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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%...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
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.
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

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Related Experiment Video

Updated: May 19, 2026

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

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Published on: February 17, 2017

A robust model for read count data in exome sequencing experiments and implications for copy number variant calling.

Vincent Plagnol1, James Curtis, Michael Epstein

  • 1UCL Genetics Institute, UCL, London, UK. v.plagnol@ucl.ac.uk

Bioinformatics (Oxford, England)
|September 4, 2012
PubMed
Summary

ExomeDepth is a new algorithm for detecting copy number variants (CNVs) from exome sequencing data, improving accuracy by controlling for technical variability. This method identified novel causative deletions in primary immunodeficiency patients.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Human Genetics

Background:

  • Exome sequencing is crucial for identifying genetic causes of Mendelian disorders.
  • Copy number variants (CNVs) are known contributors to these disorders.
  • Accurate CNV detection from exome data is challenging due to technical variability.

Purpose of the Study:

  • To introduce ExomeDepth, a novel algorithm for robust CNV calling from exome sequencing data.
  • To enhance the detection of small and heterozygous deletions by controlling for technical variability.

Main Methods:

  • ExomeDepth utilizes a robust statistical model for read count data.
  • An optimized reference set is constructed to maximize CNV detection power.
  • The algorithm is implemented as an R package available on CRAN.

Main Results:

  • ExomeDepth demonstrates improved performance across diverse exome datasets compared to existing tools.
  • Analysis of primary immunodeficiency patient data revealed 170-250 exonic CNV calls per sample.
  • Two novel causative deletions in GATA2 and DOCK8 were identified.

Conclusions:

  • ExomeDepth offers a powerful and reliable method for CNV detection in exome sequencing.
  • The algorithm facilitates the discovery of genetic variants underlying Mendelian disorders.
  • ExomeDepth is a valuable tool for genomic research and clinical diagnostics.