Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Single Nucleotide Polymorphisms-SNPs

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,...

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

Multi-species Conserved Sequences

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...

Gene Duplication and Divergence

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.

Comparing Copy Number Variations and SNPs

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%...

Genetic Variation

Genetic Variation

Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles, which...

You might also read

Related Articles

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

Sort by

Same author

HGVS Nomenclature 2024: improvements to community engagement, usability, and computability.

Genome medicine·2024

Same author

Author Correction: Standardizing variant naming in literature with VariantValidator to increase diagnostic rates.

Nature genetics·2024

Same author

Standardizing variant naming in literature with VariantValidator to increase diagnostic rates.

Nature genetics·2024

Same author

Comparison of the ABC and ACMG systems for variant classification.

European journal of human genetics : EJHG·2024

Same author

Systematic large-scale application of ClinGen InSiGHT <i>APC</i> -specific ACMG/AMP variant classification criteria substantially alleviates the burden of variants of uncertain significance in ClinVar and LOVD databases.

medRxiv : the preprint server for health sciences·2024

Same author

Hematologically important mutations: Leukocyte adhesion deficiency (second update).

Blood cells, molecules & diseases·2023

Search research articles

Related Experiment Video

Updated: Jun 4, 2026

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

Describing structural changes by extending HGVS sequence variation nomenclature.

Peter E M Taschner¹, Johan T den Dunnen

¹Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, Nederland. P.Taschner@lumc.nl

|February 11, 2011

Summary

This summary is machine-generated.

New technologies enable discovery of complex DNA sequence variants. This study proposes extensions to the Human Genome Variation Society (HGVS) nomenclature for clear, unambiguous descriptions of these complex genomic changes.

More Related Videos

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Identification and Classification of Position-specific GABA_A Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Published on: June 6, 2025

Related Experiment Videos

Last Updated: Jun 4, 2026

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Identification and Classification of Position-specific GABA_A Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Published on: June 6, 2025

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Advanced sequencing technologies facilitate the rapid identification of novel DNA sequence variants, including complex structural rearrangements.
Current Human Genome Variation Society (HGVS) nomenclature primarily addresses simple variants, posing challenges for describing complex structural changes.
Accurate and standardized description of complex genomic variations is crucial for genetic research and clinical applications.

Purpose of the Study:

To propose extensions to the HGVS nomenclature for the unambiguous description of complex DNA sequence variants.
To enhance the capacity of nomenclature systems to represent intricate genomic alterations.
To ensure consistency and reduce ambiguity in reporting complex structural variants.

Main Methods:

Development of novel nomenclature rules, including nesting for describing changes within inversions/duplications and composite changes for concatenated insertions.
Application of proposed extensions to facilitate the description of complex variants that are difficult to represent with existing nomenclature.
Integration of updated nomenclature specifications into sequence variant checkers like Mutalyzer.

Main Results:

Proposed extensions allow for the clear description of complex structural variants, such as inversions and duplications with minor differences.
The new nomenclature avoids the less informative indel description for complex variants.
The suggested additions provide flexibility and consistency, minimizing alternative interpretations and ambiguous descriptions.

Conclusions:

The extended HGVS nomenclature provides a robust framework for describing complex DNA sequence variants.
Implementation in tools like Mutalyzer will improve the standardization and accuracy of variant reporting.
These advancements are essential for advancing genomic research and understanding the impact of complex genomic alterations.