ArticleThe pharmacogenomics journal2018
Significant variation between SNP-based HLA imputations in diverse populations: the last mile is the hardest.
Article in The pharmacogenomics journal, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed, 38 citations in OpenAlex.
- Association Between Single-Nucleotide Polymorphisms in HLA Alleles and Human Immunodeficiency Virus Type 1 Viral Load in Demographically Diverse, Antiretroviral Therapy-Naive Participants From the Strategic Timing of AntiRetroviral Treatment Trial.The Journal of infectious diseases · 2019Trial
- A specific amino acid motif ofProceedings of the National Academy of Sciences of the United States of America · 2019Trial
- Shared Epitope-PositiveNeurology(R) neuroimmunology & neuroinflammation · 2026Article
- The digital keystone: how artificial intelligence is reshaping HLA research and clinical practice.Immunogenetics · 2026Review
- Risk Haplotype of BTNL2 Predisposes Male Patients to NSTEMI: A Genetic and Functional Study.Research square · 2026Article
- Article
- Pharmacogenomics predictors of aromatic antiepileptic drugs-induced SCARs in the Iraqi patients.Heliyon · 2025Article
- Accurate multi-population imputation of MICA, MICB, HLA-E, HLA-F and HLA-G alleles from genome SNP data.PLoS computational biology · 2024Article
- Fifty years of HLA-associated type 1 diabetes risk: history, current knowledge, and future directions.Frontiers in immunology · 2024Review
- Imputation-Based HLA Typing with GWAS SNPs.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Article
- The lupus susceptibility allele DRB1*03:01 encodes a disease-driving epitope.Communications biology · 2022Article
- Immunogenomics of Killer Cell Immunoglobulin-Like Receptor (KIR) and HLA Class I: Coevolution and Consequences for Human Health.The journal of allergy and clinical immunology. In practice · 2022Article
- Allele imputation for the killer cell immunoglobulin-like receptor KIR3DL1/S1.PLoS computational biology · 2022Article
- Challenges for the standardized reporting of NGS HLA genotyping: Surveying gaps between clinical and research laboratories.Human immunology · 2021Article
- HLA Loci and Recurrence of Focal Segmental Glomerulosclerosis in Pediatric Kidney Transplantation.Transplantation direct · 2021Article
- Genetic Determinants inJournal of personalized medicine · 2021Review
- Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research.Frontiers in genetics · 2021Review
- An immunogenetic view of COVID-19.Genetics and molecular biology · 2021Article
- Genomic risk scores for juvenile idiopathic arthritis and its subtypes.Annals of the rheumatic diseases · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors at 10 institutions in 3 countries.
Funding
Abstract
Four single nucleotide polymorphism (SNP)-based human leukocyte antigen (HLA) imputation methods (e-HLA, HIBAG, HLA*IMP:02 and MAGPrediction) were trained using 1000 Genomes SNP and HLA genotypes and assessed for their ability to accurately impute molecular HLA-A, -B, -C and -DRB1 genotypes in the Human Genome Diversity Project cell panel. Imputation concordance was high (>89%) across all methods for both HLA-A and HLA-C, but HLA-B and HLA-DRB1 proved generally difficult to impute. Overall, <27.8% of subjects were correctly imputed for all HLA loci by any method. Concordance across all loci was not enhanced via the application of confidence thresholds; reliance on confidence scores across methods only led to noticeable improvement (+3.2%) for HLA-DRB1. As the HLA complex is highly relevant to the study of human health and disease, a standardized assessment of SNP-based HLA imputation methods is crucial for advancing genomic research. Considerable room remains for the improvement of HLA-B and especially HLA-DRB1 imputation methods, and no imputation method is as accurate as molecular genotyping. The application of large, ancestrally diverse HLA and SNP reference data sets and multiple imputation methods has the potential to make SNP-based HLA imputation methods a tractable option for determining HLA genotypes.
Indexed as
Identifiers
What OpenQuestion holds
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.