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

19.4K
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%...
19.4K
Real Time RT-PCR02:57

Real Time RT-PCR

67.6K
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...
67.6K

You might also read

Related Articles

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

Sort by
Same author

UMI-nea: a fast, robust tool for reference-free UMI deduplication and accurate quantification.

Bioinformatics (Oxford, England)·2025
Same author

Development of a Smart Sleep Mask with Multiple Sensors.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference·2021
Same author

High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants.

Nature medicine·2019
Same author

Targeted Single Primer Enrichment Sequencing with Single End Duplex-UMI.

Scientific reports·2019
Same author

smCounter2: an accurate low-frequency variant caller for targeted sequencing data with unique molecular identifiers.

Bioinformatics (Oxford, England)·2018
Same author

Association Between Inherited Germline Mutations in Cancer Predisposition Genes and Risk of Pancreatic Cancer.

JAMA·2018

Related Experiment Video

Updated: Apr 18, 2026

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

11.9K

Quantitative analysis of differences in copy numbers using read depth obtained from PCR-enriched samples and

Frank Reinecke1, Ravi Vijaya Satya2, John DiCarlo3

  • 1Bioinformatics Assay Design & Analysis, QIAGEN GmbH, Max-Volmer-Straße 4, Hilden, 40724, Germany. frank.reinecke@qiagen.com.

BMC Bioinformatics
|January 29, 2015
PubMed
Summary

A new algorithm, quandico, accurately detects copy number variants (CNVs) in PCR-enriched next-generation sequencing (NGS) data. This method offers high sensitivity and specificity for CNV detection in clinical diagnostics and cancer research.

More Related Videos

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

12.3K
Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics
09:23

Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics

Published on: January 5, 2024

2.8K

Related Experiment Videos

Last Updated: Apr 18, 2026

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

11.9K
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

12.3K
Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics
09:23

Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics

Published on: January 5, 2024

2.8K

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Diagnostics

Background:

  • Next-generation sequencing (NGS) is increasingly used in clinical diagnostics and cancer research.
  • Detecting copy number variants (CNVs) is crucial alongside single nucleotide variants (SNVs).
  • Existing CNV detection algorithms often do not account for the unique characteristics of PCR-enriched amplicon sequencing data.

Purpose of the Study:

  • To introduce quandico, a novel algorithm for detecting copy number differences.
  • To address the specific challenges of analyzing PCR-enriched amplicon sequencing data for CNVs.
  • To provide a sensitive and specific tool for CNV detection in relevant research and clinical settings.

Main Methods:

  • Developed quandico, an algorithm specifically designed for PCR-enriched NGS data.
  • Utilized a weighted t-test statistic to calculate probabilities (p-values) for copy number alterations.
  • Evaluated performance using reference DNA with known CNVs.

Main Results:

  • Quandico achieved 98.6% sensitivity and 98.5% specificity in detecting known CNVs.
  • Performance significantly outperformed another recently described method for amplicon sequencing.
  • The algorithm demonstrated high accuracy even for single copy differences.

Conclusions:

  • The quandico algorithm is effective for calling copy number changes from PCR-enriched samples.
  • The method provides high sensitivity and specificity, suitable for clinical and research applications.
  • Quandico represents a significant advancement for CNV detection in amplicon sequencing data.