ArticleBriefings in bioinformatics2021
In silico tools for accurate HLA and KIR inference from clinical sequencing data empower immunogenetics on individual-patient and population scales.
Article in Briefings in bioinformatics, 2021. 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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15 citing papers in PubMed, 34 citations in OpenAlex.
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- A walk through the development of human leukocyte antigen typing: from serologic techniques to next-generation sequencing.Clinical transplantation and research · 2024Review
- Historical perspective and future directions: computational science in immuno-oncology.Journal for immunotherapy of cancer · 2024Review
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- Evaluation of HLA typing content of next-generation sequencing datasets from family trios and individuals of arab ethnicity.Frontiers in genetics · 2024Article
- Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data.BMC genomics · 2023Article
- Benchmarking freely available HLA typing algorithms across varying genes, coverages and typing resolutions.Frontiers in immunology · 2022Article
- KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population.PeerJ · 2022Article
- High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING.PLoS computational biology · 2021Article
- MiDAS-Meaningful Immunogenetic Data at Scale.PLoS computational biology · 2021Article
- 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
- The Immunogenic Potential of Recurrent Cancer Drug Resistance Mutations: AnFrontiers in immunology · 2020Article
- Accurate and Efficient KIR Gene and Haplotype Inference From Genome Sequencing Reads With Novel K-mer Signatures.Frontiers in immunology · 2020Article
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Authors and funding
15 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Immunogenetic variation in humans is important in research, clinical diagnosis and increasingly a target for therapeutic intervention. Two highly polymorphic loci play critical roles, namely the human leukocyte antigen (HLA) system, which is the human version of the major histocompatibility complex (MHC), and the Killer-cell immunoglobulin-like receptors (KIR) that are relevant for responses of natural killer (NK) and some subsets of T cells. Their accurate classification has typically required the use of dedicated biological specimens and a combination of in vitro and in silico efforts. Increased availability of next generation sequencing data has led to the development of ancillary computational solutions. Here, we report an evaluation of recently published algorithms to computationally infer complex immunogenetic variation in the form of HLA alleles and KIR haplotypes from whole-genome or whole-exome sequencing data. For both HLA allele and KIR gene typing, we identified tools that yielded >97% overall accuracy for four-digit HLA types, and >99% overall accuracy for KIR gene presence, suggesting the readiness of in silico solutions for use in clinical and high-throughput research settings.
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