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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.
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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.
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,...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Related Experiment Video

Updated: Jul 9, 2026

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

Likelihood-based optimization enables accurate copy number estimation for paralogous genes using exome data.

Sang Yoon Byun1, Vikas Bansal1,2

  • 1Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, United States.

Bioinformatics (Oxford, England)
|July 7, 2026
PubMed
Summary
This summary is machine-generated.

EdgeCopy accurately profiles copy number variants (CNVs) in paralogous genes using whole-exome sequencing data. This method improves upon existing tools for detecting genetic variations in challenging genomic regions.

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Last Updated: Jul 9, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing
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Rare Event Detection Using Error-corrected DNA and RNA Sequencing

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Accurate copy number variant (CNV) detection in paralogous genes using exome sequencing is challenging due to mapping ambiguity and high variation.
  • Existing CNV callers are not optimized for paralogous genes, limiting their utility in genetic studies.
  • Paralogous genes are implicated in numerous diseases, making their accurate profiling crucial.

Purpose of the Study:

  • To develop and evaluate EdgeCopy, a novel computational method for copy number profiling of paralogous genes from whole-exome sequencing data.
  • To address the limitations of current exome CNV callers in handling paralogous genes.
  • To enable more accurate genetic studies involving disease-associated paralogous genes.

Main Methods:

  • EdgeCopy aggregates reads mapping to paralogous gene copies and uses an approximate composite likelihood function to estimate copy number.
  • Numerical optimization refines gene-level fractional copy number estimates.
  • A Hidden Markov Model is employed for exon-level copy number estimation.

Main Results:

  • EdgeCopy demonstrated high concordance (0.973) with experimental data for disease-associated paralogous genes.
  • Evaluated on ~2400 samples, EdgeCopy showed robust concordance (0.974-0.982) with whole-genome sequencing estimates across 130 paralogous genes and diverse populations.
  • Compared to a state-of-the-art exome CNV caller, EdgeCopy significantly outperformed in estimating copy number for paralogous genes, achieving 0.908 concordance versus 0.565 for CNV events.

Conclusions:

  • EdgeCopy provides accurate and robust copy number profiling for paralogous genes using exome sequencing data.
  • The method overcomes limitations of existing tools, particularly for genes with high mapping ambiguity.
  • EdgeCopy is a valuable tool for genetic studies investigating CNVs in paralogous genes and their associated diseases.