ArticleBioinformatics (Oxford, England)2018
AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- PanGraphRNA: An efficient and flexible bioinformatics platform for graph pangenome-based RNA-seq data analysis.Journal of integrative plant biology · 2026Article
- eQTLs identify regulatory networks and drivers of variation in the individual response to sepsis.Cell genomics · 2024Article
- Comparison between qPCR and RNA-seq reveals challenges of quantifying HLA expression.Immunogenetics · 2023Article
- Haplotype-aware pantranscriptome analyses using spliced pangenome graphs.Nature methods · 2023Article
- Regulation of HLA class I expression by non-coding gene variations.PLoS genetics · 2022Article
- HLA allele-specific expression: Methods, disease associations, and relevance in hematopoietic stem cell transplantation.Frontiers in immunology · 2022Review
- Whole-genome sequencing and genome regions of special interest: Lessons from major histocompatibility complex, sex determination, and plant self-incompatibility.Molecular ecology · 2021Article
- Haplotype-Specific Expression Analysis of MHC Class II Genes in Healthy Individuals and Rheumatoid Arthritis Patients.Frontiers in immunology · 2021Article
- HLA RNA Sequencing With Unique Molecular Identifiers Reveals High Allele-Specific Variability in mRNA Expression.Frontiers in immunology · 2021Article
- An immunogenetic view of COVID-19.Genetics and molecular biology · 2021Article
- Pangenome Graphs.Annual review of genomics and human genetics · 2020Review
- scHLAcount: allele-specific HLA expression from single-cell gene expression data.Bioinformatics (Oxford, England) · 2020Article
- Mining GWAS and eQTL data for CF lung disease modifiers by gene expression imputation.PloS one · 2020Article
- Article
- Expression estimation and eQTL mapping for HLA genes with a personalized pipeline.PLoS genetics · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Motivation: Reliance on mapping to a single reference haplotype currently limits accurate estimation of allele or haplotype-specific expression using RNA-sequencing, notably in highly polymorphic regions such as the major histocompatibility complex. Results: We present AltHapAlignR, a method incorporating alternate reference haplotypes to generate gene- and haplotype-level estimates of transcript abundance for any genomic region where such information is available. We validate using simulated and experimental data to quantify input allelic ratios for major histocompatibility complex haplotypes, demonstrating significantly improved correlation with ground truth estimates of gene counts compared to standard single reference mapping. We apply AltHapAlignR to RNA-seq data from 462 individuals, showing how significant underestimation of expression of the majority of classical human leukocyte antigen genes using conventional mapping can be corrected using AltHapAlignR to allow more accurate quantification of gene expression for individual alleles and haplotypes. Availability and implementation: Source code freely available at https://github.com/jknightlab/AltHapAlignR. Supplementary information: Supplementary data are available at Bioinformatics online.
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