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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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%...
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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,...
Genome Copying Errors02:46

Genome Copying Errors

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.
Gene Conversion02:08

Gene Conversion

Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
Test for Homogeneity01:23

Test for Homogeneity

The goodness–of–fit test can be used to decide whether a population fits a given distribution, but it will not suffice to decide whether two populations follow the same unknown distribution. A different test, called the test for homogeneity, can be used to conclude whether two populations have the same distribution. To calculate the test statistic for a test for homogeneity, follow the same procedure as with the test of independence. The hypotheses for the test for homogeneity can be stated as...
Genetic Variation01:25

Genetic Variation

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.
Genes exist in different versions called alleles, which...

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Related Experiment Video

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Detection of Copy Number Alterations Using Single Cell Sequencing
09:45

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

Finding recurrent copy number alterations preserving within-sample homogeneity.

Sandro Morganella1, Stefano Maria Pagnotta, Michele Ceccarelli

  • 1Department of Science, University of Sannio, 82100, Benevento, Italy. morganella@unisannio.it

Bioinformatics (Oxford, England)
|August 30, 2011
PubMed
Summary

Genomic Analysis of Important Alterations (GAIA) identifies recurrent copy number alterations (CNAs) by integrating statistical significance and within-sample homogeneity. This novel approach improves the accuracy of detecting functionally relevant genomic changes in diseases.

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Characterizing Mutational Load and Clonal Composition of Human Blood
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Last Updated: May 29, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing
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Published on: February 17, 2017

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
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Characterizing Mutational Load and Clonal Composition of Human Blood
07:58

Characterizing Mutational Load and Clonal Composition of Human Blood

Published on: July 11, 2019

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Copy number alterations (CNAs) are key genetic variations implicated in human diseases.
  • Array comparative genomic hybridization (aCGH) enables CNA identification.
  • Distinguishing functional CNAs from random events is a major challenge.

Purpose of the Study:

  • To develop a novel computational approach for identifying recurrent CNAs.
  • To enhance CNA detection accuracy by incorporating within-sample homogeneity.
  • To provide a comprehensive comparison of different recurrent CNA detection methods.

Main Methods:

  • Proposed Genomic Analysis of Important Alterations (GAIA) method.
  • Extended statistical hypothesis framework to include within-sample homogeneity.
  • Iterative procedure combining statistical significance and homogeneity for region extraction.
  • Validation using real aCGH datasets and simulation studies.

Main Results:

  • GAIA effectively identifies recurrent CNAs by leveraging within-sample homogeneity.
  • The proposed method demonstrates comparable or superior performance to existing approaches.
  • A detailed comparison with other algorithms was conducted using real and simulated data.

Conclusions:

  • GAIA offers a robust alternative for recurrent CNA detection.
  • Incorporating within-sample homogeneity improves the identification of functionally relevant genomic alterations.
  • The GAIA R/Bioconductor package is available for public use.