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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...
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Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
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In addition to multiple alleles at the same locus influencing traits, numerous genes or alleles at different locations may interact and influence phenotypes in a phenomenon called epistasis. For example, rabbit fur can be black or brown depending on whether the animal is homozygous dominant or heterozygous at a TYRP1 locus. However, if the rabbit is also homozygous recessive at a locus on the tyrosinase gene (TYR), it will have an unshaded coat that appears white, regardless of its TYRP1...
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Protein-coding repeat polymorphisms strongly shape diverse human phenotypes.

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    Variable number tandem repeats (VNTRs) in human genomes influence phenotypes like height and hair. New methods analyze VNTRs from sequencing data, revealing strong associations with human traits previously missed by genetic studies.

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    Area of Science:

    • Human Genetics
    • Genomics
    • Molecular Biology

    Background:

    • Hundreds of human proteins contain variable number tandem repeats (VNTRs) in coding exons, affecting protein structure.
    • VNTRs have been difficult to analyze with standard genetic methods like SNP arrays and high-throughput sequencing, leaving their phenotypic impact largely unknown.
    • Understanding VNTRs is crucial for a comprehensive view of human genetic variation and its relation to health.

    Approach:

    • Developed novel computational methods to estimate VNTR lengths from whole-exome sequencing data.
    • Integrated VNTR allele identification with SNP haplotype analysis and imputation into large SNP datasets.
    • Analyzed 118 protein-altering VNTRs across 415,280 UK Biobank participants for associations with 791 phenotypes.

    Key Points:

    • Identified strong associations between VNTRs and human phenotypes, including height (e.g., ACAN VNTR influencing height by 3.4 cm), hair morphology, and health biomarkers.
    • Demonstrated that VNTRs, like the LPA kringle IV-2 VNTR, explain a significant portion (90%) of heritability for biomarkers such as lipoprotein(a) in Europeans.
    • Revealed substantial, previously hidden effects of common, highly polymorphic structural variants on human traits.

    Conclusions:

    • VNTRs represent a significant, underappreciated source of genetic variation impacting human phenotypes.
    • The developed analytical framework allows for the incorporation of VNTRs into large-scale genetic studies, enhancing our understanding of genotype-phenotype relationships.
    • These findings open new avenues for research into the genetic basis of human diseases and population-specific traits.