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

Cancer Survival Analysis01:21

Cancer Survival Analysis

788
Cancer survival analysis focuses on quantifying and interpreting the time from a key starting point, such as diagnosis or the initiation of treatment, to a specific endpoint, such as remission or death. This analysis provides critical insights into treatment effectiveness and factors that influence patient outcomes, helping to shape clinical decisions and guide prognostic evaluations. A cornerstone of oncology research, survival analysis tackles the challenges of skewed, non-normally...
788
Cancer-Critical Genes II: Tumor Suppressor Genes01:05

Cancer-Critical Genes II: Tumor Suppressor Genes

9.9K
Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
9.9K
Cancer-Critical Genes I: Proto-oncogenes01:33

Cancer-Critical Genes I: Proto-oncogenes

11.5K
Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
11.5K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

18.8K
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%...
18.8K
Adaptive Mechanisms in Cancer Cells02:53

Adaptive Mechanisms in Cancer Cells

7.2K
Cancer cells accumulate genetic changes at an abnormally rapid rate due to the defects in the DNA repair mechanisms. From an evolutionary perspective, such genetic instability is advantageous for cancer development. Mutant cell lines accumulate a series of beneficial mutations that contribute to their progression into cancer.
Some of the advantages that cancer cells have on normal cells include - enhanced ability to divide without terminally differentiating, induce new blood vessel formation,...
7.2K
Mouse Models of Cancer Study02:43

Mouse Models of Cancer Study

6.6K
Mice have long served as models for studying human biology and pathology because of their phylogenetic and physiological similarity with humans. They are also easy to maintain and breed in the laboratory, and hence, many inbred strains are now available for research. Studies on mice have contributed immeasurably to our understanding of cancer biology.
The development of transgenic, knockout, and knock-in mice has led to an exponential increase in their use as model organisms in research,...
6.6K

You might also read

Related Articles

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

Sort by
Same author

Clinical Validation of the Belay Ascent™ Test to Report on Chromosomal Arm-Level Aneuploidy and Gene-Level Copy Number Variants in Cerebrospinal Fluid Using Low-Pass Whole-Genome Sequencing.

Cancers·2026
Same author

A plasma-based DNA test for quantification of disease burden in acute myeloid leukemia patients undergoing bone marrow transplantation.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Deep Learning Enabled 3D Multi-Omic Analysis Reveals Molecular Signatures of Heterogeneous Response to Chemotherapy in Pancreatic Cancer.

bioRxiv : the preprint server for biology·2026
Same author

A plasma-based DNA test for quantification of disease burden in acute myeloid leukemia patients undergoing bone marrow transplantation.

medRxiv : the preprint server for health sciences·2026
Same author

Evidence that extra copies of chromosome 1q play a role in the early phases of pancreatic neoplasia.

Science advances·2026
Same author

Monitoring of plasma and urine tumor-derived DNA to inform bladder-sparing approaches for patients with muscle-invasive bladder cancer.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same journal

Editor's Note: Heterodimerization of Insulin-like Growth Factor Receptor/Epidermal Growth Factor Receptor and Induction of Survivin Expression Counteract the Antitumor Action of Erlotinib.

Cancer research·2026
Same journal

Editor's Note: Deguelin Analogue SH-1242 Inhibits Hsp90 Activity and Exerts Potent Anticancer Efficacy with Limited Neurotoxicity.

Cancer research·2026
Same journal

Retraction: Two Functional Epitopes of Pigment Epithelial-Derived Factor Block Angiogenesis and Induce Differentiation in Prostate Cancer.

Cancer research·2026
Same journal

Editor's Note: Chronic Stress Facilitates Lung Tumorigenesis by Promoting Exocytosis of IGF2 in Lung Epithelial Cells.

Cancer research·2026
Same journal

MIF-CD74 Signaling Defines a Brain-Specific Immune Vulnerability in Metastasis and Neurologic Disease.

Cancer research·2026
Same journal

Forging New Pathways in Oncology: Strategic Insights from the 17th Annual Frontiers in Cancer Science Conference.

Cancer research·2026
See all related articles

Related Experiment Video

Updated: Feb 19, 2026

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
13:24

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

12.3K

CRAVAT 4: Cancer-Related Analysis of Variants Toolkit.

David L Masica1,2, Christopher Douville1,2, Collin Tokheim1,2

  • 1Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland.

Cancer Research
|November 3, 2017
PubMed
Summary
This summary is machine-generated.

Cancer sequencing generates many mutations, making interpretation challenging. The Cancer-Related Analysis of Variants Toolkit (CRAVAT) aids researchers by providing integrated tools for comprehensive mutation analysis and interpretation.

More Related Videos

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
11:02

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

20.0K
Comparative Lesions Analysis Through a Targeted Sequencing Approach
08:16

Comparative Lesions Analysis Through a Targeted Sequencing Approach

Published on: November 5, 2019

7.3K

Related Experiment Videos

Last Updated: Feb 19, 2026

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
13:24

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

12.3K
Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
11:02

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

20.0K
Comparative Lesions Analysis Through a Targeted Sequencing Approach
08:16

Comparative Lesions Analysis Through a Targeted Sequencing Approach

Published on: November 5, 2019

7.3K

Area of Science:

  • Computational biology
  • Genomics
  • Cancer research

Background:

  • Cancer sequencing studies yield extensive somatic mutation data, posing interpretation challenges.
  • Existing computational tools for mutation analysis are often disparate, complicating workflows.
  • Efficient interpretation of complex genomic data is crucial for advancing cancer research.

Purpose of the Study:

  • To introduce the Cancer-Related Analysis of Variants Toolkit (CRAVAT) as a solution for cancer mutation interpretation.
  • To provide a comprehensive suite of tools for analyzing and prioritizing somatic mutations.
  • To facilitate the user-friendly exploration of mutation data in large-scale cancer studies.

Main Methods:

  • CRAVAT integrates mutation mapping, quality control, impact prediction, and extensive annotation.
  • The toolkit offers gene- and mutation-level interpretation, including joint prioritization of mutation consequences.
  • Structural and mechanistic visualization tools are incorporated for enhanced data understanding.

Main Results:

  • CRAVAT provides an interactive web environment for exploring analysis results.
  • Dynamic filtering and sorting capabilities highlight informative mutations within large datasets.
  • The toolkit supports public web portal, cloud, and local deployments for flexible use.

Conclusions:

  • CRAVAT offers a unified and user-friendly approach to cancer mutation interpretation.
  • The toolkit simplifies the analysis of complex genomic data from cancer sequencing studies.
  • CRAVAT is easily integrated with other cancer omics analysis methods.