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KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population

The killer cell immunoglobulin-like receptor (KIR) gene cluster on chromosome 19 encodes cell surface glycoproteins that bind class I human leukocyte antigen (HLA) molecules as well as some other ligands. Through regulation of natural killer (NK) cell activity KIRs participate in tumour surveillance...

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Autores principales: Ritari, Jarmo, Hyvärinen, Kati, Partanen, Jukka, Koskela, Satu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8744484/
https://www.ncbi.nlm.nih.gov/pubmed/35036093
http://dx.doi.org/10.7717/peerj.12692
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author Ritari, Jarmo
Hyvärinen, Kati
Partanen, Jukka
Koskela, Satu
author_facet Ritari, Jarmo
Hyvärinen, Kati
Partanen, Jukka
Koskela, Satu
author_sort Ritari, Jarmo
collection PubMed
description The killer cell immunoglobulin-like receptor (KIR) gene cluster on chromosome 19 encodes cell surface glycoproteins that bind class I human leukocyte antigen (HLA) molecules as well as some other ligands. Through regulation of natural killer (NK) cell activity KIRs participate in tumour surveillance and clearing viral infections. KIR gene gene copy number variation associates with the outcome of transplantations and susceptibility to immune-mediated diseases. Inferring KIR gene content from genetic variant data is therefore desirable for immunogenetic analysis, particularly in the context of growing biobank genome data collections that rely on genotyping by microarray. Here we describe a stand-alone and freely available gene content imputation for 12 KIR genes. The models were trained using 807 Finnish biobank samples genotyped for 5900 KIR-region SNPs and analysed for KIR gene content with targeted sequencing. Cross-validation results demonstrate a high mean overall accuracy of 98.5% (95% CI [97.0–99.2]%) which compares favourably with previous methods including short-read sequencing based approaches.
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spelling pubmed-87444842022-01-14 KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population Ritari, Jarmo Hyvärinen, Kati Partanen, Jukka Koskela, Satu PeerJ Bioinformatics The killer cell immunoglobulin-like receptor (KIR) gene cluster on chromosome 19 encodes cell surface glycoproteins that bind class I human leukocyte antigen (HLA) molecules as well as some other ligands. Through regulation of natural killer (NK) cell activity KIRs participate in tumour surveillance and clearing viral infections. KIR gene gene copy number variation associates with the outcome of transplantations and susceptibility to immune-mediated diseases. Inferring KIR gene content from genetic variant data is therefore desirable for immunogenetic analysis, particularly in the context of growing biobank genome data collections that rely on genotyping by microarray. Here we describe a stand-alone and freely available gene content imputation for 12 KIR genes. The models were trained using 807 Finnish biobank samples genotyped for 5900 KIR-region SNPs and analysed for KIR gene content with targeted sequencing. Cross-validation results demonstrate a high mean overall accuracy of 98.5% (95% CI [97.0–99.2]%) which compares favourably with previous methods including short-read sequencing based approaches. PeerJ Inc. 2022-01-07 /pmc/articles/PMC8744484/ /pubmed/35036093 http://dx.doi.org/10.7717/peerj.12692 Text en ©2022 Ritari et al. https://creativecommons.org/licenses/by-nc/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by-nc/4.0/) , which permits using, remixing, and building upon the work non-commercially, as long as it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Ritari, Jarmo
Hyvärinen, Kati
Partanen, Jukka
Koskela, Satu
KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population
title KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population
title_full KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population
title_fullStr KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population
title_full_unstemmed KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population
title_short KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population
title_sort kir gene content imputation from single-nucleotide polymorphisms in the finnish population
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8744484/
https://www.ncbi.nlm.nih.gov/pubmed/35036093
http://dx.doi.org/10.7717/peerj.12692
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