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%...
Single Nucleotide Polymorphisms-SNPs01:05

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,...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

You might also read

Related Articles

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

Sort by
Same author

Corrigendum to "A Pre-symptomatic phase of tumefactive multiple sclerosis mirrors radiologically isolated syndrome" [Multiple Sclerosis and Related Disorders 112 (2026) 107312].

Multiple sclerosis and related disorders·2026
Same author

A Pre-symptomatic phase of tumefactive multiple sclerosis mirrors radiologically isolated syndrome.

Multiple sclerosis and related disorders·2026
Same author

Determinants of Quality of Life in Patients with Immune-Checkpoint-Inhibitor Induced Secondary Adrenal Insufficiency.

The Journal of clinical endocrinology and metabolism·2026
Same author

Evaluating the current neuro-oncology capacity in Sub-Saharan Africa: A questionnaire-based survey.

Neuro-oncology practice·2026
Same author

Presentation and Clinical Patterns of Bilateral Adrenal Lesions: A Retrospective Cohort Study.

The Journal of clinical endocrinology and metabolism·2026
Same author

MRI Deep Learning for Differentiating Glioblastoma, IDH Wild-type from Central Nervous System Diffuse Large B-cell Lymphoma.

Cancer research communications·2026

Related Experiment Video

Updated: Jun 1, 2026

Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform
09:30

Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform

Published on: August 17, 2022

Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform.

Jeanette E Eckel-Passow1, Elizabeth J Atkinson, Sooraj Maharjan

  • 1Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA. eckel@mayo.edu

BMC Bioinformatics
|June 2, 2011
PubMed
Summary

This study compared four software packages for copy number variation (CNV) detection. PennCNV demonstrated optimal performance for statistical analysis of both locus-level and segmented copy number data, offering comprehensive quality control.

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

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
09:16

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants

Published on: February 21, 2015

Related Experiment Videos

Last Updated: Jun 1, 2026

Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform
09:30

Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform

Published on: August 17, 2022

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

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
09:16

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants

Published on: February 21, 2015

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Copy number data are routinely extracted from genome-wide association study (GWAS) chips.
  • Evaluating software for accurate copy number estimation is crucial for genetic studies.
  • Four software packages (Affymetrix Power Tools, Aroma.Affymetrix, PennCNV, CRLMM) were assessed for Affymetrix SNP chips.

Purpose of the Study:

  • To empirically evaluate and compare four freely-available software packages for copy number estimation.
  • To assess bias, variance, concordance, and false-positive rates of copy number variation (CNV) detection.
  • To guide the selection of optimal software for analyzing GWAS copy number data.

Main Methods:

  • Utilized 1,418 GENOA samples genotyped on the Affymetrix Genome-Wide Human SNP Array 6.0.
  • Compared locus-level copy number bias and variance across software.
  • Assessed concordance of copy number gains/deletions and false-positive rates for deletions.

Main Results:

  • PennCNV and Aroma.Affymetrix showed the smallest variability in median copy number.
  • PennCNV provided CNV-specific quality-control metrics and identified 136 poor CNV samples.
  • PennCNV detected more CNVs than CRLMM/VanillaIce with high concordance for duplications and deletions.

Conclusions:

  • PennCNV is recommended for statistical tests on both locus-level and segmented copy number data.
  • PennCNV offers a single-package solution for copy number estimation, segmentation, and quality control.
  • Researchers should consider multiple algorithms and evaluate concordance for downstream association tests.