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

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%...

You might also read

Related Articles

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

Sort by
Same author

BMP/Ventx1.1 axis modulates the multiciliogenesis in the early Xenopus epidermis.

Genes & genomics·2026
Same author

Direct Reciprocal Repression between Goosecoid and Ventx1.1 Modulates Dorsoventral Patterning in Xenopus.

Differentiation; research in biological diversity·2026
Same author

Multifaceted role of Iroquois signaling in development and diseases.

Molecules and cells·2025
Same author

Machine learning-based estimation of the mild cognitive impairment stage using multimodal physical and behavioral measures.

Scientific reports·2025
Same author

Bone morphogenetic protein-mediated Ventx3.2 regulates mesendoderm patterning and gut morphogenesis during Xenopus embryogenesis.

Biochemical and biophysical research communications·2025
Same author

Corrigendum to "Sizzled (Frzb3) physically interacts with noncanonical Wnt ligands to inhibit gastrulation cell movement" [Volume 47, Issue 6, June 2024, 100068. start page - end page].

Molecules and cells·2024

Related Experiment Video

Updated: May 14, 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

A computational method for detecting copy number variations using scale-space filtering.

Jongkeun Lee1, Unjoo Lee, Baeksop Kim

  • 1Cancer Genomics Branch and Research Institute and Hospital, National Cancer Center, Goyang, Korea.

BMC Bioinformatics
|February 20, 2013
PubMed
Summary

A new method, CNV_SS, accurately detects copy number variations (CNVs) from low-coverage sequencing data. This computational approach significantly improves detection accuracy compared to existing methods, even with limited data.

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

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

Related Experiment Videos

Last Updated: May 14, 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

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

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

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Next-generation sequencing necessitates advanced computational methods for analyzing genomic data.
  • Accurate detection of copy number variations (CNVs) is crucial for genome projects, especially with low-coverage sequencing data.
  • There is a need for robust methods to identify CNV types and locations from low-coverage read data.

Purpose of the Study:

  • To develop a novel computational method for precise CNV detection.
  • To address the challenge of analyzing low-coverage sequencing data for CNVs.
  • To improve the accuracy and efficiency of CNV identification.

Main Methods:

  • The study proposes CNV_SS, a new CNV detection method utilizing scale-space filtering.
  • Gaussian convolution is applied to read coverage data across various scales.
  • Zero-crossing points and inflection points are calculated to generate a fingerprint map for CNV analysis.

Main Results:

  • CNV_SS demonstrates low false negative rates (FNR) of 1.27%–2.43% and false positive rates (FPR) of 1.14%–2.44% at low coverage (0.5x–2x).
  • The method significantly outperforms conventional approaches in FNR, achieving improvements between 3.82% and 76.97% with low-coverage data.
  • CNV_SS accurately identifies the types and locations of CNVs.

Conclusions:

  • CNV_SS is an effective tool for detecting CNVs, particularly from low-coverage sequencing data.
  • The method offers superior performance compared to existing techniques for CNV analysis.
  • The source code for CNV_SS is publicly available for research use.