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

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

15.9K
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...
15.9K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

18.8K
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,...
18.8K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

18.9K
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%...
18.9K

You might also read

Related Articles

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

Sort by
Same author

Decoding disease and therapy through multiomics integration and systems analysis.

Briefings in bioinformatics·2026
Same author

Impaired Brain Growth in Children Perinatally Infected With Chikungunya.

Pediatric neurology·2026
Same author

Immunogenetic Variants in Major Mental and Neurodevelopmental Disorders.

Biological psychiatry·2026
Same author

The 12 o'clock assay: an optimized dodecaplex droplet digital PCR assay for robust DNA methylation quantification and epigenetic clock-based age-predictions.

Clinical epigenetics·2026
Same author

HaploExplore, a software specifically designed for the detection of minor allele (MiA-) haploblocks.

NAR genomics and bioinformatics·2025
Same author

Genetic Background Predicts Uveal Melanoma Patients' Outcomes.

Ophthalmology science·2025
Same journal

Covariance decomposition for distance based species tree estimation.

BMC bioinformatics·2026
Same journal

SNPio: a Python interface for population genomic data processing.

BMC bioinformatics·2026
Same journal

SpaHNR: a spatial domain identification method via sparse attention-based hierarchical node representation and multi-view contrastive learning.

BMC bioinformatics·2026
Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026
Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026
Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Feb 26, 2026

Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation
08:07

Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation

Published on: September 6, 2017

10.7K

HLA-check: evaluating HLA data from SNP information.

Marc Jeanmougin1, Josselin Noirel1, Cédric Coulonges1

  • 1Laboratoire Génomique, Bioinformatique et Applications, EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint-Martin, Paris, 75003, France.

BMC Bioinformatics
|July 13, 2017
PubMed
Summary
This summary is machine-generated.

This study introduces HLA-check, a bioinformatics tool that significantly improves the accuracy of human leukocyte antigen (HLA) imputation from SNP data. HLA-check identifies and helps correct erroneous HLA typings, enhancing genetic association studies.

Keywords:
Human leukocyte antigenImputationMajor histocompatibility complex

More Related Videos

Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration
04:41

Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration

Published on: January 9, 2020

19.5K
An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

23.4K

Related Experiment Videos

Last Updated: Feb 26, 2026

Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation
08:07

Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation

Published on: September 6, 2017

10.7K
Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration
04:41

Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration

Published on: January 9, 2020

19.5K
An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

23.4K

Area of Science:

  • Genomics
  • Human Leukocyte Antigen (HLA) research
  • Bioinformatics

Background:

  • The Major Histocompatibility Complex (MHC) and its Human Leukocyte Antigen (HLA) genes are crucial in human diseases.
  • Next-Generation Sequencing (NGS) enables accurate HLA genotyping but is expensive.
  • Bioinformatics tools like SNP2HLA and HIBAG infer HLA types from SNP data using linkage disequilibrium.

Purpose of the Study:

  • To develop and validate a tool for detecting aberrant HLA allele calls.
  • To enhance the accuracy of existing HLA imputation software.

Main Methods:

  • Implemented an imputation method similar to SNP2HLA using ShapeIT and Impute2.
  • Developed a novel tool, HLA-check, to identify inconsistencies between SNP genotypes and HLA allele calls.
  • Evaluated imputation quality on a European dataset.

Main Results:

  • Achieved imputation quality comparable to existing methods (SNP2HLA) on a European dataset.
  • HLA-check significantly increased the accuracy of HLA imputation, particularly for HLA class I genes.
  • Identified a small percentage (less than 10%) of implausible HLA typings in the studied population.

Conclusions:

  • HLA-check effectively detects unreliable HLA typings derived from SNP data.
  • The tool can be integrated with existing HLA imputation software to improve data quality.
  • Identified samples can be excluded or re-genotyped using NGS for more robust HLA association analyses.