Cargando…
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...
Autores principales: | , , , |
---|---|
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 |
_version_ | 1784630124396675072 |
---|---|
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. |
format | Online Article Text |
id | pubmed-8744484 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT ritarijarmo kirgenecontentimputationfromsinglenucleotidepolymorphismsinthefinnishpopulation AT hyvarinenkati kirgenecontentimputationfromsinglenucleotidepolymorphismsinthefinnishpopulation AT partanenjukka kirgenecontentimputationfromsinglenucleotidepolymorphismsinthefinnishpopulation AT koskelasatu kirgenecontentimputationfromsinglenucleotidepolymorphismsinthefinnishpopulation |