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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.
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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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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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The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...
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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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Detection of Copy Number Alterations Using Single Cell Sequencing
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Large multiallelic copy number variations in humans.

Robert E Handsaker1, Vanessa Van Doren1, Jennifer R Berman2

  • 11] Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [3] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.

Nature Genetics
|January 27, 2015
PubMed
Summary

Multiallelic copy number variations (mCNVs) drive most human gene dosage variation, impacting gene expression. This study identifies numerous mCNVs and their alleles across thousands of genomes, revealing novel insights into genetic diversity.

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Area of Science:

  • Genomics
  • Human Genetics
  • Population Genetics

Background:

  • Genomic segments vary widely in copy number across human genomes.
  • Understanding copy number variations (CNVs) is crucial for comprehending human genetic diversity and its impact on gene dosage.

Purpose of the Study:

  • To develop methods for identifying copy numbers, alleles, and haplotypes at large multiallelic CNVs (mCNVs) using whole-genome sequence data.
  • To quantify the contribution of mCNVs to human gene dosage variation and gene expression.

Main Methods:

  • Analysis of 849 genomes from the 1000 Genomes Project.
  • Identification of large ( >5-kb) mCNVs, including duplications with multiple segregating alleles.
  • Development of initial strategies for mCNV analysis via imputation.

Main Results:

  • Identification of most large mCNVs, including 3,878 duplications, with 1,356 having 3 or more segregating alleles.
  • mCNVs account for the majority of human gene dosage variation, exceeding deletions and biallelic duplications sevenfold.
  • Discovery of 'runaway duplication haplotypes' for genes like HPR and ORM1.

Conclusions:

  • mCNVs are a major source of human genetic variation influencing gene dosage and expression.
  • The study provides a foundational dataset and analytical approaches for studying mCNVs.
  • Further research into mCNVs and their functional consequences is warranted.