Genome-Wide Copy Number Variant Analysis in Inbred Chickens Lines With Different Susceptibility to Marek’s Disease

Luo, Juan; Yu, Ying; Mitra, Apratim; Chang, Shuang; Zhang, Huanmin; Liu, George E.; Yang, Ning; Song, Jiuzhou

doi:10.1534/g3.112.005132

Cited by 41 publications

(63 citation statements)

References 39 publications

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“…These unique CNVRs may be recent events in evolution and contribute to breed-specific phenotype and performance [44]. Compared with the eight previous chicken CNV studies [9,[32][33][34]36,[39][40][41], far more CNVRs both on average and in total were found. A total of 6,478 (86.0%) autosomal CNVRs with slightly smaller average size (10.6 kb) were novel, likely due to the higher resolution and sensitivity of NGS method than aCGH and SNP array.…”

Section: Genome-wide Cnv Landscape In the Chicken Genomementioning

confidence: 78%

“…The NGS technology and RD method employed in our work has advantages in both technology platform and genetic diversity compared with the eight previous reports [9,[32][33][34]36,[39][40][41]. Because a significant fraction of CNVs falls into genomic regions not well-covered by microarrays, especially for SD regions lacking sufficient probes [16,23], CNV as a major source of genetic variation is complementary to SNP and could account for a substantial part of missing heritability [14].…”

Section: Discussionmentioning

confidence: 96%

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Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing

Liu

et al. 2014

Preprint

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Background: Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we performed a genome-wide CNV analysis in 12 diversified chicken genomes based on whole genome sequencing. Results: A total of 8,840 CNV regions (CNVRs) covering 98.2 Mb and representing 9.4% of the chicken genome were identified, ranging in size from 1.1 to 268.8 kb with an average of 11.1 kb. Sequencing-based predictions were confirmed at a high validation rate by two independent approaches, including array comparative genomic hybridization (aCGH) and quantitative PCR (qPCR). The Pearson's correlation coefficients between sequencing and aCGH results ranged from 0.435 to 0.755, and qPCR experiments revealed a positive validation rate of 91.71% and a false negative rate of 22.43%. In total, 2,214 (25.0%) predicted CNVRs span 2,216 (36.4%) RefSeq genes associated with specific biological functions. Besides two previously reported copy number variable genes EDN3 and PRLR, we also found some promising genes with potential in phenotypic variation. Two genes, FZD6 and LIMS1, related to disease susceptibility/resistance are covered by CNVRs. The highly duplicated SOCS2 may lead to higher bone mineral density. Entire or partial duplication of some genes like POPDC3 may have great economic importance in poultry breeding. Conclusions: Our results based on extensive genetic diversity provide a more refined chicken CNV map and genome-wide gene copy number estimates, and warrant future CNV association studies for important traits in chickens.

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Section: Genome-wide Cnv Landscape In the Chicken Genomementioning

confidence: 78%

Section: Discussionmentioning

confidence: 96%

Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing

Liu

et al. 2014

Preprint

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“…CNVs related to MD resistance were reported before using array CGH and next-generation sequencing [36,37]. However, most of them were reported in only parental lines, i.e., MD-resistant Line 63 and susceptible Line 72.…”

Section: Introductionmentioning

confidence: 99%

Characterization of Copy Number Variation’s Potential Role in Marek’s Disease

Ding

et al. 2017

IJMS

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Marek’s Disease (MD) is a highly contagious pathogenic and oncogenic disease primarily affecting chickens. Chicken Lines 63 and 72, as well as their recombinant congenic strains (RCS) with varied susceptibility to MD, are ideal models to study the complex mechanisms of genetic resistance to MD. In this study, we investigated copy number variation (CNV) in these inbred chicken lines using the Affymetrix Axiom HD 600 K SNP genotyping array. We detected 393 CNV segments across all ten chicken lines, of which 12 CNVs were specifically identified in Line 72. We then assessed genetic structure based on CNV and observed markedly different patterns. Finally, we validated two deletion events in Line 72 and correlated them with genes expression using qPCR and RNA-seq, respectively. Our combined results indicated that these two CNV deletions were likely to contribute to MD susceptibility.

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“…The concept of CNVs associated with cancer susceptibility can explain well a difference in the frequency of sporadic cancers between individuals under the same environment. The CNVs associated with cancer susceptibility have been reported in dogs [19], mice [7] and chickens [20] as well as in human. The analysis of CNVs associated with cancer susceptibility CNVs allows us to estimate individual susceptibility to each type of cancers.…”

Section: Introductionmentioning

confidence: 99%

CNVs Associated with Susceptibility to Cancers: A Mini-Review

Furuya¹,

Suehiro²,

Namiki³

et al. 2015

JCT

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Copy number variations (CNVs) that are frequent in genome influence on susceptibility of various diseases including cancers. The present mini-review focuses on CNVs associated with susceptibility to the cancers. Since CNVs are different between cancer types, the analysis of the specific CNV makes it possible to estimate the susceptibility to the cancers of interest in individuals. Although it is true that available data on CNVs associated with cancer susceptibility are limited at present, accumulation of the data is accelerated with the research progression of CNVs in near future. Information on CNVs associated with cancer susceptibility is useful for not only cancer research but also personalized healthcare including cancer prevention.

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Genome-Wide Copy Number Variant Analysis in Inbred Chickens Lines With Different Susceptibility to Marek’s Disease

Cited by 41 publications

References 39 publications

Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing

Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing

Characterization of Copy Number Variation’s Potential Role in Marek’s Disease

CNVs Associated with Susceptibility to Cancers: A Mini-Review

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