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%...
Real Time RT-PCR02:57

Real Time RT-PCR

Real-time reverse transcription-polymerase chain reaction, or Real-time RT-PCR, is an analytical tool used to determine the expression level of target genes. The method involves converting mRNA to complementary DNA with the help of an enzyme known as reverse transcriptase, followed by the PCR amplification of the cDNA. These two processes can be performed simultaneously in a single tube or separately as a two-step reaction.
The real-time quantification of the number of amplified products is...

You might also read

Related Articles

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

Sort by
Same author

Precision-guided immunomodulatory therapy in sepsis.

The Lancet. Respiratory medicine·2026
Same author

Tremelimumab with or without durvalumab in combination with paclitaxel in metastatic urothelial cancer: phase I/II ICRA trial.

Nature communications·2026
Same author

On the state of protein function prediction: a report on the fourth CAFA challenge.

bioRxiv : the preprint server for biology·2026
Same author

Enabling DCIS subtyping: leveraging foundation models for robust grading and molecular biomarker scoring.

NPJ breast cancer·2026
Same author

From prediction to precision: Biomarker discovery and predictive modeling for personalized immune checkpoint blockade therapy.

European journal of cancer (Oxford, England : 1990)·2026
Same author

Effects of a Combined Dietary and Physical Activity Intervention on Bone Density, Lean Mass and Fat Mass in Adults: The GOTO Trial.

Journal of cachexia, sarcopenia and muscle·2026

Related Experiment Video

Updated: May 13, 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 scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control.

Ewald van Dyk1, Marcel J T Reinders, Lodewyk F A Wessels

  • 1Bioinformatics and Statistics group, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.

Nucleic Acids Research
|March 12, 2013
PubMed
Summary

A new method, Analytical Multi-scale Identification of Recurrent Events (ADMIRE), accurately detects copy number alterations in tumors. ADMIRE improves upon existing tools by controlling false discovery rates on events, not probes, and identifies key events missed by other methods.

More Related Videos

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Serum and Plasma Copy Number Detection Using Real-time PCR
09:21

Serum and Plasma Copy Number Detection Using Real-time PCR

Published on: December 15, 2017

Related Experiment Videos

Last Updated: May 13, 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

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Serum and Plasma Copy Number Detection Using Real-time PCR
09:21

Serum and Plasma Copy Number Detection Using Real-time PCR

Published on: December 15, 2017

Area of Science:

  • Genomics
  • Cancer Research
  • Bioinformatics

Background:

  • DNA copy number changes are key drivers of tumor formation.
  • Existing methods like GISTIC detect recurring copy number alterations but have limitations in false discovery rate control.
  • Accurate detection of both broad and focal copy number alterations is crucial for understanding cancer development.

Purpose of the Study:

  • To introduce Analytical Multi-scale Identification of Recurrent Events (ADMIRE), a novel method for detecting recurring copy number alterations.
  • To address limitations in existing methods, particularly GISTIC's probe-level false discovery rate control.
  • To provide a robust tool for identifying both broad and focal copy number alterations across multiple tumor samples.

Main Methods:

  • ADMIRE employs a multi-scale Gaussian smoothing approach for copy number alteration detection.
  • False discovery rate control is performed analytically on events, eliminating the need for permutations.
  • The method operates without requiring prior data segmentation or calling, preserving information.

Main Results:

  • Simulations demonstrate ADMIRE's effectiveness in detecting recurring copy number alterations.
  • Application to a glioblastoma SNP array dataset showcases its utility.
  • ADMIRE successfully identified focal events missed by GISTIC, including those involving tumor-suppressor genes CDKN2C and NF1.

Conclusions:

  • ADMIRE offers an improved approach for identifying recurring copy number alterations in cancer.
  • The method's analytical false discovery rate control and multi-scale nature enhance detection accuracy.
  • ADMIRE is a valuable tool for cancer genomics research, particularly for discovering focal events and potential therapeutic targets.