, and then copy number invariant regions were detected among the study subjects. These copy number invariant regions would be used as good internal controls for further CNV studies. Lastly, we demonstrated that the CNV information could stratify even a single ethnic population with a proper reference genome assembly from multiple heterogeneous populations.
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Affiliation(s)
- Jae Pil Jeon
- Division of Biobank for Health Sciences, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul 122-701, Korea
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24
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Enhanced fixation and preservation of a newly arisen duplicate gene by masking deleterious loss-of-function mutations. Genet Res (Camb) 2009; 91:267-80. [PMID: 19640322 DOI: 10.1017/s0016672309000196] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Segmental duplications are enriched within many eukaryote genomes, and their potential consequence is gene duplication. While previous theoretical studies of gene duplication have mainly focused on the gene silencing process after fixation, the process leading to fixation is even more important for segmental duplications, because the majority of duplications would be lost before reaching a significant frequency in a population. Here, by a series of computer simulations, we show that purifying selection against loss-of-function mutations increases the fixation probability of a new duplicate gene, especially when the gene is haplo-insufficient. Theoretically, the probability of simultaneous preservation of both duplicate genes becomes twice the loss-of-function mutation rate (u(c)) when the population size (N), the degree of dominance of mutations (h) and the recombination rate between the duplicate genes (c) are all sufficiently large (Nu(c)>1, h>0.1 and c>u(c)). The preservation probability declines rapidly with h and becomes 0 when h=0 (haplo-sufficiency). We infer that masking deleterious loss-of-function mutations give duplicate genes an immediate selective advantage and, together with effects of increased gene dosage, would predominantly determine the fates of the duplicate genes in the early phase of their evolution.
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25
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Asuni AA, Hilton K, Siskova Z, Lunnon K, Reynolds R, Perry VH, O'Connor V. Alpha-synuclein deficiency in the C57BL/6JOlaHsd strain does not modify disease progression in the ME7-model of prion disease. Neuroscience 2009; 165:662-74. [PMID: 19879926 DOI: 10.1016/j.neuroscience.2009.10.047] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 10/22/2009] [Accepted: 10/22/2009] [Indexed: 11/28/2022]
Abstract
We previously detailed how intrahippocampal inoculation of C57BL/6J mice with murine modified scrapie (ME7) leads to chronic neurodegeneration (Cunningham C, Deacon R, Wells H, Boche D, Waters S, Diniz CP, Scott H, Rawlins JN, Perry VH (2003) Eur J Neurosci 17:2147-2155.). Our characterization of the ME7-model is based on inoculation of this murine modified scrapie agent into C57BL/6J mice from Harlan laboratories. This agent in the C57BL/6J host generates a disease that spans a 24-week time course. The hippocampal pathology shows progressive misfolded prion (PrP(Sc)) deposition, astrogliosis and leads to behavioural dysfunction underpinned by the early synaptic loss that precedes neuronal death. The Harlan C57BL/6J, although widely used as a wild type mouse, are a sub-strain harbouring a spontaneous deletion of alpha-synuclein with the full description C57BL/6JOlaHsd. Recently alpha-synuclein has been shown to ameliorate the synaptic loss in a mouse model lacking the synaptic chaperone CSP-alpha. This opens a potential confound of the ME7-model, particularly with respect to the signature synaptic loss that underpin the physiological and behavioural dysfunction. To investigate if this strain-selective loss of a candidate disease modifier impacts on signature ME7 pathology, we compared cohorts of C57BL/6JOlaHsd (alpha-synuclein negative) with the founder strain from Charles Rivers (C57BL/6JCrl, alpha-synuclein positive). There were subtle changes in behaviour when comparing control animals from the two sub-strains indicating potentially significant consequences for studies assuming neurobiogical identity of both strains. However, there was no evidence that the absence of alpha-synuclein modifies disease. Indeed, accumulation of PrP(Sc), synaptic loss and the behavioural dysfunction associated with the ME7-agent was the same in both genetic backgrounds. Our data suggest that alpha-synuclein deficiency does not contribute to the compartment specific processes that give rise to prion disease mediated synaptotoxicity and neurodegeneration.
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Affiliation(s)
- A A Asuni
- CNS Inflammation Group, University of Southampton, UK.
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26
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Freeman JL, Ceol C, Feng H, Langenau DM, Belair C, Stern HM, Song A, Paw BH, Look AT, Zhou Y, Zon LI, Lee C. Construction and application of a zebrafish array comparative genomic hybridization platform. Genes Chromosomes Cancer 2009; 48:155-70. [PMID: 18973135 DOI: 10.1002/gcc.20623] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The zebrafish is emerging as a prominent model system for studying the genetics of human development and disease. Genetic alterations that underlie each mutant model can exist in the form of single base changes, balanced chromosomal rearrangements, or genetic imbalances. To detect genetic imbalances in an unbiased genome-wide fashion, array comparative genomic hybridization (CGH) can be used. We have developed a 5-Mb resolution array CGH platform specifically for the zebrafish. This platform contains 286 bacterial artificial chromosome (BAC) clones, enriched for orthologous sequences of human oncogenes and tumor suppressor genes. Each BAC clone has been end-sequenced and cytogenetically assigned to a specific location within the zebrafish genome, allowing for ease of integration of array CGH data with the current version of the genome assembly. This platform has been applied to three zebrafish cancer models. Significant genomic imbalances were detected in each model, identifying different regions that may potentially play a role in tumorigenesis. Hence, this platform should be a useful resource for genetic dissection of additional zebrafish developmental and disease models as well as a benchmark for future array CGH platform development.
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Affiliation(s)
- Jennifer L Freeman
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
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27
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Henrichsen CN, Chaignat E, Reymond A. Copy number variants, diseases and gene expression. Hum Mol Genet 2009; 18:R1-8. [PMID: 19297395 DOI: 10.1093/hmg/ddp011] [Citation(s) in RCA: 292] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Copy number variation (CNV) has recently gained considerable interest as a source of genetic variation likely to play a role in phenotypic diversity and evolution. Much effort has been put into the identification and mapping of regions that vary in copy number among seemingly normal individuals in humans and a number of model organisms, using bioinformatics or hybridization-based methods. These have allowed uncovering associations between copy number changes and complex diseases in whole-genome association studies, as well as identify new genomic disorders. At the genome-wide scale, however, the functional impact of CNV remains poorly studied. Here we review the current catalogs of CNVs, their association with diseases and how they link genotype and phenotype. We describe initial evidence which revealed that genes in CNV regions are expressed at lower and more variable levels than genes mapping elsewhere, and also that CNV not only affects the expression of genes varying in copy number, but also have a global influence on the transcriptome. Further studies are warranted for complete cataloguing and fine mapping of CNVs, as well as to elucidate the different mechanisms by which they influence gene expression.
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Affiliation(s)
- Charlotte N Henrichsen
- The Center for Integrative Genomics, Genopode Building, University of Lausanne, Lausanne, Switzerland
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28
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Perry GH. The evolutionary significance of copy number variation in the human genome. Cytogenet Genome Res 2009; 123:283-7. [PMID: 19287166 DOI: 10.1159/000184719] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2008] [Indexed: 12/27/2022] Open
Abstract
Copy number variation provides the raw material for gene family expansion and diversification, which is an important evolutionary force. Moreover, copy number variants (CNVs) can influence gene transcriptional and translational levels and have been associated with complex disease susceptibility. Therefore, natural selection may have affected at least some of the greater than one thousand CNVs thus far discovered among the genomes of phenotypically normal humans. While identifying and understanding particular instances of natural selection may shed light on important aspects of human evolutionary history, our ability to analyze CNVs in traditional population genetic frameworks has been limited. However, progress has been made by adapting some of these frameworks for use with copy number data. Moving forward, these efforts will be aided by non-human organism studies of the population genetics of copy number variation, and by more direct comparisons of within-species copy number variation and between-species copy number fixation.
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Affiliation(s)
- G H Perry
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
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29
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Cutler G, Kassner PD. Copy number variation in the mouse genome: implications for the mouse as a model organism for human disease. Cytogenet Genome Res 2009; 123:297-306. [PMID: 19287168 DOI: 10.1159/000184721] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2008] [Indexed: 11/19/2022] Open
Abstract
Individuals within a species have genetic differences which ultimately result in the spectrum of phenotypic variation that we observe. Genetic variation exists at the nucleotide level in the form of single nucleotide polymorphisms (SNPs), and at a structural level as inversions, deletions and amplifications of larger stretches of nucleotides. Profiling of human and mouse genomes has identified numerous genomic segmental copy number variations (CNVs) throughout these genomes. Since inbred mice are widely used laboratory models for the study of both normal and disease biology, it is crucial that we understand the full scope of genetic variation, including CNVs, within these animals. These genetic differences can inform us about the history of a population or species, enlighten us on gene function, and guide our selection of a model system for the study of human disease.
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Affiliation(s)
- G Cutler
- Lead Discovery, Amgen, South San Francisco, CA, USA.
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Henrichsen CN, Vinckenbosch N, Zöllner S, Chaignat E, Pradervand S, Schütz F, Ruedi M, Kaessmann H, Reymond A. Segmental copy number variation shapes tissue transcriptomes. Nat Genet 2009; 41:424-9. [PMID: 19270705 DOI: 10.1038/ng.345] [Citation(s) in RCA: 241] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Accepted: 01/05/2009] [Indexed: 01/08/2023]
Abstract
Copy number variation (CNV) is a key source of genetic diversity, but a comprehensive understanding of its phenotypic effect is only beginning to emerge. We have generated a CNV map in wild mice and classical inbred strains. Genome-wide expression data from six major organs show not only that expression of genes within CNVs tend to correlate with copy number changes, but also that CNVs influence the expression of genes in their vicinity, an effect that extends up to half a megabase. Genes within CNVs show lower expression and more specific spatial expression patterns than genes mapping elsewhere. Our analyses reveal differential constraint on copy number changes of genes expressed in different tissues. Dosage alterations of brain-expressed genes are less frequent than those of other genes and are buffered by tighter transcriptional regulation. Our study provides initial evidence that CNVs shape tissue transcriptomes on a global scale.
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Cahan P, Li Y, Izumi M, Graubert TA. The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells. Nat Genet 2009; 41:430-7. [PMID: 19270704 PMCID: PMC2728431 DOI: 10.1038/ng.350] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Accepted: 01/13/2009] [Indexed: 11/09/2022]
Abstract
The extent to which differences in germline DNA copy number contribute to natural phenotypic variation is unknown. We analyzed the copy number content of the mouse genome to sub-10-kb resolution. We identified over 1,300 copy number variant regions (CNVRs), most of which are <10 kb in length, are found in more than one strain, and, in total, span 3.2% (85 Mb) of the genome. To assess the potential functional impact of copy number variation, we mapped expression profiles of purified hematopoietic stem and progenitor cells, adipose tissue and hypothalamus to CNVRs in cis. Of the more than 600 significant associations between CNVRs and expression profiles, most map to CNVRs outside of the transcribed regions of genes. In hematopoietic stem and progenitor cells, up to 28% of strain-dependent expression variation is associated with copy number variation, supporting the role of germline CNVs as key contributors to natural phenotypic variation in the laboratory mouse.
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Affiliation(s)
- Patrick Cahan
- Department of Internal Medicine, Division of Oncology, Stem Cell Biology Section, Washington University, St Louis, MO, USA
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Williams R, Lim JE, Harr B, Wing C, Walters R, Distler MG, Teschke M, Wu C, Wiltshire T, Su AI, Sokoloff G, Tarantino LM, Borevitz JO, Palmer AA. A common and unstable copy number variant is associated with differences in Glo1 expression and anxiety-like behavior. PLoS One 2009; 4:e4649. [PMID: 19266052 PMCID: PMC2650792 DOI: 10.1371/journal.pone.0004649] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Accepted: 01/05/2009] [Indexed: 12/15/2022] Open
Abstract
Glyoxalase 1 (Glo1) has been implicated in anxiety-like behavior in mice and in multiple psychiatric diseases in humans. We used mouse Affymetrix exon arrays to detect copy number variants (CNV) among inbred mouse strains and thereby identified a ∼475 kb tandem duplication on chromosome 17 that includes Glo1 (30,174,390–30,651,226 Mb; mouse genome build 36). We developed a PCR-based strategy and used it to detect this duplication in 23 of 71 inbred strains tested, and in various outbred and wild-caught mice. Presence of the duplication is associated with a cis-acting expression QTL for Glo1 (LOD>30) in BXD recombinant inbred strains. However, evidence for an eQTL for Glo1 was not obtained when we analyzed single SNPs or 3-SNP haplotypes in a panel of 27 inbred strains. We conclude that association analysis in the inbred strain panel failed to detect an eQTL because the duplication was present on multiple highly divergent haplotypes. Furthermore, we suggest that non-allelic homologous recombination has led to multiple reversions to the non-duplicated state among inbred strains. We show associations between multiple duplication-containing haplotypes, Glo1 expression and anxiety-like behavior in both inbred strain panels and outbred CD-1 mice. Our findings provide a molecular basis for differential expression of Glo1 and further implicate Glo1 in anxiety-like behavior. More broadly, these results identify problems with commonly employed tests for association in inbred strains when CNVs are present. Finally, these data provide an example of biologically significant phenotypic variability in model organisms that can be attributed to CNVs.
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Affiliation(s)
- Richard Williams
- Committee on Computational Neuroscience, University of Chicago, Chicago, Illinois, United States of America
| | - Jackie E. Lim
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Bettina Harr
- Max-Planck-Institute for Evolutionary Biology, Department of Evolutionary Genetics, Ploen, Germany
| | - Claudia Wing
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Ryan Walters
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Margaret G. Distler
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Meike Teschke
- Max-Planck-Institute for Evolutionary Biology, Department of Evolutionary Genetics, Ploen, Germany
| | - Chunlei Wu
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Tim Wiltshire
- Department of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Andrew I. Su
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Greta Sokoloff
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Lisa M. Tarantino
- Department of Psychiatry, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Justin O. Borevitz
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Abraham A. Palmer
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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Fadista J, Nygaard M, Holm LE, Thomsen B, Bendixen C. A snapshot of CNVs in the pig genome. PLoS One 2008; 3:e3916. [PMID: 19079605 PMCID: PMC2596487 DOI: 10.1371/journal.pone.0003916] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Accepted: 11/14/2008] [Indexed: 11/18/2022] Open
Abstract
Recent studies of mammalian genomes have uncovered the extent of copy number variation (CNV) that contributes to phenotypic diversity, including health and disease status. Here we report a first account of CNVs in the pig genome covering part of the chromosomes 4, 7, 14, and 17 already sequenced and assembled. A custom tiling oligonucleotide array was used with a median probe spacing of 409 bp for screening 12 unrelated Duroc boars that are founders of a large family material. After a strict CNV calling pipeline, 37 copy number variable regions (CNVRs) across all four chromosomes were identified, with five CNVRs overlapping segmental duplications, three overlapping pig unigenes and one overlapping a RefSeq pig mRNA. This CNV snapshot analysis is the first of its kind in the porcine genome and constitutes the basis for a better understanding of porcine phenotypes and genotypes with the prospect of identifying important economic traits.
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Affiliation(s)
- João Fadista
- Group of Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Tjele, Denmark
| | - Marianne Nygaard
- Group of Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Tjele, Denmark
| | - Lars-Erik Holm
- Group of Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Tjele, Denmark
| | - Bo Thomsen
- Group of Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Tjele, Denmark
| | - Christian Bendixen
- Group of Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Tjele, Denmark
- * E-mail:
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Mozhui K, Ciobanu DC, Schikorski T, Wang X, Lu L, Williams RW. Dissection of a QTL hotspot on mouse distal chromosome 1 that modulates neurobehavioral phenotypes and gene expression. PLoS Genet 2008; 4:e1000260. [PMID: 19008955 PMCID: PMC2577893 DOI: 10.1371/journal.pgen.1000260] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Accepted: 10/14/2008] [Indexed: 11/18/2022] Open
Abstract
A remarkably diverse set of traits maps to a region on mouse distal chromosome 1 (Chr 1) that corresponds to human Chr 1q21-q23. This region is highly enriched in quantitative trait loci (QTLs) that control neural and behavioral phenotypes, including motor behavior, escape latency, emotionality, seizure susceptibility (Szs1), and responses to ethanol, caffeine, pentobarbital, and haloperidol. This region also controls the expression of a remarkably large number of genes, including genes that are associated with some of the classical traits that map to distal Chr 1 (e.g., seizure susceptibility). Here, we ask whether this QTL-rich region on Chr 1 (Qrr1) consists of a single master locus or a mixture of linked, but functionally unrelated, QTLs. To answer this question and to evaluate candidate genes, we generated and analyzed several gene expression, haplotype, and sequence datasets. We exploited six complementary mouse crosses, and combed through 18 expression datasets to determine class membership of genes modulated by Qrr1. Qrr1 can be broadly divided into a proximal part (Qrr1p) and a distal part (Qrr1d), each associated with the expression of distinct subsets of genes. Qrr1d controls RNA metabolism and protein synthesis, including the expression of approximately 20 aminoacyl-tRNA synthetases. Qrr1d contains a tRNA cluster, and this is a functionally pertinent candidate for the tRNA synthetases. Rgs7 and Fmn2 are other strong candidates in Qrr1d. FMN2 protein has pronounced expression in neurons, including in the dendrites, and deletion of Fmn2 had a strong effect on the expression of few genes modulated by Qrr1d. Our analysis revealed a highly complex gene expression regulatory interval in Qrr1, composed of multiple loci modulating the expression of functionally cognate sets of genes.
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Affiliation(s)
- Khyobeni Mozhui
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Daniel C. Ciobanu
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Thomas Schikorski
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Xusheng Wang
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Lu Lu
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Robert W. Williams
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- * E-mail:
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36
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Extensive genomic copy number variation in embryonic stem cells. Proc Natl Acad Sci U S A 2008; 105:17453-6. [PMID: 18988746 DOI: 10.1073/pnas.0805638105] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Recent analysis of the human and mouse genomes has revealed that highly identical duplicated elements account for >5% of the sequence content. These elements vary in copy number between individuals. Copy number variations (CNVs) contribute significantly to genetic differences among individuals and are increasingly recognized as a causal factor in human diseases with different etiologies. In inbred mouse strains, CNVs have been fixed by inbreeding, but they are highly variable among strains. Within strains, de novo germ-line CNVs can occur, leading to interindividual variation. By analyzing the genome of clonal isolates of mouse ES cells derived from common parental lines, we have uncovered extensive and recurrent CNVs. This variation arises during mitosis and can be cotransmitted into the mouse germ line along with engineered alleles, contributing to genetic variability. The frequency and extent of these genomic changes in ES cells suggests that all somatic tissues in individuals will be mosaics composed of variants of the zygotic genome. Human ES (hES) cells and derived somatic lineages may be similarly affected, challenging the concept of a stable somatic genome.
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She X, Cheng Z, Zöllner S, Church DM, Eichler EE. Mouse segmental duplication and copy number variation. Nat Genet 2008; 40:909-14. [PMID: 18500340 PMCID: PMC2574762 DOI: 10.1038/ng.172] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Accepted: 05/14/2008] [Indexed: 11/08/2022]
Abstract
Detailed analyses of the clone-based genome assembly reveal that the recent duplication content of mouse (4.94%) is now comparable to that of human (5.5%), in contrast to previous estimates from the whole-genome shotgun sequence assembly. However, the architecture of mouse and human genomes differs markedly: most mouse duplications are organized into discrete clusters of tandem duplications that show depletion of genes and transcripts and enrichment of long interspersed nuclear element (LINE) and long terminal repeat (LTR) retroposons. We assessed copy number variation of the C57BL/6J duplicated regions within 15 mouse strains previously used for genetic association studies, sequencing and the Mouse Phenome Project. We determined that over 60% of these base pairs are polymorphic among the strains (on average, there was 20 Mb of copy-number-variable DNA between different mouse strains). Our data suggest that different mouse strains show comparable, if not greater, copy number polymorphism when compared to human; however, such variation is more locally restricted. We show large and complex patterns of interstrain copy number variation restricted to large gene families associated with spermatogenesis, pregnancy, viviparity, pheromone signaling and immune response.
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Affiliation(s)
- Xinwei She
- Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Seattle, Washington 98195, USA
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Lgals6, a 2-million-year-old gene in mice: a case of positive Darwinian selection and presence/absence polymorphism. Genetics 2008; 178:1533-45. [PMID: 18385114 DOI: 10.1534/genetics.107.082792] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Duplications of genes are widely considered to be a driving force in the evolutionary process. The fate of such duplicated genes (paralogs) depends mainly on the early stages of their evolution. Therefore, the study of duplications that have already started to diverge is useful to better understand their evolution. We present here the example of a 2-million-year-old segmental duplication at the origin of the Lgals4 and Lgals6 genes in the mouse genome. We analyzed the distribution of these genes in samples from 110 wild individuals and wild-derived inbred strains belonging to eight mouse species from Mus (Coelomys) pahari to M. musculus and 28 laboratory strains. Using a maximum-likelihood method, we show that the sequence of the Lgals6 gene has evolved under the influence of strong positive selection that is likely to result in its neofunctionalization. Surprisingly, despite this selection pressure, the Lgals6 gene is present in some mouse species, but not all. Furthermore, even within the species and populations where it is present, the Lgals6 gene is never fixed. To explain this paradox, we propose different hypotheses such as balanced selection and neutral retention of ancient polymophism and we discuss this unexpected result with regard to known galectin properties and response to infections by pathogens.
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Korbel JO, Kim PM, Chen X, Urban AE, Weissman S, Snyder M, Gerstein MB. The current excitement about copy-number variation: how it relates to gene duplications and protein families. Curr Opin Struct Biol 2008; 18:366-74. [PMID: 18511261 DOI: 10.1016/j.sbi.2008.02.005] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2008] [Accepted: 02/13/2008] [Indexed: 01/28/2023]
Abstract
Following recent technological advances there has been an increasing interest in genome structural variants (SVs), in particular copy-number variants (CNVs)--large-scale duplications and deletions. Although not immediately evident, CNV surveys make a conceptual connection between the fields of population genetics and protein families, in particular with regard to the stability and expandability of families. The mechanisms giving rise to CNVs can be considered as fundamental processes underlying gene duplication and loss; duplicated genes being the results of 'successful' copies, fixed and maintained in the population. Conversely, many 'unsuccessful' duplicates remain in the genome as pseudogenes. Here, we survey studies on CNVs, highlighting issues related to protein families. In particular, CNVs tend to affect specific gene functional categories, such as those associated with environmental response, and are depleted in genes related to basic cellular processes. Furthermore, CNVs occur more often at the periphery of the protein interaction network. In comparison, protein families associated with successful and unsuccessful duplicates are associated with similar functional categories but are differentially placed in the interaction network. These trends are likely reflective of CNV formation biases and natural selection, both of which differentially influence distinct protein families.
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Affiliation(s)
- Jan O Korbel
- Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
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40
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Guryev V, Saar K, Adamovic T, Verheul M, van Heesch SAAC, Cook S, Pravenec M, Aitman T, Jacob H, Shull JD, Hubner N, Cuppen E. Distribution and functional impact of DNA copy number variation in the rat. Nat Genet 2008; 40:538-45. [PMID: 18443591 DOI: 10.1038/ng.141] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Accepted: 03/17/2008] [Indexed: 12/13/2022]
Abstract
The abundance and dynamics of copy number variants (CNVs) in mammalian genomes poses new challenges in the identification of their impact on natural and disease phenotypes. We used computational and experimental methods to catalog CNVs in rat and found that they share important functional characteristics with those in human. In addition, 113 one-to-one orthologous genes overlap CNVs in both human and rat, 80 of which are implicated in human disease. CNVs are nonrandomly distributed throughout the genome. Chromosome 18 is a cold spot for CNVs as well as evolutionary rearrangements and segmental duplications, suggesting stringent selective mechanisms underlying CNV genesis or maintenance. By exploiting gene expression data available for rat recombinant inbred lines, we established the functional relationship of CNVs underlying 22 expression quantitative trait loci. These characteristics make the rat an excellent model for studying phenotypic effects of structural variation in relation to human complex traits and disease.
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Affiliation(s)
- Victor Guryev
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences & University Medical Centre Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
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Bloomfield G, Tanaka Y, Skelton J, Ivens A, Kay RR. Widespread duplications in the genomes of laboratory stocks of Dictyostelium discoideum. Genome Biol 2008; 9:R75. [PMID: 18430225 PMCID: PMC2643946 DOI: 10.1186/gb-2008-9-4-r75] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Revised: 03/19/2008] [Accepted: 04/22/2008] [Indexed: 12/01/2022] Open
Abstract
Background Duplications of stretches of the genome are an important source of individual genetic variation, but their unrecognized presence in laboratory organisms would be a confounding variable for genetic analysis. Results We report here that duplications of 15 kb or more are common in the genome of the social amoeba Dictyostelium discoideum. Most stocks of the axenic 'workhorse' strains Ax2 and Ax3/4 obtained from different laboratories can be expected to carry different duplications. The auxotrophic strains DH1 and JH10 also bear previously unreported duplications. Strain Ax3/4 is known to carry a large duplication on chromosome 2 and this structure shows evidence of continuing instability; we find a further variable duplication on chromosome 5. These duplications are lacking in Ax2, which has instead a small duplication on chromosome 1. Stocks of the type isolate NC4 are similarly variable, though we have identified some approximating the assumed ancestral genotype. More recent wild-type isolates are almost without large duplications, but we can identify small deletions or regions of high divergence, possibly reflecting responses to local selective pressures. Duplications are scattered through most of the genome, and can be stable enough to reconstruct genealogies spanning decades of the history of the NC4 lineage. The expression level of many duplicated genes is increased with dosage, but for others it appears that some form of dosage compensation occurs. Conclusion The genetic variation described here must underlie some of the phenotypic variation observed between strains from different laboratories. We suggest courses of action to alleviate the problem.
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Affiliation(s)
- Gareth Bloomfield
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.
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Cahan P, Godfrey LE, Eis PS, Richmond TA, Selzer RR, Brent M, McLeod HL, Ley TJ, Graubert TA. wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data. Nucleic Acids Res 2008; 36:e41. [PMID: 18334530 PMCID: PMC2367727 DOI: 10.1093/nar/gkn110] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Copy number variants (CNVs) are currently defined as genomic sequences that are polymorphic in copy number and range in length from 1000 to several million base pairs. Among current array-based CNV detection platforms, long-oligonucleotide arrays promise the highest resolution. However, the performance of currently available analytical tools suffers when applied to these data because of the lower signal:noise ratio inherent in oligonucleotide-based hybridization assays. We have developed wuHMM, an algorithm for mapping CNVs from array comparative genomic hybridization (aCGH) platforms comprised of 385 000 to more than 3 million probes. wuHMM is unique in that it can utilize sequence divergence information to reduce the false positive rate (FPR). We apply wuHMM to 385K-aCGH, 2.1M-aCGH and 3.1M-aCGH experiments comparing the 129X1/SvJ and C57BL/6J inbred mouse genomes. We assess wuHMM's performance on the 385K platform by comparison to the higher resolution platforms and we independently validate 10 CNVs. The method requires no training data and is robust with respect to changes in algorithm parameters. At a FPR of <10%, the algorithm can detect CNVs with five probes on the 385K platform and three on the 2.1M and 3.1M platforms, resulting in effective resolutions of 24 kb, 2–5 kb and 1 kb, respectively.
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Affiliation(s)
- Patrick Cahan
- Department of Internal Medicine and Department of Genetics, Division of Oncology, Stem Cell Biology Section, Washington University, St Louis, MO, USA
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Genome-wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements. PLoS Genet 2008; 4:e1000007. [PMID: 18454193 PMCID: PMC2265474 DOI: 10.1371/journal.pgen.1000007] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Accepted: 01/15/2008] [Indexed: 11/19/2022] Open
Abstract
Endogenous retroviral elements (ERVs) in mice are significant genomic mutagens, causing ∼10% of all reported spontaneous germ line mutations in laboratory strains. The majority of these mutations are due to insertions of two high copy ERV families, the IAP and ETn/MusD elements. This significant level of ongoing retrotranspositional activity suggests that inbred mice are highly variable in content of these two ERV groups. However, no comprehensive genome-wide studies have been performed to assess their level of polymorphism. Here we compared three test strains, for which sufficient genomic sequence is available, to each other and to the reference C57BL/6J genome and detected very high levels of insertional polymorphism for both ERV families, with an estimated false discovery rate of only 0.4%. Specifically, we found that at least 60% of IAP and 25% of ETn/MusD elements detected in any strain are absent in one or more of the other three strains. The polymorphic nature of a set of 40 ETn/MusD elements found within gene introns was confirmed using genomic PCR on DNA from a panel of mouse strains. For some cases, we detected gene-splicing abnormalities involving the ERV and obtained additional evidence for decreased gene expression in strains carrying the insertion. In total, we identified nearly 700 polymorphic IAP or ETn/MusD ERVs or solitary LTRs that reside in gene introns, providing potential candidates that may contribute to gene expression differences among strains. These extreme levels of polymorphism suggest that ERV insertions play a significant role in genetic drift of mouse lines. The laboratory mouse is the most widely used mammal for biological research. Hundreds of inbred mouse strains have been developed that vary in characteristics such as susceptibility to cancer or other diseases. There is much interest in uncovering differences between strains that result in different traits and, to aid this effort, millions of single nucleotide differences or polymorphisms between strains have been cataloged. To date, there has been less emphasis placed on other sources of genetic variation. In this study, we have conducted a genome-wide analysis to examine the level of polymorphism of mouse endogenous retroviral sequences (ERVs). ERVs are derived from infectious retroviruses that now exist in the genome and are inherited as part of chromosomes. Unlike in humans, genomic insertions of ERVs cause many new mutations in mice but their extent of variation between strains has been difficult to study because of their high copy numbers. By comparing genomic sequences of four common mouse strains, we found very high levels of polymorphism for two large active families of ERVs. Moreover, we documented nearly 700 polymorphic ERVs located within gene introns and found evidence that some of these affect gene transcript levels. This study demonstrates that ERV polymorphisms are a major source of genetic variability among mouse strains and likely contribute to strain-specific traits.
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Lee AS, Gutiérrez-Arcelus M, Perry GH, Vallender EJ, Johnson WE, Miller GM, Korbel JO, Lee C. Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies. Hum Mol Genet 2008; 17:1127-36. [PMID: 18180252 DOI: 10.1093/hmg/ddn002] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Copy number variants (CNVs) are heritable gains and losses of genomic DNA in normal individuals. While copy number variation is widely studied in humans, our knowledge of CNVs in other mammalian species is more limited. We have designed a custom array-based comparative genomic hybridization (aCGH) platform with 385 000 oligonucleotide probes based on the reference genome sequence of the rhesus macaque (Macaca mulatta), the most widely studied non-human primate in biomedical research. We used this platform to identify 123 CNVs among 10 unrelated macaque individuals, with 24% of the CNVs observed in multiple individuals. We found that segmental duplications were significantly enriched at macaque CNV loci. We also observed significant overlap between rhesus macaque and human CNVs, suggesting that certain genomic regions are prone to recurrent CNV formation and instability, even across a total of approximately 50 million years of primate evolution ( approximately 25 million years in each lineage). Furthermore, for eight of the CNVs that were observed in both humans and macaques, previous human studies have reported a relationship between copy number and gene expression or disease susceptibility. Therefore, the rhesus macaque offers an intriguing, non-human primate outbred model organism with which hypotheses concerning the specific functions of phenotypically relevant human CNVs can be tested.
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Affiliation(s)
- Arthur S Lee
- Department of Pathology, Brigham and Women's Hospital, 221 Longwood Ave., Boston, MA 02115, USA
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46
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Watkins-Chow DE, Pavan WJ. Genomic copy number and expression variation within the C57BL/6J inbred mouse strain. Genes Dev 2008; 18:60-6. [PMID: 18032724 PMCID: PMC2134784 DOI: 10.1101/gr.6927808] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Accepted: 10/16/2007] [Indexed: 12/14/2022]
Abstract
The C57BL/6J strain is one of the most widely used animal models for biomedical research, and individual mice within the strain are often assumed to be genetically identical after more than 70 yr of inbreeding. Using a single nucleotide polymorphism (SNP) genotyping panel, we assessed if copy number variations (CNVs) could be detected within the C57BL/6J strain by comparing relative allele frequencies in first generation (F(1)) progeny of C57BL/6J mice. Sequencing, quantitative PCR, breeding, and array comparative genomic hybridization (CGH) together confirmed the presence of two CNVs. Both CNVs span genes encoded on chromosome 19, and quantitative RT-PCR demonstrated that they result in altered expression of the insulin-degrading enzyme (Ide) and fibroblast growth factor binding protein 3 (Fgfbp3) genes. Analysis of 39 different C57BL/6J breeders revealed that 64% of mice from the Jackson Laboratory colony were heterozygous for the CNV spanning Ide. Homozygotes with and without the duplication were present in concordance with Hardy-Weinberg equilibrium (13% and 23%, respectively), and analysis of archived samples from the C57BL/6J colony suggests that the duplication has rapidly reached a high frequency in the colony since 1994. The identification of two CNVs in the small portion of the genome screened demonstrates that individual mice of highly inbred strains are not isogenic and suggests other CNVs may be segregating within C57BL/6J as well as other carefully maintained inbred strains. These differences can influence interpretations of physiological, biomedical, and behavioral experiments and can be exploited to model CNVs apparent in the human genome.
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Affiliation(s)
- Dawn E. Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - William J. Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Estivill X, Armengol L. Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies. PLoS Genet 2007; 3:1787-99. [PMID: 17953491 PMCID: PMC2039766 DOI: 10.1371/journal.pgen.0030190] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Genome-wide association scans (GWASs) using single nucleotide polymorphisms (SNPs) have been completed successfully for several common disorders and have detected over 30 new associations. Considering the large sample sizes and genome-wide SNP coverage of the scans, one might have expected many of the common variants underpinning the genetic component of various disorders to have been identified by now. However, these studies have not evaluated the contribution of other forms of genetic variation, such as structural variation, mainly in the form of copy number variants (CNVs). Known CNVs account for over 15% of the assembled human genome sequence. Since CNVs are not easily tagged by SNPs, might have a wide range of copy number variability, and often fall in genomic regions not well covered by whole-genome arrays or not genotyped by the HapMap project, current GWASs have largely missed the contribution of CNVs to complex disorders. In fact, some CNVs have already been reported to show association with several complex disorders using candidate gene/region approaches, underpinning the importance of regions not investigated in current GWASs. This reveals the need for new generation arrays (some already in the market) and the use of tailored approaches to explore the full dimension of genome variability beyond the single nucleotide scale.
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Affiliation(s)
- Xavier Estivill
- Center for Genomic Regulation (CRG), National Genotyping Center (CeGen), CIBERESP, Pompeu Fabra University (UPF), Barcelona, Catalonia, Spain.
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Cutler G, Marshall LA, Chin N, Baribault H, Kassner PD. Significant gene content variation characterizes the genomes of inbred mouse strains. Genome Res 2007; 17:1743-54. [PMID: 17989247 DOI: 10.1101/gr.6754607] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The contribution to genetic diversity of genomic segmental copy number variations (CNVs) is less well understood than that of single-nucleotide polymorphisms (SNPs). While less frequent than SNPs, CNVs have greater potential to affect phenotype. In this study, we have performed the most comprehensive survey to date of CNVs in mice, analyzing the genomes of 42 Mouse Phenome Consortium priority strains. This microarray comparative genomic hybridization (CGH)-based analysis has identified 2094 putative CNVs, with an average of 10 Mb of DNA in 51 CNVs when individual mouse strains were compared to the reference strain C57BL/6J. This amount of variation results in gene content that can differ by hundreds of genes between strains. These genes include members of large families such as the major histocompatibility and pheromone receptor genes, but there are also many singleton genes including genes with expected phenotypic consequences from their deletion or amplification. Using a whole-genome association analysis, we demonstrate that complex multigenic phenotypes, such as food intake, can be associated with specific copy number changes.
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Affiliation(s)
- Gene Cutler
- Lead Discovery, Amgen, South San Francisco, California 94080, USA.
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Recurrent DNA copy number variation in the laboratory mouse. Nat Genet 2007; 39:1384-9. [PMID: 17965714 DOI: 10.1038/ng.2007.19] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Accepted: 08/27/2007] [Indexed: 11/08/2022]
Abstract
Different species, populations and individuals vary considerably in the copy number of discrete segments of their genomes. The manner and frequency with which these genetic differences arise over generational time is not well understood. Taking advantage of divergence among lineages sharing a recent common ancestry, we have conducted a genome-wide analysis of spontaneous copy number variation (CNV) in the laboratory mouse. We used high-resolution microarrays to identify 38 CNVs among 14 colonies of the C57BL/6 strain spanning approximately 967 generations of inbreeding, and we examined these loci in 12 additional strains. It is clear from our results that many CNVs arise through a highly nonrandom process: 18 of 38 were the product of recurrent mutation, and rates of change varied roughly four orders of magnitude across different loci. Recurrent CNVs are found throughout the genome, affect 43 genes and fluctuate in copy number over mere hundreds of generations, observations that raise questions about their contribution to natural variation.
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