Copy number variation in the domestic dog

Álvarez, Carlos E.; Akey, Joshua M.

doi:10.1007/s00335-011-9369-8

Cited by 46 publications

(49 citation statements)

References 80 publications

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“…Recurrent DNA copy number aberrations (CNA) exceed the frequency expected from normal copy number variability (Alvarez and Akey, 2012), but even within each WHO subtype, there is sufficient heterogeneity such that CNAs that are fundamentally associated with disease pathogenesis have remained largely elusive (Thomas et al, 2011). …”

Section: Comparative Molecular Pathogenesis Of Human Nhl and Caninmentioning

confidence: 99%

Canine lymphoma as a comparative model for human non-Hodgkin lymphoma: recent progress and applications

Ito

Frantz

Modiano

2014

Veterinary Immunology and Immunopathology

127

130

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The term “lymphoma” describes a heterogeneous group of disorders involving monoclonal proliferation of malignant lymphocytes. As a group, lymphomas are among the most common tumors of dogs. Yet our enumeration and understanding of the many subtypes of lymphoma have been relatively slow, perhaps in part because for many years lymphoma was treated as a singular entity rather than a group of distinct diseases. The recognition that the full spectrum of lymphoid malignancies seen in humans also occurs in dogs, and that these tumors retain not only morphologic similarities and biological behavior but also synonymous driver molecular abnormalities, sets an ideal stage for dual-purpose research that can accelerate progress for these diseases in both species. Specifically, dogs represent exceptional models for defining causality, understanding progression, and developing new treatments for lymphoma in comparatively brief windows of time. Unique advantages of canine models include (1) spontaneous disease occurring without an isogenic background or genetic engineering; (2) chronology of disease adapted to lifespan, (3) shared environment and societal status that allows dogs to be treated as “patients,” while at the same time being able to ethically explore translational innovations that are not possible in human subjects; and (4) organization of dogs into breeds with relatively homogeneous genetic backgrounds and distinct predisposition for lymphomas. Here, we will review recent studies describing intrinsic and extrinsic factors that contribute to the pathogenesis of canine and human lymphomas, as well as newly developed tools that will enhance the fidelity of these models to improve diagnosis and develop new treatments.

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Section: Comparative Molecular Pathogenesis Of Human Nhl and Caninmentioning

confidence: 99%

Canine lymphoma as a comparative model for human non-Hodgkin lymphoma: recent progress and applications

Ito

Frantz

Modiano

2014

Veterinary Immunology and Immunopathology

127

130

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“…For example, in animals, copy number variation has major effects on developmental traits and disease (Henrichsen et al, 2009;Craddock et al, 2010;Stankiewicz and Lupski, 2010;Alvarez and Akey, 2012). In plants, copy number variation has been identified in multiple species and demonstrated to affect important agronomic traits (Horiguchi et al, 2009;Pearce et al, 2011;Cook et al, 2012;Díaz et al, 2012;Li et al, 2012;Wingen et al, 2012;Ma et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

A System for Dosage-Based Functional Genomics in Poplar

et al. 2015

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Altering gene dosage through variation in gene copy number is a powerful approach to addressing questions regarding gene regulation, quantitative trait loci, and heterosis, but one that is not easily applied to sexually transmitted species. Elite poplar (Populus spp) varieties are created through interspecific hybridization, followed by clonal propagation. Altered gene dosage relationships are believed to contribute to hybrid performance. Clonal propagation allows for replication and maintenance of meiotically unstable ploidy or structural variants and provides an alternative approach to investigating gene dosage effects not possible in sexually propagated species. Here, we built a genome-wide structural variation system for dosage-based functional genomics and breeding of poplar. We pollinated Populus deltoides with gamma-irradiated Populus nigra pollen to produce >500 F1 seedlings containing dosage lesions in the form of deletions and insertions of chromosomal segments (indel mutations). Using high-precision dosage analysis, we detected indel mutations in ;55% of the progeny. These indels varied in length, position, and number per individual, cumulatively tiling >99% of the genome, with an average of 10 indels per gene. Combined with future phenotype and transcriptome data, this population will provide an excellent resource for creating and characterizing dosage-based variation in poplar, including the contribution of dosage to quantitative traits and heterosis.

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“…In the past few years, a significant amount of research on genome-wide CNV identification was conducted in various domestic animal species, including cattle [15, 16], dog [17–19], sheep [20], goat [21], chicken [22], turkey [23] and pig [24, 25]. A suite of genes with copy number alteration were exploited contributing to variation of either Mendelian phenotypes [26–28] or complex production traits [29].…”

Section: Introductionmentioning

confidence: 99%

Global copy number analyses by next generation sequencing provide insight into pig genome variation

Jiang

Wang

et al. 2014

BMC Genomics

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BackgroundCopy number variations (CNVs) confer significant effects on genetic innovation and phenotypic variation. Previous CNV studies in swine seldom focused on in-depth characterization of global CNVs.ResultsUsing whole-genome assembly comparison (WGAC) and whole-genome shotgun sequence detection (WSSD) approaches by next generation sequencing (NGS), we probed formation signatures of both segmental duplications (SDs) and individualized CNVs in an integrated fashion, building the finest resolution CNV and SD maps of pigs so far. We obtained copy number estimates of all protein-coding genes with copy number variation carried by individuals, and further confirmed two genes with high copy numbers in Meishan pigs through an enlarged population. We determined genome-wide CNV hotspots, which were significantly enriched in SD regions, suggesting evolution of CNV hotspots may be affected by ancestral SDs. Through systematically enrichment analyses based on simulations and bioinformatics analyses, we revealed CNV-related genes undergo a different selective constraint from those CNV-unrelated regions, and CNVs may be associated with or affect pig health and production performance under recent selection.ConclusionsOur studies lay out one way for characterization of CNVs in the pig genome, provide insight into the pig genome variation and prompt CNV mechanisms studies when using pigs as biomedical models for human diseases.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-593) contains supplementary material, which is available to authorized users.

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Copy number variation in the domestic dog

Cited by 46 publications

References 80 publications

Canine lymphoma as a comparative model for human non-Hodgkin lymphoma: recent progress and applications

Canine lymphoma as a comparative model for human non-Hodgkin lymphoma: recent progress and applications

A System for Dosage-Based Functional Genomics in Poplar

Global copy number analyses by next generation sequencing provide insight into pig genome variation

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