ArticleBMC bioinformatics2017
PyHLA: tests for the association between HLA alleles and diseases.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 48 citations in OpenAlex.
- HLA Class II GenesFrontiers in immunology · 2019Trial
- Prognostic Impact of ERAP1 Genetic Variants and Haplotypes in Cervical Cancer: Insights From TCGA-CESC and a Brazilian Patient Cohort.Molecular genetics & genomic medicine · 2026Article
- Whole exome sequencing analysis of suicidal thoughts and behaviors in a veteran cohort implicates inflammatory pathways and genes previously associated with psychiatric and neurodegenerative diseases.Journal of affective disorders · 2026Article
- Investigating HLA haplotypes as a potential risk factor for nodding syndrome: A case-control study in the Mahenge area, Tanzania.PLoS neglected tropical diseases · 2025Article
- HLA-DRB1*15:01 is associated with a reduced likelihood of longevity in northern European men.Genome medicine · 2025Article
- Risk and Association of Specific HLA Alleles With Nintedanib-Induced Gastrointestinal Adverse Reactions: A Discovery Study in an Italian Population.Clinical and translational science · 2025Article
- HLA variation associated with peanut allergy and anaphylaxis among non-Hispanic Black individuals.The journal of allergy and clinical immunology. Global · 2025Article
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- Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation.American journal of human genetics · 2024Article
- Exploration of potential immune mechanisms in cervical dystonia.Parkinsonism & related disorders · 2024Article
- A web-based genome-wide association study reveals the susceptibility loci of common adverse events following COVID-19 vaccination in the Japanese population.Scientific reports · 2023Article
- The Association of Human Leukocyte Antigens Complex with Type 1 Diabetes in the Omani Population.Sultan Qaboos University medical journal · 2023Article
- PGG.MHC: toward understanding the diversity of major histocompatibility complexes in human populations.Nucleic acids research · 2023Article
- HLA-B evolutionary divergence is associated with outcomes after SARS-CoV-2 infection.Human immunology · 2022Article
- Genome-wide Association Study Identifies 2 New Loci Associated With Anti-NMDAR Encephalitis.Neurology(R) neuroimmunology & neuroinflammation · 2021Article
- HLA genetic polymorphism in patients with Coronavirus Disease 2019 in Midwestern United States.HLA · 2021Article
- Association of ProtectiveFrontiers in genetics · 2021Article
- Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research.Frontiers in genetics · 2021Review
- Exome Sequencing Reveals a Putative Role for HLA-C*03:02 in Control of HIV-1 in African Pediatric Populations.Frontiers in genetics · 2021Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRecently, several tools have been designed for human leukocyte antigen (HLA) typing using single nucleotide polymorphism (SNP) array and next-generation sequencing (NGS) data. These tools provide high-throughput and cost-effective approaches for identifying HLA types. Therefore, tools for downstream association analysis are highly desirable. Although several tools have been designed for multi-allelic marker association analysis, they were designed only for microsatellite markers and do not scale well with increasing data volumes, or they were designed for large-scale data but provided a limited number of tests.
resultsWe have developed a Python package called PyHLA, which implements several methods for HLA association analysis, to fill the gap. PyHLA is a tailor-made, easy to use, and flexible tool designed specifically for the association analysis of the HLA types imputed from genome-wide genotyping and NGS data. PyHLA provides functions for association analysis, zygosity tests, and interaction tests between HLA alleles and diseases. Monte Carlo permutation and several methods for multiple testing corrections have also been implemented.
conclusionsPyHLA provides a convenient and powerful tool for HLA analysis. Existing methods have been integrated and desired methods have been added in PyHLA. Furthermore, PyHLA is applicable to small and large sample sizes and can finish the analysis in a timely manner on a personal computer with different platforms. PyHLA is implemented in Python. PyHLA is a free, open source software distributed under the GPLv2 license. The source code, tutorial, and examples are available at https://github.com/felixfan/PyHLA.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.