File Name: copy number variation in human health disease and evolution .zip
Copy number variation CNV is a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals. Copy number variations can be generally categorized into two main groups: short repeats and long repeats. However, there are no clear boundaries between the two groups and the classification depends on the nature of the loci of interest. Short repeats include mainly bi-nucleotide repeats two repeating nucleotides e. Long repeats include repeats of entire genes. This classification based on size of the repeat is the most obvious type of classification as size is an important factor in examining the types of mechanisms that most likely gave rise to the repeats,  hence the likely effects of these repeats on phenotype.
Autism spectrum disorders ASDs are characterized by language impairments, social deficits, and repetitive behaviors. The onset of symptoms occurs by the age of 3 and shows a lifelong persistence. Genetics plays a major role in the etiology of ASD. Except genetics, several potential risk factors environmental factors and epigenetics may contribute to ASD. Copy number variations CNVs are the most widespread structural variations in the human genome. These variations can alter the genome structure either by deletion or by duplication. CNVs can be de novo or inherited.
Metrics details. Copy number variation CNV has been examined in many species and is recognized as a major source of genetic variation that directly contributes to phenotypic variation such as resistance to infectious diseases. Two highly inbred chicken lines, 6 3 MD-resistant and 7 2 MD-susceptible , as well as their F 1 generation and six recombinant congenic strains RCSs with varied susceptibility to MD, are considered as ideal models to identify the complex mechanisms of genetic and molecular resistance to MD. In the present study, to unravel the potential genetic mechanisms underlying resistance to MD, we performed a genome-wide CNV detection using next generation sequencing on the inbred chicken lines with the assistance of CNVnator. Within these shared regions, harbored genes were identified.
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Copy number variation CNV can promote phenotypic diversification and adaptive evolution. However, the genomic architecture of CNVs among Macaca species remains scarcely reported, and the roles of CNVs in adaptation and evolution of macaques have not been well addressed. Here, we identified and characterized 1, genome-wide hetero-specific CNVs across nine Macaca species with bioinformatic methods, along with 26 CNV-dense regions and dozens of lineage-specific CNVs.
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. However, reliably determining copy number of a particular DNA sequence for a large number of samples can be challenging.
People have two copies of most genes, one copy inherited from each parent. In some cases, however, the number of copies varies—meaning that a person can be born with one, three, or more copies of particular genes. Less commonly, one or more genes may be entirely missing. This type of genetic difference is known as copy number variation CNV. Copy number variation results from insertions, deletions, and duplications of large segments of DNA. These segments are big enough to include whole genes.
A computational tool to detect both germline and mosaic chromosomal alterations at low allelic fractions based on phased haplotype data. Mosaic chromsomal alterations in diploid cells affect the overall balance of alleles from the two haplotypes at consecutive heterozygous sites. Long-range phase information allows the careful integration of this imbalance across long chromosomal segments. By carefully performing this integration, MoChA is capable of detecting mosaic chromosomal alterations present in as little as one percent of the cells that comprise the DNA library. The ability to identify events at such low cell fractions greatly enhances the ability to detect clonality in samples from blood, cancer, and cell lines. MoChA is entirely written in C and based on HTSlib and BCFtools libraries and is equally capable of processing data from DNA microarray and whole-genome sequencing experiments, providing a simple unifying framework for researchers.
Molecular methods, by which copy number variants CNVs detection is available, have been gradually introduced into routine diagnostics over the last 15 years. Despite this, some CNVs continue to be a huge challenge when it comes to clinical interpretation. CNVs are an important source of normal and pathogenic variants, but, in many cases, their impact on human health depends on factors that are not yet known. Therefore, perception of their clinical consequences can change over time, as our knowledge grows. This review summarises guidelines that facilitate correct classification of identified changes and discusses difficulties with the interpretation of rare, small CNVs.
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