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

17.8K
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%...
17.8K
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

13.6K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
13.6K
RNA-seq03:21

RNA-seq

10.1K
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...
10.1K
Next-generation Sequencing03:00

Next-generation Sequencing

91.6K
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....
91.6K
Sanger Sequencing01:57

Sanger Sequencing

755.1K
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...
755.1K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

15.3K
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,...
15.3K

You might also read

Related Articles

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

Sort by
Same author

Circulating tumor-associated autoantibody signatures for diagnosis and prognosis in small-cell lung cancer and lung adenocarcinoma.

British journal of cancer·2026
Same author

Machine Learning Reveals the Contribution of Rare Genetic Variants and Enhances Risk Prediction for Coronary Artery Disease in the Japanese Population.

Circulation. Genomic and precision medicine·2026
Same author

Deletion of neurosecretory proteins GL and GM drives dual anti-obesity effects via appetite suppression and enhanced energy expenditure.

Communications biology·2026
Same author

Publisher Correction: Multi-ancestry genome-wide association analyses of refractive error augment genetic discovery and polygenic prediction.

Nature genetics·2026
Same author

Correction: Annotation of nuclear lncRNAs based on chromatin interactions.

PloS one·2026
Same author

Multi-ancestry genome-wide association analyses of refractive error augment genetic discovery and polygenic prediction.

Nature genetics·2026
Same journal

The Single-Cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors.

Cell genomics·2026
Same journal

NERINE reveals rare variant associations in gene networks across phenotypes and implicates an SNCA-PRL-LRRK2 subnetwork in Parkinson's disease.

Cell genomics·2026
Same journal

Single-cell profiling of DNA methylation in autism spectrum disorder prefrontal cortex reveals distinct regulatory and aging signatures.

Cell genomics·2026
Same journal

BMI-genome interactions regulate global gene expression with emphasis in brain and gut.

Cell genomics·2026
Same journal

Translating genome-wide association studies at multiple scales: Drug target prioritization, cellular architectures, and organ imaging.

Cell genomics·2026
Same journal

CellBouncer, a unified toolkit for single-cell demultiplexing and ambient RNA analysis, reveals hominid mitochondrial incompatibilities.

Cell genomics·2026
See all related articles

Related Experiment Video

Updated: Jul 25, 2025

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

1.0K

Detection of trait-associated structural variations using short-read sequencing.

Shunichi Kosugi1,2, Yoichiro Kamatani3, Katsutoshi Harada1

  • 1Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

Cell Genomics
|June 30, 2023
PubMed
Summary
This summary is machine-generated.

A new computational tool, MOPline, enhances the detection of genomic structural variations (SVs) from short-read whole-genome sequencing data, enabling better genetic analysis and trait association studies.

Keywords:
CNVGWASMOPlineSVWGSimputationshort readstructural variantstructural variationwhole-genome sequencing

More Related Videos

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
11:35

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

13.0K
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

15.3K

Related Experiment Videos

Last Updated: Jul 25, 2025

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

1.0K
Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
11:35

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

13.0K
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

15.3K

Area of Science:

  • Genomics
  • Bioinformatics
  • Population Genetics

Background:

  • Genomic structural variations (SVs) significantly influence genetic and phenotypic traits.
  • Limited reliable methods for SV detection have historically hindered comprehensive genetic analysis.

Purpose of the Study:

  • To develop and validate a computational algorithm (MOPline) for improved SV detection and genotyping using short-read whole-genome sequencing (WGS) data.
  • To leverage MOPline for large-scale imputation of SVs and subsequent association studies with diseases and quantitative traits.

Main Methods:

  • Development of the MOPline algorithm incorporating missing call recovery and high-confidence SV call selection.
  • Application of MOPline to 3,672 high-coverage WGS datasets for SV detection and genotyping.
  • Imputation of SVs in 181,622 Japanese individuals and subsequent genome-wide association studies (GWAS).

Main Results:

  • MOPline detected approximately 16,000 SVs per individual, a 1.7-3.3-fold increase compared to previous large-scale projects, with comparable statistical quality.
  • Genome-wide association studies identified 41 significant SVs associated with 42 diseases and 60 quantitative traits.
  • Discovery of 8 exonic SVs, including 5 novel associations, and identification of enriched mobile element insertions.

Conclusions:

  • Short-read WGS data, when analyzed with advanced algorithms like MOPline, can effectively identify both rare and common structural variations.
  • This approach significantly enhances the power to detect SVs associated with diverse human traits and diseases.
  • MOPline represents a substantial advancement in the field of structural variation detection and its application in genetic association studies.