PMID- 35036093
OWN - NLM
STAT- MEDLINE
DCOM- 20230106
LR  - 20230111
IS  - 2167-8359 (Print)
IS  - 2167-8359 (Electronic)
IS  - 2167-8359 (Linking)
VI  - 10
DP  - 2022
TI  - KIR gene content imputation from single-nucleotide polymorphisms in the Finnish 
      population.
PG  - e12692
LID - 10.7717/peerj.12692 [doi]
LID - e12692
AB  - 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.
CI  - (c)2022 Ritari et al.
FAU - Ritari, Jarmo
AU  - Ritari J
AD  - Finnish Red Cross Blood Service, Helsinki, Finland.
FAU - Hyvarinen, Kati
AU  - Hyvarinen K
AD  - Finnish Red Cross Blood Service, Helsinki, Finland.
FAU - Partanen, Jukka
AU  - Partanen J
AD  - Finnish Red Cross Blood Service, Helsinki, Finland.
FAU - Koskela, Satu
AU  - Koskela S
AD  - Finnish Red Cross Blood Service, Helsinki, Finland.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20220107
PL  - United States
TA  - PeerJ
JT  - PeerJ
JID - 101603425
RN  - 0 (Receptors, KIR)
MH  - Humans
MH  - *Polymorphism, Single Nucleotide/genetics
MH  - Finland
MH  - *DNA Copy Number Variations
MH  - Receptors, KIR/genetics
MH  - Genotype
PMC - PMC8744484
OTO - NOTNLM
OT  - Biobank
OT  - Imputation
OT  - KIR
OT  - Killer-cell immunoglobulin-like receptor
OT  - SNP
OT  - Single-nucleotide polymorphisms
COIS- The authors declare there are no competing interests.
EDAT- 2022/01/18 06:00
MHDA- 2022/01/18 06:01
PMCR- 2022/01/07
CRDT- 2022/01/17 06:01
PHST- 2021/08/26 00:00 [received]
PHST- 2021/12/06 00:00 [accepted]
PHST- 2022/01/17 06:01 [entrez]
PHST- 2022/01/18 06:00 [pubmed]
PHST- 2022/01/18 06:01 [medline]
PHST- 2022/01/07 00:00 [pmc-release]
AID - 12692 [pii]
AID - 10.7717/peerj.12692 [doi]
PST - epublish
SO  - PeerJ. 2022 Jan 7;10:e12692. doi: 10.7717/peerj.12692. eCollection 2022.