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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%...
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.
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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,...
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

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 characterized.

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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

Comparative analysis of copy number variation detection methods and database construction.

Asako Koike1, Nao Nishida, Daiki Yamashita

  • 1Central Research Laboratory, Hitachi Ltd., Tokyo, Japan. asako.koike.ea@hitachi.com

BMC Genetics
|March 10, 2011
PubMed
Summary
This summary is machine-generated.

Copy number variations (CNVs) detection accuracy varies by program. Hidden Markov model-based tools like PennCNV and Birdsuite offer better performance. Repeat sequences, especially LINEs, are involved in common CNV formation.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Array-based detection of copy number variations (CNVs) is crucial for identifying genetic variations linked to diseases.
  • Current CNV detection methods lack sufficient accuracy, with results varying significantly based on the software and parameters used.

Purpose of the Study:

  • To evaluate the performance of five prominent CNV detection programs (Birdsuite, Birdseye, PennCNV, CGHseg, DNAcopy) on the Affymetrix platform.
  • To identify and characterize CNVs in 180 healthy Japanese individuals using optimized detection parameters.

Main Methods:

  • Comparative analysis of CNV detection programs using HapMap and experimental data.
  • Identification of CNVs in a cohort of 180 healthy Japanese individuals.
  • Investigation of sequence characteristics within detected CNVs, including repeat sequences and conservation scores.

Main Results:

  • Hidden Markov model-based programs (PennCNV, Birdseye, Birdsuite) demonstrated superior performance in terms of reproducibility and Mendelian consistency.
  • Birdsuite exhibited the highest sensitivity for CNV detection but may include false positives and negatives.
  • Commonly detected CNVs in Japanese individuals showed a higher prevalence of segmental and LINE repeat sequences and lower primate conservation scores compared to random regions.

Conclusions:

  • Interspersed repeats, particularly LINE sequences, play a significant role in the formation of common CNVs.
  • The study provides valuable insights into CNV detection accuracy and the genomic features associated with CNV formation.
  • Detected CNV data is available in a new repository for collaborative research.