Diversity Of Human Copy Number Variation And Multicopy Genes Pdf
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- Diversity of Human Copy Number Variation and Multicopy Genes
- Distribution and Functionality of Copy Number Variation across European Cattle Populations
- Human gene copy number variation and infectious disease
- Expandable and reversible copy number amplification drives rapid adaptation to antifungal drugs
Protocol DOI: Copy number variation CNV , where a segment of DNA differs in copy number between different individuals, is an extensive and often underappreciated source of genetic variation within species. However, reliably determining copy number of a particular.
Diversity of Human Copy Number Variation and Multicopy Genes
Previously, we identified long repeat sequences that are frequently associated with genome rearrangements, including copy number variation CNV , in many diverse isolates of the human fungal pathogen Candida albicans Todd et al. Here, we describe the rapid acquisition of novel, high copy number CNVs during adaptation to azole antifungal drugs. Single-cell karyotype analysis indicates that these CNVs appear to arise via a dicentric chromosome intermediate and breakage-fusion-bridge cycles that are repaired using multiple distinct long inverted repeat sequences. Subsequent removal of the antifungal drug can lead to a dramatic loss of the CNV and reversion to the progenitor genotype and drug susceptibility phenotype. These findings support a novel mechanism for the rapid acquisition of antifungal drug resistance and provide genomic evidence for the heterogeneity frequently observed in clinical settings. The evolution of antifungal drug resistance is an urgent threat to human health worldwide, particularly for hospitalized and immune-compromised individuals Perea and Patterson, ; Pfaller, ; Vandeputte et al.
The Y chromosome harbors nine multi-copy ampliconic gene families expressed exclusively in testis. Recent studies demonstrated high variation in Y ampliconic gene copy number among humans. However, how this variation affects expression levels in human testis remains understudied. Here we developed a novel computational tool Ampliconic Copy Number Estimator AmpliCoNE that utilizes read sequencing depth information to estimate Y ampliconic gene copy number per family. We applied this tool to whole-genome sequencing data of men with matched testis expression data whose samples are part of the Genotype-Tissue Expression GTEx project. We found that the Y ampliconic gene families with low copy number in humans were deleted or pseudogenized in non-human great apes, suggesting relaxation of functional constraints.
Derek M. Bickhart, Lingyang Xu, Jana L. Hutchison, John B. Cole, Daniel J. Null, Steven G. Sonstegard, Curtis P. Van Tassell, Robert D.
Distribution and Functionality of Copy Number Variation across European Cattle Populations
Copy number variation CNV , which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. Animals originating from several breeds of British Isles, and Balkan and Italian regions, on average, displayed higher abundance of CNV counts than Dutch or Alpine animals. Various CNVRs identified in the present study overlapped with olfactory receptor genes and genes related to immune system. In addition, we also detected a CNV overlapping the Kit gene in English longhorn cattle which has previously been associated with color-sidedness. To conclude, we provide a comprehensive overview of CNV distribution in genome of European cattle.
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Variability in the susceptibility to infectious disease and its clinical manifestation can be determined by variation in the environment and by genetic variation in the pathogen and the host. Despite several successes based on candidate gene studies, defining the host variation affecting infectious disease has not been as successful as for other multifactorial diseases. In this review we focus on CNV, particularly on complex multiallelic CNV that is often not well characterised either directly by hybridisation methods or indirectly by analysis of genotypes and flanking single nucleotide variants. We also highlight some understudied areas that might prove fruitful areas for further research. Infectious disease can be regarded as a complex multifactorial disease, with both genetic and environmental variation contributing to differing susceptibilities to infection, and differing effects of infection Chapman and Hill Like any other multifactorial disease, the variation in who is infected has been divided into a genetic component and an environmental component, with heritability estimates equivalent to other multifactorial diseases [for example, heritability of malaria in Kenya is 0. Like any other multifactorial disease, both rare and common genetic variations are likely to play a role.
These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and.
Human gene copy number variation and infectious disease
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Metrics details. Copy number variations CNVs are an important type of structural variations in the genome that usually affect gene expression levels by gene dosage effect. Understanding CNVs as part of genome evolution may provide insights into the genetic basis of important agricultural traits and contribute to the crop breeding in the future.
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Expandable and reversible copy number amplification drives rapid adaptation to antifungal drugs
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