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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

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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 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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Genetic Variation01:25

Genetic Variation

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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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Gene Duplication and Divergence02:37

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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
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Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
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Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
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SCNVSim: somatic copy number variation and structure variation simulator.

Maochun Qin1, Biao Liu2, Jeffrey M Conroy3

  • 1Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA. Maochun.Qin@RoswellPark.org.

BMC Bioinformatics
|April 19, 2015
PubMed
Summary

SCNVSim simulates cancer genomes with structural variations (SVs) and copy number variations (CNVs), including tumor features like aneuploidy and heterogeneity. This tool aids in developing and evaluating methods for detecting these crucial genomic alterations in cancer.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Somatic structural variations (SVs) and copy number variations (CNVs) are key drivers of tumor genesis.
  • Detecting somatic SVs/CNVs from next-generation sequencing (NGS) data is challenging due to tumor ploidy, heterogeneity, and purity.
  • A simulated cancer genome with known SVs/CNVs serves as a benchmark for evaluating detection tools.

Purpose of the Study:

  • To introduce SCNVSim, a novel tool for simulating somatic copy number variations (CNVs) and structural variations (SVs).
  • To enable the simulation of complex tumor sample characteristics, including aneuploidy, heterogeneity, and purity.

Main Methods:

  • SCNVSim simulates various types of SV and CNV events.
  • The tool incorporates critical tumor-specific features such as aneuploidy, heterogeneity, and purity.
  • It generates detailed genomic information for simulated cancer cell populations.

Main Results:

  • SCNVSim can simulate diverse SV and CNV events.
  • The simulation accounts for key tumor characteristics like aneuploidy, heterogeneity, and purity.
  • The tool generates comprehensive genomic data, including copy number status, LOH, and breakpoints.

Conclusions:

  • SCNVSim provides essential simulated cancer genomes for developing and evaluating somatic SV/CNV detection methods.
  • The tool's ability to model tumor features enhances the reliability of benchmark datasets.
  • This facilitates advancements in cancer genomics research and diagnostic tool development.