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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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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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Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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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Genome Copying Errors02:46

Genome Copying Errors

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DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their  survival. Therefore, the copying errors are checked and repaired at three levels.
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Pleiotropy01:33

Pleiotropy

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Pleiotropy is the phenomenon in which a single gene impacts multiple, seemingly unrelated phenotypic traits. For example, defects in the SOX10 gene cause Waardenburg Syndrome Type 4, or WS4, which can cause defects in pigmentation, hearing impairments, and an absence of intestinal contractions necessary for elimination. This diversity of phenotypes results from the expression pattern of SOX10 in early embryonic and fetal development. SOX10 is found in neural crest cells that form melanocytes,...
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Histone Variants at the Centromere02:30

Histone Variants at the Centromere

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Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3...
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Polygenic Traits01:18

Polygenic Traits

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When more than one gene is responsible for a given phenotype, the trait is considered polygenic. Human height is a polygenic trait. Studies have uncovered hundreds of loci that influence height, and there are believed to be many more. Due to the high number of genes involved, as well as environmental and nutritional factors, height varies significantly within a given population. The distribution of height forms a bell-shaped curve, with relatively few individuals in the population at the...
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Related Experiment Video

Updated: Jun 29, 2025

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

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Protein-altering variants at copy number-variable regions influence diverse human phenotypes.

Margaux L A Hujoel1,2,3, Robert E Handsaker4,5,6, Maxwell A Sherman7,8,4,9,10

  • 1Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA. mhujoel@broadinstitute.org.

Nature Genetics
|March 29, 2024
PubMed
Summary

Copy number variants (CNVs) analysis revealed significant associations between genetic variations and 41 quantitative traits. This study highlights the impact of previously overlooked genomic variations on human health and disease risk.

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Detection of Copy Number Alterations Using Single Cell Sequencing
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Detection of Copy Number Alterations Using Single Cell Sequencing
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Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
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Area of Science:

  • Genomics
  • Human Genetics
  • Bioinformatics

Background:

  • Copy number variants (CNVs) represent large genetic variations but are often under-ascertained in genetic association studies.
  • Previous analyses have limitations in detecting subexonic CNVs and variations within segmental duplications.

Purpose of the Study:

  • To ascertain protein-altering CNVs from large-scale whole-exome sequencing data.
  • To investigate the association of these CNVs with quantitative traits.
  • To explore the contribution of previously undetected genomic variations to human traits and diseases.

Main Methods:

  • Utilized UK Biobank whole-exome sequencing data (n=468,570).
  • Employed haplotype-informed methods for ascertaining protein-altering CNVs, including subexonic CNVs and variations in segmental duplications.
  • Integrated CNVs into analyses of rare variants predicted to cause gene loss of function (LOF).

Main Results:

  • Identified 100 associations between predicted LOF variants (including CNVs) and 41 quantitative traits.
  • A partial deletion in RGL3 exon 6 showed a strong protective effect against hypertension risk (OR=0.86).
  • Variations in segmental duplications contributed significantly to type 2 diabetes risk, chronotype, and blood cell traits.

Conclusions:

  • Protein-altering CNVs and variations in segmental duplications are crucial genetic factors influencing quantitative traits.
  • New insights into human genetics can be gained by analyzing genomic variations previously missed by standard methods.
  • This study underscores the importance of comprehensive CNV analysis in understanding genetic contributions to health and disease.