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

11.6K
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%...
11.6K
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
Sanger Sequencing01:57

Sanger Sequencing

800.8K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
800.8K

You might also read

Related Articles

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

Sort by
Same author

177Lu-FAP-2286 Therapy in a Patient of Advanced Metastatic Malignant Solitary Fibrous Tumor.

Clinical nuclear medicine·2026
Same author

Ultrasound-Recharged Sub-Nanometer Palladium Catalysts for on-Demand and Self-Terminating Bioorthogonal Prodrug Activation in Cancer Therapy.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same author

An Adaptive Ionic Sieve: Flexible Hydrogen-Bonded Organic Frameworks Decouple the Trade-Off Between Zn Ions Desolvation and Mass Transfer.

Angewandte Chemie (International ed. in English)·2026
Same author

Efficient one-pot lactic acid production from cellulose via a Trichoderma reesei and Bacillus coagulans cooperation leveraging substrate-induced secretomes.

Bioresource technology·2026
Same author

Unexpected Bilateral Lacrimal and Salivary Gland Uptake of 68Ga-DOTA-Ibandronic Acid on PET/CT.

Clinical nuclear medicine·2026
Same author

Insufficient ferroptosis in radiation-induced tumor cells promote Treg cell generation to induce radiotherapy resistance.

Communications biology·2026

Related Experiment Video

Updated: May 3, 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

12.6K

PSCC: sensitive and reliable population-scale copy number variation detection method based on low coverage

Xuchao Li1, Shengpei Chen2, Weiwei Xie1

  • 1BGI-Shenzhen, Shenzhen, China.

Plos One
|January 28, 2014
PubMed
Summary
This summary is machine-generated.

This study introduces a population-scale copy number variation calling (PSCC) method for accurate genetic variation detection using low-coverage whole-genome sequencing (LCS). The PSCC method demonstrates high sensitivity and specificity, even with ultra-low sequencing coverage.

More Related Videos

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

16.5K
Serum and Plasma Copy Number Detection Using Real-time PCR
09:21

Serum and Plasma Copy Number Detection Using Real-time PCR

Published on: December 15, 2017

10.7K

Related Experiment Videos

Last Updated: May 3, 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

12.6K
Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

16.5K
Serum and Plasma Copy Number Detection Using Real-time PCR
09:21

Serum and Plasma Copy Number Detection Using Real-time PCR

Published on: December 15, 2017

10.7K

Area of Science:

  • Genetics
  • Genomics
  • Bioinformatics

Background:

  • Copy number variations (CNVs) are key genetic variations influencing phenotypes and diseases.
  • High-throughput sequencing advances CNV discovery but existing methods struggle with low coverage.
  • Current CNV detection methods often lack stability under low sequence coverage conditions.

Purpose of the Study:

  • To develop an effective population-scale CNV calling (PSCC) method for low-coverage whole-genome sequencing (LCS).
  • To address the instability of existing CNV detection methods with low sequence coverage.
  • To enable reliable CNV detection in population-scale studies using cost-effective sequencing.

Main Methods:

  • Developed a novel population-scale CNV calling (PSCC) method utilizing low-coverage sequencing (LCS).
  • Implemented a two-step correction strategy to mitigate biases from GC content and genomic complexity.
  • Employed binary segmentation for CNV segment localization and combined statistics tests for false positive control.

Main Results:

  • PSCC achieved 99.7%/100% sensitivity and 98.6%/100% specificity for CNVs >300 kb under LCS (∼2×) and ultra-LCS (∼0.2×).
  • Analysis of 34 clinical samples with 2× LCS successfully identified all 31 pathogenic CNVs detected by aCGH.
  • The PSCC method demonstrated significant performance advantages over existing approaches using ultra-low coverage data.

Conclusions:

  • The PSCC method enables sensitive and reliable detection of CNVs from low-coverage or ultra-low-coverage sequencing data.
  • Population-scale sequencing combined with PSCC offers a powerful approach for CNV discovery.
  • This method enhances the utility of LCS for genetic variation studies, particularly in large cohorts.