Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Genome-wide Association Studies-GWAS

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...

Single Nucleotide Polymorphisms-SNPs

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,...

You might also read

Related Articles

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

Sort by

Same author

The Biobank Rare Variant consortium powers the discovery of rare genetic associations through global collaboration.

medRxiv : the preprint server for health sciences·2026

Same author

Examining the association between fetal HLA-C, maternal KIR haplotypes and birth weight.

PLoS genetics·2026

Same author

Identification of genetic risk loci associated with aquaporin 4-positive neuromyelitis optica spectrum disorder: a genome-wide association study.

The Lancet. Neurology·2026

Same author

Host control of persistent Epstein-Barr virus infection.

Nature·2026

Same author

How to Unmask an Unknown: The Restriction-Modification System <i>Mho</i>VII of <i>Mycoplasma hominis</i> Expresses Two Complementary Methylation Activities in One Enzyme.

International journal of molecular sciences·2026

Same author

Preventing premature deaths through polygenic risk scores.

Nature communications·2026

Search research articles

Related Experiment Video

Updated: Jun 4, 2026

Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation

Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation

Published on: September 6, 2017

HLA*IMP--an integrated framework for imputing classical HLA alleles from SNP genotypes.

Alexander T Dilthey¹, Loukas Moutsianas, Stephen Leslie

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

Bioinformatics (Oxford, England)

|February 9, 2011

Summary

This study introduces HLA*IMP, a free software for imputing human leukocyte antigen (HLA) alleles from SNP data, improving accuracy and call rates for large genetic studies. This powerful tool aids in understanding genetic risk factors for diseases.

More Related Videos

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Related Experiment Videos

Last Updated: Jun 4, 2026

Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation

Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation

Published on: September 6, 2017

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Area of Science:

Immunogenetics
Human Leukocyte Antigen (HLA) research
Genomic imputation

Background:

Classical HLA alleles significantly impact disease susceptibility and drug responses.
Current HLA typing methods are costly for large-scale genetic studies.
Previous work established SNP-based HLA allele imputation; this study refines the method.

Purpose of the Study:

To present an improved, freely available software suite (HLA*IMP) for imputing classical HLA alleles.
To enhance the accuracy and efficiency of HLA imputation from SNP data.
To provide a tool for large-scale genetic studies investigating HLA-associated phenotypes.

Main Methods:

Modified the original HLA imputation algorithm with a novel SNP selection function for increased call rates.
Developed a parallelized model building algorithm to process large reference datasets (>2500 individuals).
Validated the framework using independent datasets, assessing imputation accuracy at two- and four-digit resolution.

Main Results:

Achieved imputation call rates of 95-99% with accuracy between 92-98% (four-digit) and >97% (two-digit).
Demonstrated improved performance with a 40% increase in call rates in some scenarios.
Successfully applied HLA*IMP to a psoriasis GWAS, showing imputed HLA alleles had stronger disease association than individual SNPs.

Conclusions:

HLA*IMP offers a powerful and accurate tool for HLA imputation in large genetic studies.
The enhanced method facilitates the dissection of genetic architecture within the HLA region.
The software is freely available, promoting wider research accessibility.