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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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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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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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Gene Duplication and Divergence02:37

Gene Duplication and Divergence

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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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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.
Genes exist in different versions called alleles,...
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Variability: Analysis01:11

Variability: Analysis

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Measures of variability are statistical metrics that reveal the dispersion pattern within a dataset. They are pivotal in biostatistics, providing insights into the heterogeneity within health and biological data. Variability signifies the degree to which data points diverge from one another, helping researchers understand the potential range of values and associated uncertainty within the data.
The range is a simple measure of variability, indicating the difference between the highest and...
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Detection of Copy Number Alterations Using Single Cell Sequencing
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CONSERTING: integrating copy-number analysis with structural-variation detection.

Xiang Chen1, Pankaj Gupta1, Jianmin Wang2

  • 11] Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. [2] Pediatric Cancer Genome Project, St. Jude Children's Research Hospital and Washington University School of Medicine, Memphis, Tennessee, USA.

Nature Methods
|May 5, 2015
PubMed
Summary
This summary is machine-generated.

We developed a new algorithm, CONSERTING, to accurately detect copy-number alterations in cancer genomes using whole-genome sequencing. This method identified novel genetic changes missed by other approaches in pediatric and adult cancer patients.

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Related Experiment Videos

Last Updated: Apr 13, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing
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Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • Somatic copy-number alterations (CNAs) are key drivers of cancer.
  • Accurate detection of CNAs is crucial for understanding cancer development and treatment.

Purpose of the Study:

  • To develop and validate a novel algorithm for detecting somatic CNAs from whole-genome sequencing (WGS) data.
  • To identify novel oncogenic CNAs, complex rearrangements, and subclonal CNAs in cancer genomes.

Main Methods:

  • Developed CONSERTING (Copy Number Segmentation by Regression Tree in Next Generation Sequencing).
  • Employed iterative segmentation analysis based on read depth changes and localized structural variations.
  • Applied the algorithm to analyze 43 pediatric and adult cancer genomes.

Main Results:

  • CONSERTING demonstrated high accuracy and sensitivity in CNA detection.
  • Identified novel oncogenic CNAs, complex rearrangements, and subclonal CNAs.
  • Detected alterations missed by alternative CNA detection methods.

Conclusions:

  • CONSERTING is an effective tool for detecting somatic CNAs using WGS data.
  • The algorithm facilitates the discovery of clinically relevant genetic alterations in cancer.