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

Mismatch Repair01:20

Mismatch Repair

5.3K
Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
5.3K
Mutations in Microorganisms01:18

Mutations in Microorganisms

156
Mutations are heritable changes in an organism’s genome involving alterations in the base sequence of DNA or RNA. These changes can influence cellular processes and phenotypic traits, potentially transforming the unaltered wild type into a mutant form. Such changes, termed forward mutations, are pivotal in shaping the genetic diversity of organisms.RNA viruses exhibit the highest mutation rates due to the absence of robust proofreading mechanisms during genome replication. In contrast,...
156
Spontaneous and Induced Mutations01:30

Spontaneous and Induced Mutations

272
Spontaneous mutations arise infrequently during DNA replication due to errors in the process. A key factor behind these errors is tautomeric shifts in nitrogenous bases, where bases transition from keto to enol forms or amino to imino forms. This shift can alter base-pairing rules, leading to mutations. Additionally, reactive oxygen species (ROS) arising from aerobic metabolism can damage DNA, resulting in depurination (loss of a purine base) or depyrimidination (loss of a pyrimidine base).
272
Mutations01:39

Mutations

85.2K
Overview
85.2K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.4K
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...
6.4K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

222
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
222

You might also read

Related Articles

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

Sort by
Same author

Genomics comes of age: From research tool to routine care.

Journal of internal medicine·2026
Same author

Single-cell whole-genome sequencing reveals convergent evolution in Burkitt lymphoma.

Nature communications·2026
Same author

High-resolution single-cell mapping of clonal hematopoiesis and structural variation in aplastic anemia.

Nature genetics·2026
Same author

UV-induced mutations accumulate during early clonal expansion in aneuploid subtypes of pediatric B-cell precursor acute lymphoblastic leukemia.

Haematologica·2026
Same author

Author Correction: Real-world clinical utility of tumor whole-genome sequencing in solid cancers.

Nature medicine·2026
Same author

Real-world clinical utility of tumor whole-genome sequencing in solid cancers.

Nature medicine·2026

Related Experiment Video

Updated: Oct 3, 2025

Characterizing Mutational Load and Clonal Composition of Human Blood
07:58

Characterizing Mutational Load and Clonal Composition of Human Blood

Published on: July 11, 2019

7.5K

MutationalPatterns: the one stop shop for the analysis of mutational processes.

Freek Manders1,2, Arianne M Brandsma1,2, Jurrian de Kanter1,2

  • 1Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands.

BMC Genomics
|February 16, 2022
PubMed
Summary

The updated MutationalPatterns R package enhances the analysis of somatic mutations, improving the identification of mutational signatures and their biological impact. This tool aids in understanding mutation accumulation and cancer diagnostics.

Keywords:
Base substitutionsIndelsMutagenic processesMutational signaturesRRegional mutation patternsSomatic mutations

More Related Videos

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

1.1K
Implementation of In Vitro Drug Resistance Assays: Maximizing the Potential for Uncovering Clinically Relevant Resistance Mechanisms
08:46

Implementation of In Vitro Drug Resistance Assays: Maximizing the Potential for Uncovering Clinically Relevant Resistance Mechanisms

Published on: December 9, 2015

10.7K

Related Experiment Videos

Last Updated: Oct 3, 2025

Characterizing Mutational Load and Clonal Composition of Human Blood
07:58

Characterizing Mutational Load and Clonal Composition of Human Blood

Published on: July 11, 2019

7.5K
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

1.1K
Implementation of In Vitro Drug Resistance Assays: Maximizing the Potential for Uncovering Clinically Relevant Resistance Mechanisms
08:46

Implementation of In Vitro Drug Resistance Assays: Maximizing the Potential for Uncovering Clinically Relevant Resistance Mechanisms

Published on: December 9, 2015

10.7K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Somatic mutations within a genome record cellular mutational processes.
  • Investigating these processes requires extracting mutational patterns from sequencing data.

Purpose of the Study:

  • To introduce an updated R/Bioconductor package, MutationalPatterns, for in-depth analysis of somatic mutations.
  • To enhance capabilities for analyzing single/double base substitutions, small indels, and their associated mutational signatures.

Main Methods:

  • The package offers regional mutation spectra analysis and detection of strand asymmetry phenomena.
  • Includes functions to assess the potential for signatures to cause damaging mutations.
  • Features stricter signature refitting to prevent overfitting and bootstrapped refitting for robustness.

Main Results:

  • Demonstrated reliable signature refitting even with as few as 50 mutations per signature using simulated data.
  • Applied the package to genome mutation data from cell lines with deleted DNA repair processes.
  • Successfully generated novel biological insights from large cancer datasets.

Conclusions:

  • The novel MutationalPatterns version enables comprehensive analysis and visualization of mutational patterns.
  • Facilitates deeper understanding of mutation accumulation mechanisms.
  • Aids in cancer diagnostics and provides freely available software.