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

16.4K
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...
16.4K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

7.2K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
7.2K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

812
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
812
What is Population Genetics?01:25

What is Population Genetics?

65.3K
A population is composed of members of the same species that simultaneously live and interact in the same area. When individuals in a population breed, they pass down their genes to their offspring. Many of these genes are polymorphic, meaning that they occur in multiple variants. Such variations of a gene are referred to as alleles. The collective set of all the alleles within a population is known as the gene pool.
65.3K

You might also read

Related Articles

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

Sort by
Same author

Career Intentions in Academic Medicine: Factors Influencing Pursuit and Gender Disparities.

Advances in medical education and practice·2026
Same author

A scalable high-throughput serolomics platform for profiling serum antibody responses in large-scale population-based cohorts.

Nature protocols·2026
Same author

Blood cytotoxic natural killer-like CD8 + CD94+ T cells migrate to the brain and predict multiple sclerosis severity.

Brain : a journal of neurology·2026
Same author

Academic medicine career intentions among medical residents: a social cognitive career theory approach.

BMC medical education·2026
Same author

Complete genomes reveal a refined map of Mycobacterium tuberculosis genetic diversity across evolutionary scales.

Nature communications·2026
Same author

Are there gender differences in academic medical career aspirations related to research, mentoring and discrimination? A national cross-sectional study of French medical residents.

BMJ open·2026

Related Experiment Video

Updated: Mar 12, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.9K

High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs.

Alexander T Dilthey1,2, Pierre-Antoine Gourraud3,4, Alexander J Mentzer1

  • 1Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

Plos Computational Biology
|October 30, 2016
PubMed
Summary

Accurately determining Human Leucocyte Antigen (HLA) gene types from whole-genome sequencing data is challenging. The new HLA*PRG algorithm, using a Population Reference Graph, achieves high accuracy, comparable to gold standards, but requires significant computational resources.

More Related Videos

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
11:10

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Published on: December 27, 2010

12.8K
Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

412.1K

Related Experiment Videos

Last Updated: Mar 12, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.9K
Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
11:10

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Published on: December 27, 2010

12.8K
Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

412.1K

Area of Science:

  • Genomics
  • Immunogenetics
  • Bioinformatics

Background:

  • Human Leucocyte Antigen (HLA) gene variation is critical for distinguishing self from non-self and is linked to autoimmune and infectious diseases.
  • Accurate HLA typing from whole-genome sequencing (WGS) data is highly desirable for immunogenetic characterization in large population studies.
  • The hyperpolymorphism and sequence similarity of HLA genes present significant challenges for accurate read mapping and type inference.

Purpose of the Study:

  • To develop a method for accurate HLA typing directly from standard whole-genome sequencing data.
  • To overcome the challenges of mapping and inferring HLA alleles in highly polymorphic regions.
  • To enable immunogenetic characterization within existing population sequencing projects.

Main Methods:

  • Construction of a Population Reference Graph (PRG) encompassing 46 HLA genes, pseudogenes, their genomic context, and over 10,000 known allele sequences.
  • Development of a sequence-to-PRG paired-end read mapping algorithm optimized for HLA gene accuracy.
  • Implementation of a likelihood framework for inferring the most probable HLA allele pairs from IMGT/HLA database at each locus.

Main Results:

  • The HLA*PRG algorithm demonstrated superior performance compared to existing methods.
  • Evaluation on six classical HLA genes across 14 samples resulted in 99.4% (157 out of 158) allele inference accuracy.
  • The method successfully identified and corrected two erroneous alleles in the validation dataset.

Conclusions:

  • HLA*PRG achieves accuracies comparable to gold-standard methods using standard whole-genome sequencing data for the first time.
  • The developed PRG framework and mapping algorithm effectively address HLA gene hyperpolymorphism and sequence similarity challenges.
  • High computational demands remain a significant barrier for widespread practical application of the HLA*PRG method.