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Mouse Segmental Duplication and Copy-Number Variation

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. The architecture of mouse and human genomes differ dramatically; most mouse duplications are organized into discrete clusters of tandem duplications that are depleted for genes/transcripts and enriched for LINE1 and LTR retroposons. We assessed copy-number variation of the C57BL/6J duplicated regions within 15 mouse strains used for genetic association studies, sequencing, and the mouse phenome project. We determined that over 60% of these basepairs are polymorphic between the strains (on average 20 Mbp 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 inter-strain copy-number variation restricted to large gene families associated with spermatogenesis, pregnancy, viviparity, phermone signaling, and immune response. Keywords: comparative genomic hybridization

ORGANISM(S): Mus musculus

PROVIDER: GSE11369 | GEO | 2008/05/10

SECONDARY ACCESSION(S): PRJNA106591

REPOSITORIES: GEO

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Mouse Segmental Duplication and Copy-Number Variation

Project description: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. The architecture of mouse and human genomes differ dramatically; most mouse duplications are organized into discrete clusters of tandem duplications that are depleted for genes/transcripts and enriched for LINE1 and LTR retroposons. We assessed copy-number variation of the C57BL/6J duplicated regions within 15 mouse strains used for genetic association studies, sequencing, and the mouse phenome project. We determined that over 60% of these basepairs are polymorphic between the strains (on average 20 Mbp 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 inter-strain copy-number variation restricted to large gene families associated with spermatogenesis, pregnancy, viviparity, phermone signaling, and immune response. Keywords: comparative genomic hybridization Genomic DNA of 14 inbred mouse strains was tested against reference C57BL/6J sample. C57BL/6J DNA sample from another individual was tested as negative control.

2008-05-10 | E-GEOD-11369 | biostudies-arrayexpress

Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans

Project description:Background: Copy number variation is an important component of genetic variation in higher eukaryotes. The extent of natural copy number variation in C. elegans is unknown outside of 2 highly divergent wild isolates and the canonical N2 Bristol strain. Results: We have used array comparative genomic hybridization (aCGH) to detect copy number variation in the genomes of 12 natural isolates of Caenorhabditis elegans. Deletions relative to the canonical N2 strain are more common in these isolates than duplications, and indels are enriched in multigene families on the autosome arms. Among the strains in our study, the Hawaiian and Madeiran strains (CB4856 and JU258) carry the largest number of deletions, followed by the Vancouver strain (KR314). Overall we detected 510 different deletions affecting 1136 genes, or over 5% of the genes in the canonical N2 genome. The indels we identified had a median length of 2.7 kb. Since many deletions are found in multiple isolates, deletion loci were used as markers to derive an unrooted tree to estimate genetic relatedness among the strains. Conclusion: Copy number variation is extensive in C. elegans, affecting over 5% of the genes in the genome. The deletions we have detected in natural isolates of C. elegans contribute significantly to the number of deletion alleles available to researchers. The relationships between strains are complex and different regions of the genome possess different genealogies due to recombination throughout the natural history of the species, which may not be apparent in studies utilizing smaller numbers of genetic markers.

2009-12-17 | GSE19440 | GEO

Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans

2010-05-17 | E-GEOD-19440 | biostudies-arrayexpress

Mus musculus

Project description:Mouse Segmental Duplication and Copy-Number Variation

| PRJNA106591 | ENA

Polyploidy can drive rapid adaptation in yeast

Project description:Analysis of copy number variation in evolved haploid, diploid, tetraploid strains.

2015-02-28 | GSE51017 | GEO

Natural selection shapes genome wide patterns of copy number polymorphism in D. melanogaster

Project description:The role natural selection plays in governing the locations and early evolution of copy number mutations remains largely unexplored. Here we employ high-density full-genome tiling arrays to create a fine-scale genomic map of copy number polymorphisms (CNPs) in Drosophila melanogaster. We inferred a total of 2,658 independent CNPs, 56% of which overlap genes. These include CNPs likely to be under positive selection, most notably high frequency duplications encompassing toxin-response genes. The locations and frequencies of CNPs are strongly shaped by purifying selection with deletions under stronger purifying selection than duplications. Among duplications, those overlapping exons or introns and those falling on the X-chromosome seem to be subject to the strongest purifying selection. In order to characterize copy number polymorphisms (CNPs) in Drosophila malanogaster, we applied comparative genome hybridization (CGH) using tiling arrays covering the full euchromatic genome of Drosophila melanogaster. We inferred copy number changes with a Hidden Markov Model (HMM) that returned the posterior probabilities for copy number by comparing DNA hybridization intensities between natural isolates and the reference genome strain. Training data for copy number changes were obtained via hybridization with a line known to contain a ~200kb homozygous duplication and from a set of 52 validated homozygous deletions. The probabilities of mutation were parsed to make CNP calls. Key words: comparative genomic hybridization, CGH, copy number polymorphism, CNP, copy number variation, CNV, duplication, deletion

2008-06-06 | GSE11326 | GEO

Array-CGH and Next-generation sequencing of duplication CNVs reveals that most are tandem and some disrupt genes at breakpoints

Project description:Interpreting the genomic and phenotypic consequences of copy number variation (CNV) is essential to understand the etiology of genetic disorders. Whereas deletion CNVs obviously lead to haploinsufficiency, duplications may cause disease through triplosensitivity, gene disruption, or gene fusion at breakpoints. The mutational spectrum of duplications has been studied at certain loci and in some cases these copy number gains are complex chromosome rearrangements involving triplications and/or inversions. However, the organization of clinically relevant duplications throughout the genome has not been investigated on a large scale. Here, we fine mapped 184 germline duplications (14.7 kb-25.3 Mb; median 532 kb) ascertained from individuals referred for diagnostic cytogenetics testing. We performed next-generation sequencing (NGS) and whole-genome sequencing (WGS) to sequence 130 breakpoints from 112 subjects with 119 CNVs and found that most (83%) were tandem duplications in direct orientation. The remainder were triplications embedded within duplications (8.4%), adjacent duplications (4.2%), insertional translocations (2.5%), or other complex rearrangements (1.7%). In addition, we predicted six in-frame fusion genes at sequenced duplication breakpoints. Four gene fusions were formed by tandem duplications, one by two interconnected duplications, and one by duplication inserted at another locus. These novel fusion genes could be related to clinical phenotypes and warrant further study. Though most duplications are positioned head-to-tail adjacent to the original locus, those that are inverted, triplicated, or inserted can disrupt or fuse genes in a manner that may not be predicted by conventional copy number analysis. Thus, interpreting the genetic consequences of duplication CNVs requires breakpoint-level analysis.

2014-10-25 | GSE62657 | GEO

Oenococcus oeni CGH 11strains vs AWRIB515

Project description:CGH analysis of copy number variation in 11 strains of Oenococcus oeni compared to strain AWRIB515.

2010-05-24 | GSE16736 | GEO

Recurrent DNA copy number variation in the laboratory mouse

Project description: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 between 14 colonies of the C57BL/6 strain spanning ~967 generations of inbreeding, and examined these loci in 12 additional strains. It is clear from our results that many CNVs arise through a highly non-random process: 18 of 38 were the product of recurrent mutation, and rates of change vary roughly four orders of magnitude across different loci. These recurrent CNVs are distributed 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. Keywords: Representational oligonucleotide microarray analysis, comparative genomic hybridization, DNA copy number variation, structural variation, inbred mice, spontaneous mutation rate

2007-10-28 | GSE8980 | GEO

Recurrent DNA copy number variation in the laboratory mouse

Project description: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 between 14 colonies of the C57BL/6 strain spanning ~967 generations of inbreeding, and examined these loci in 12 additional strains. It is clear from our results that many CNVs arise through a highly non-random process: 18 of 38 were the product of recurrent mutation, and rates of change vary roughly four orders of magnitude across different loci. These recurrent CNVs are distributed 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. Keywords: comparative genomic hybridization, DNA copy number variation, structural variation, inbred mice, spontaneous mutation rate

2007-10-28 | GSE8885 | GEO

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