Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

17.9K
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%...
17.9K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

15.5K
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,...
15.5K
Next-generation Sequencing03:00

Next-generation Sequencing

92.1K
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....
92.1K
Genome Copying Errors02:46

Genome Copying Errors

4.3K
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.
4.3K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Transport discovery of emerging robust helical surface States in Z2 = 0 systems.

Physical review letters·2014
Same author

Aromatic triazole foldamers induced by C-H···X (X = F, Cl) intramolecular hydrogen bonding.

The Journal of organic chemistry·2014
Same author

Human heat shock protein-specific cytotoxic T lymphocytes display potent antitumour immunity in multiple myeloma.

British journal of haematology·2014
Same author

ATG-Fresenius S combined with cyclosporine a: an effective immunosuppressive therapy for children with aplastic anemia.

Journal of pediatric hematology/oncology·2014
Same author

Priming of Toll-like receptor 4 pathway in mesenchymal stem cells increases expression of B cell activating factor.

Biochemical and biophysical research communications·2014
Same author

Central adiponectin administration reveals new regulatory mechanisms of bone metabolism in mice.

American journal of physiology. Endocrinology and metabolism·2014

Related Experiment Video

Updated: Aug 16, 2025

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

11.7K

CNV-PCC: An efficient method for detecting copy number variations from next-generation sequencing data.

Tong Zhang1, Jinxin Dong1, Hua Jiang1

  • 1School of Computer Science and Technology, Liaocheng University, Liaocheng, China.

Frontiers in Bioengineering and Biotechnology
|December 19, 2022
PubMed
Summary
This summary is machine-generated.

A new method, CNV-PCC, improves the detection of copy number variations (CNVs) in human genomes. It accurately identifies challenging low copy number duplications and small CNVs using whole genome sequencing data.

Keywords:
copy number variationsnext-generation sequencing technologypccread depthsegmentation

More Related Videos

Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants
09:16

Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants

Published on: February 21, 2015

19.7K
Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform
09:30

Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform

Published on: August 17, 2022

3.2K

Related Experiment Videos

Last Updated: Aug 16, 2025

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

11.7K
Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants
09:16

Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants

Published on: February 21, 2015

19.7K
Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform
09:30

Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform

Published on: August 17, 2022

3.2K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Copy number variations (CNVs) are crucial in human genome diversity and complex disease development.
  • Next-generation sequencing (NGS) facilitates CNV detection, with read depth (RD) being a common approach.
  • Existing RD-based methods struggle with low copy number duplications (3-4 copies) and small CNVs, often yielding imprecise breakpoints.

Purpose of the Study:

  • To introduce CNV-PCC, a novel computational method for accurate CNV detection in whole genome sequencing data.
  • To address the limitations of current methods in identifying low copy number duplications and small CNVs.
  • To improve breakpoint resolution in CNV analysis.

Main Methods:

  • CNV-PCC utilizes split read signals to identify potential CNV breakpoints.
  • A two-stage segmentation strategy enhances the detection of low copy number duplications and small CNVs.
  • Principal Component Classifier (PCC) calculates outlier scores, and the OTSU algorithm determines CNV regions.

Main Results:

  • CNV-PCC demonstrates superior sensitivity and F1-score compared to existing methods on simulated data.
  • The method significantly improves breakpoint accuracy for CNV detection.
  • CNV-PCC exhibits high consistency with established methods when applied to real sequencing data.

Conclusions:

  • CNV-PCC is an effective and accurate tool for detecting copy number variations, including challenging low copy number duplications and small variants.
  • The method enhances the capabilities of whole genome sequencing in CNV analysis.
  • CNV-PCC offers improved precision and reliability for genomic research and disease association studies.