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,...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
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...
Pharmacogenomics: Identification of New Drug Targets01:29

Pharmacogenomics: Identification of New Drug Targets

Advances in genomics have profoundly influenced drug discovery by increasing both the speed and accuracy of pharmaceutical development. Pharmacogenomics, which examines how genetic variation influences drug response, facilitates the identification of novel therapeutic targets and enables patient stratification for personalized treatment. These strategies contribute to improved drug efficacy, minimized adverse effects, and more efficient clinical trial design.Mapping genetic differences...

You might also read

Related Articles

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

Sort by
Same author

ASO Visual Abstract: Disparities in the Surgical Management of the Axilla by Self-Identified Race in the Multicenter Neoadjuvant I-SPY2 Trial.

Annals of surgical oncology·2025
Same author

Combined prognostic impact of initial clinical stage and residual cancer burden after neoadjuvant systemic therapy in triple-negative and HER2-positive breast cancer: an analysis of the I-SPY2 randomized clinical trial.

Breast cancer research : BCR·2025
Same author

Pathologic complete response (pCR) rates for patients with HR+/HER2- high-risk, early-stage breast cancer (EBC) by clinical and molecular features in the phase II I-SPY2 clinical trial.

Annals of oncology : official journal of the European Society for Medical Oncology·2024
Same author

Treatment Efficacy Score-continuous residual cancer burden-based metric to compare neoadjuvant chemotherapy efficacy between randomized trial arms in breast cancer trials.

Annals of oncology : official journal of the European Society for Medical Oncology·2022
Same author

Predicted sensitivity to endocrine therapy for stage II-III hormone receptor-positive and HER2-negative (HR+/HER2-) breast cancer before chemo-endocrine therapy.

Annals of oncology : official journal of the European Society for Medical Oncology·2021
Same author

Circulating tumor DNA in neoadjuvant-treated breast cancer reflects response and survival.

Annals of oncology : official journal of the European Society for Medical Oncology·2020
Same journal

Genomic Organization of Ribosomal DNA and Karyotypic Diversity in Vicia sativa and Vicia villosa.

Cytogenetic and genome research·2026
Same journal

George Martin and Werner's Syndrome.

Cytogenetic and genome research·2026
Same journal

The Spectrum of Mosaic Double Aneuploidy of Monosomy X and Trisomy 18: Two New Cases and Review of the Literature.

Cytogenetic and genome research·2026
Same journal

Familial Robertsonian Translocation, rob(14;21), with High Risk for Down Syndrome.

Cytogenetic and genome research·2026
Same journal

Radiosensitivity and Bystander Response in X-Ray-Irradiated Tumour and Normal Epithelial Cells of Breast and Prostate Origin.

Cytogenetic and genome research·2026
Same journal

Cytogenetic Profile of Acute Lymphoblastic Leukaemia in South India: A Series of 1,819 Patients from a Single Centre.

Cytogenetic and genome research·2026
See all related articles

Related Experiment Video

Updated: Jun 24, 2026

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

CNV discovery using SNP genotyping arrays.

C Yau1, C C Holmes

  • 1Department of Statistics, University of Oxford, Oxford, UK.

Cytogenetic and Genome Research
|March 17, 2009
PubMed
Summary
This summary is machine-generated.

Genome-wide SNP genotyping platforms can now identify copy number variants (CNVs). This review covers statistical methods for CNV calling from SNP data, offering cost and analysis benefits.

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

Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Related Experiment Videos

Last Updated: Jun 24, 2026

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

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

Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Genome-wide single nucleotide polymorphism (SNP) genotyping is crucial for population genetics and genetic epidemiology.
  • Emerging applications reveal SNP platforms' utility for copy number variant (CNV) typing.

Purpose of the Study:

  • To review statistical approaches for calling CNVs from SNP data.
  • To highlight algorithms based on varying levels of information utilization.

Main Methods:

  • Review of existing statistical methodologies for CNV detection using SNP data.
  • Categorization of algorithms into three tiers based on information usage.

Main Results:

  • SNP genotyping platforms can simultaneously type both SNPs and CNVs.
  • This generalized genotyping offers advantages in cost-effectiveness and unified analysis.

Conclusions:

  • CNV calling from SNP data is a feasible and advantageous approach.
  • The reviewed statistical methods provide a framework for analyzing both SNPs and CNVs.