84
Views
2
CrossRef citations to date
0
Altmetric
Research Article

Killer cell immunoglobulin-like receptors (KIR) genes can be an adequate tool in forensic anthropological studies: evaluation in a wide Caucasian Spanish population

ORCID Icon, ORCID Icon, , ORCID Icon, ORCID Icon & ORCID Icon
Pages 168-190 | Received 25 Jan 2021, Accepted 29 Apr 2021, Published online: 31 May 2021

References

  • Pereira R, Phillips C, Pinto N, Santos C, Santos SEBD, Amorim A, Carracedo Á, Gusmão L. Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing. Kayser M, ed. PLoS One. 2012;7(1):e29684. doi:10.1371/journal.pone.0029684.
  • ArrayExpress update—trends in database growth and links to data analysis tools. academic.oup.com. [ accessed 2021 Jan 3]. https://academic.oup.com/nar/article-abstract/41/D1/D987/1066874.
  • Johnson MD, Leighton T, Murch R. Genetic analysis and attribution of microbial forensics evidence cyberbiosecurity: securing the emerging domain of biomanufacturing view project NYC native air sampling pilot project view project. Taylor Fr. 2014;31(4):233–254. doi:10.1080/10408410500304082.
  • Gomes I, Kohlmeier F, International PS-FS. Genetic markers for body fluid and tissue identification in forensics. Elsevier; 2011. [ accessed 2021 Jan 3]. https://www.sciencedirect.com/science/article/pii/S1875176811002356?casa_token=ePGtLEFghkAAAAAA:f9sw-bkDHO7GEgOSXcDDFJZPkDC3XzHhqTRbOFBdxjR0HOsHAWvYdvx8UfYnhMlVd90AYhum.
  • Kidd K, Pakstis A, Speed W, RL-FS. Current sequencing technology makes microhaplotypes a powerful new type of genetic marker for forensics. Elsevier; 2014. [ accessed 2021 Jan 3]. https://www.sciencedirect.com/science/article/pii/S187249731400132X
  • Berglund EC, Kiialainen A, Syvänen AC. Next-generation sequencing technologies and applications for human genetic history and forensics. Investig Genet. 2011;2(1):23. doi:10.1186/2041-2223-2-23.
  • Fondevila M, Phillips C, Naveran N, Fernandez L, Cerezo M, Salas A, Carracedo A, Lareu MV. Case report: identification of skeletal remains using short-amplicon marker analysis of severely degraded DNA extracted from a decomposed and charred femur. Forensic Sci Int Genet. 2008;2(3):212–218. doi:10.1016/j.fsigen.2008.02.005.
  • Colucci F, Caligiuri MA, Di Santo JP. What does it take to make a natural killer? Nat Rev Immunol. 2003;3(5):413–425. doi:10.1038/nri1088.
  • Sun JC, Lanier LL. Cutting edge: viral infection breaks NK cell tolerance to “missing self”. J Immunol. 2008;181(11):7453–7457. doi:10.4049/jimmunol.181.11.7453.
  • Yawata M, Yawata N, McQueen KL, Cheng N, Guethlein L, Rajalingam R, Shilling H, Parham P. Predominance of group A KIR haplotypes in Japanese associated with diverse NK cell repertoires of KIR expression. Immunogenetics. 2002;54(8):543–550. doi:10.1007/s00251-002-0497-x.
  • Vilches C, Parham P. KIR: diverse, rapidly evolving receptors of innate and adaptive immunity. Annu Rev Immunol. 2002;20(1):217–251. doi:10.1146/annurev.immunol.20.092501.134942.
  • Selvakumar A, Steffens U, Dupont B. Polymorphism and domain variability of human killer cell inhibitory receptors. Immunol Rev. 1997;155(1):183–196. doi:10.1111/j.1600-065X.1997.tb00951.x.
  • Wende H, Colonna M, Ziegler A, Volz A. Organization of the leukocyte receptor cluster (LRC) on human chromosome 19q13.4. Springer. 1999;10(2):154–160. doi:10.1007/s003359900961.
  • Uhrberg M, Valiante NM, Shum BP, Shilling HG, Lienert-Weidenbach K, Corliss B, Tyan D, Lanier LL, Parham P. Human diversity in killer cell inhibitory receptor genes. Immunity. 1997;7(6):753–763. doi:10.1016/S1074-7613(00)80394-5.
  • Wilson MJ, Torkar M, Haude A, Milne S, Jones T, Sheer D, Beck S, Trowsdale J. Plasticity in the organization and sequences of human KIR/ILT gene families. Proc Natl Acad Sci U S A. 2000;97(9):4778–4783. doi:10.1073/pnas.080588597.
  • Shilling HG, Lienert-Weidenbach K, Valiante NM, Uhrberg M, Parham P. Evidence for recombination as a mechanism for KIR diversification. Immunogenetics. 1998;48(6):413–416. doi:10.1007/s002510050453.
  • Middleton D, Gonzelez F. The extensive polymorphism of KIR genes. Immunology. 2010;129(1):8–19. doi:10.1111/j.1365-2567.2009.03208.x.
  • Martin A, Freitas E, Witt C, Immunogenetics FC. The genomic organization and evolution of the natural killer immunoglobulin-like receptor (KIR) gene cluster. Springer; 2000. [ accessed 2021 Jan 3]. https://link.springer.com/content/pdf/10.1007/s002510050620.pdf.
  • Trowsdale J, Barten R, Haude A, Andrew Stewart C, Beck S, Wilson MJ. The genomic context of natural killer receptor extended gene families. Immunol Rev. 2001;181(1):20–38. doi:10.1034/j.1600-065X.2001.1810102.x.
  • Faure M, Long EO. KIR2DL4 (CD158d), an NK cell-activating receptor with inhibitory potential. J Immunol. 2002;168(12):6208–6214. doi:10.4049/jimmunol.168.12.6208.
  • Rajagopalan S, Long EO. A human histocompatibility leukocyte antigen (HLA)-G-specific receptor expressed on all natural killer cells. J Exp Med. 1999;189(7):1093–1099. doi:10.1084/jem.189.7.1093.
  • Middleton D, Curran M, Maxwell L. Natural killer cells and their receptors. Transpl Immunol. 2002;10(2–3):147–164. doi:10.1016/S0966-3274(02)00062-X.
  • Parham P. Influence of KIR diversity on human immunity. In: Advances in Experimental Medicine and Biology. Vol. 560:Springer Science and Business Media Deutschland GmbH;2005. p. 47–50. doi:10.1007/0-387-24180-9_6
  • González-Galarza FF, Takeshita LC, Santos EM, Kempson F, Maia M, Silva A, Silva A, Ghattaoraya G, Alfirevic A, Jones A, et al. Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations. Nucleic Acids Res. 2015;43(D1):D784–D788. doi:10.1093/nar/gku1166.
  • Norman PJ, Stephens HAF, Verity DH, Chandanayingyong D, Vaughan RW. Distribution of natural killer cell immunoglobulin-like receptor sequences in three ethnic groups. Immunogenetics. 2001;52(3–4):195–205. doi:10.1007/s002510000281.
  • Single RM, Martin MP, Gao X, Meyer D, Yeager M, Kidd JR, Kidd KK, Carrington M. Global diversity and evidence for coevolution of KIR and HLA. Nat Genet. 2007;39(9):1114–1119. doi:10.1038/ng2077.
  • Yawata M, Yawata N, Abi-Rached L, Parham P. Variation within the human killer cell immunoglobulin-like receptor (KIR) gene family. Crit Rev Immunol. 2002;22(5–6):463–482. doi:10.1615/critrevimmunol.v22.i5-6.70.
  • Alvarado-Hernández DL, Hernández-Ramírez D, Noyola DE, García-Sepúlveda CA. KIR gene diversity in Mexican mestizos of San Luis Potosí. Immunogenetics. 2011;63(9):561–575. doi:10.1007/s00251-011-0540-x.
  • Cisneros E, Moraru M, Gómez-Lozano N, Muntasell A, López-Botet M, Vilches C. Haplotype-based analysis of KIR-gene profiles in a South European population—distribution of standard and variant haplotypes, and identification of novel recombinant structures. Front Immunol. 2020;11:440. doi:10.3389/fimmu.2020.00440.
  • Augusto DG, Piovezan BZ, Tsuneto LT, Callegari-Jacques SM, Petzl-Erler ML. KIR gene content in amerindians indicates influence of demographic factors. Barbour JD, ed. PLoS One. 2013;8(2):e56755. doi:10.1371/journal.pone.0056755.
  • Yang Y, Xu J, Ying Z, Ott J. Testing linkage disequilibrium from pooled dna: a contingency table perspective. Stat Med. 2008;27(28):5801–5815. doi:10.1002/sim.3407.
  • Home | HUGO Gene Nomenclature Committee. [ accessed 2021 Jan 3]. https://www.genenames.org/.
  • Mattiuz PL. New approaches to the population genetic segregation analysis of the HLA system. Histocompat Test; 1970. [ accessed 2021 Jan 8]. https://ci.nii.ac.jp/naid/10014800526.
  • Lewontin R, Evolution KK. The evolutionary dynamics of complex polymorphisms. JSTOR; 1960. [ accessed 2021 Jan 4]. https://www.jstor.org/stable/2405995?casa_token=EU8XO0Zgea4AAAAA:6lPL0-hNKwmSEL2CLCjscCZLJ3bMMMGUgycUXhuB1B3lvex0vlFbYGEc3-xsID1ZDHnd_raNW9-R9iUOI6JlvsnfcE20RaxoWYqUX9K3ieNIaiPAbw.
  • Lewontin RC. The interaction of selection and linkage. I. General considerations; heterotic models. Genetics. 1964;49(1):49–67. [ accessed 2021 Jan 4]. http://www.ncbi.nlm.nih.gov/pubmed/17248194.
  • Gonzalez-Galarza FF, McCabe A, Dos Santos EJM, Jones J, Takeshita L, Ortega-Rivera ND, Cid-Pavon GMD, Ramsbottom K, Ghattaoraya G, Alfirevic A, et al. Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools. Nucleic Acids Res. 2020;48(D1):D783–D788. doi:10.1093/nar/gkz1029.
  • Toh KC, Todd MJ, Tütüncü RH. SDPT3 - a MATLAB software package for semidefinite programming, version 1.3. Optim Methods Softw. 1999;11(1):545–581. doi:10.1080/10556789908805762.
  • Santos C, Phillips C, Fondevila M, Daniel R, Van Oorschot RAH, Burchard EG, Schanfield MS, Souto L, Uacyisrael J, Via M, et al. Pacifiplex: an ancestry-informative SNP panel centred on Australia and the Pacific region. Forensic Sci Int Genet. 2016;20:71–80. doi:10.1016/j.fsigen.2015.10.003.
  • Phillips C, Santos C, Fondevila M, Carracedo Á, Lareu MV. Inference of ancestry in forensic analysis I: autosomal ancestry-informative marker sets. Methods Mol Biol. 2016;1420:233–253. doi:10.1007/978-1-4939-3597-0_18.
  • Mehta B, Daniel R, Phillips C, McNevin D. Forensically relevant SNaPshot® assays for human DNA SNP analysis: a review. Int J Legal Med. 2017;131(1):21–37. doi:10.1007/s00414-016-1490-5.
  • Phillips C, Fernandez-Formoso L, Gelabert-Besada M, Garcia-Magariños M, Santos C, Fondevila M, Carracedo Á, Lareu MV. Development of a novel forensic STR multiplex for ancestry analysis and extended identity testing. Electrophoresis. 2013;34(8):1151–1162. doi:10.1002/elps.201200621.
  • Phillips C. Forensic genetic analysis of bio-geographical ancestry. Forensic Sci Int Genet. 2015;18:49–65. doi:10.1016/j.fsigen.2015.05.012.
  • Kayser M, De Knijff P. Improving human forensics through advances in genetics, genomics and molecular biology. Nat Rev Genet. 2011;12(3):179–192. doi:10.1038/nrg2952.
  • Flores AC, Marcos CY, Paladino N, Capucchio M, Theiler G, Arruvito L, Pardo R, Habegger A, Williams F, Middleton D, et al. KIR genes polymorphism in Argentinean Caucasoid and Amerindian populations. Tissue Antigens. 2007;69(6):568–576. doi:10.1111/j.1399-0039.2007.00824.x.
  • Maccari G, Robinson J, Hammond JA, Marsh SGE. The IPD project: a centralised resource for the study of polymorphism in genes of the immune system. Immunogenetics. 2020;72(1–2):49–55. doi:10.1007/s00251-019-01133-w.
  • Parham P. MHC class I molecules and KIRS in human history, health and survival. Nat Rev Immunol. 2005;5(3):201–214. doi:10.1038/nri1570.
  • Uhrberg M, Parham P, Wernet P. Definition of gene content for nine common group B haplotypes of the Caucasoid population: KIR haplotypes contain between seven and eleven KIR genes. Immunogenetics. 2002;54(4):221–229. doi:10.1007/s00251-002-0463-7.
  • Pyo C-W, Guethlein LA, Vu Q, Wang R, Abi-Rached L, Norman PJ, Marsh SGE, Miller JS, Parham P, Geraghty DE, et al. Different patterns of evolution in the centromeric and telomeric regions of group A and B haplotypes of the human killer cell Ig-like receptor locus. Matsunami H, ed. PLoS One. 2010;5(12):e15115. doi:10.1371/journal.pone.0015115.
  • Santourlidis S, Trompeter H-I, Weinhold S, Eisermann B, Meyer KL, Wernet P, Uhrberg M. Crucial role of DNA methylation in determination of clonally distributed killer cell Ig-like receptor expression patterns in NK cells. J Immunol. 2002;169(8):4253–4261. doi:10.4049/jimmunol.169.8.4253.
  • Méndez A, Granda H, Meenagh A, Contreras S, Zavaleta R, Mendoza MF, Izquierdo L, Sarmiento ME, Acosta A, Middleton D, et al. Study of KIR genes in tuberculosis patients. Tissue Antigens. 2006;68(5):386–389. doi:10.1111/j.1399-0039.2006.00685.x.
  • Gagne K, Brizard G, Gueglio B, et al. Relevance of KIR gene polymorphisms in bone marrow transplantation outcome. Hum Immunol. 2002;63(4):271–280. doi:10.1016/S0198-8859(02)00373-7.
  • Leone P, De Re V, Vacca A, Dammacco F, Racanelli V. Cancer treatment and the KIR–HLA system: an overview. Clin Exp Med. 2017;17(4):419–429. doi:10.1007/s10238-017-0455-4.
  • Niokou D, Spyropoulou-Vlachou M, Darlamitsou A, Stavropoulos-Giokas C. Distribution of killer cell immunoglobulin-like receptors in the Greek population. Hum Immunol. 2003;64(12):1167–1176. doi:10.1016/j.humimm.2003.08.100.
  • Denis L, Sivula J, Gourraud P-A, Kerdudou N, Chout R, Ricard C, Moisan J-P, Gagne K, Partanen J, Bignon J-D, et al. Genetic diversity of KIR natural killer cell markers in populations from France, Guadeloupe, Finland, Senegal and Reunion. Tissue Antigens. 2005;66(4):267–276. doi:10.1111/j.1399-0039.2005.00473.x.
  • Bontadini A, Testi M, Arnadei M, Battarra M, Chiesa A. Multicentric evaluation of the KIR genotypes in the Italian Caucasian population; 2005. [ accessed 2021 Jan 3].https://iris.unica.it/handle/11584/35271.
  • Pavlova Y, Kolesar L, Striz I, Jabor A, Slavcev A. Distribution of KIR genes in the Czech population. Int J Immunogenet. 2008;35(1):57–61. doi:10.1111/j.1744-313X.2007.00737.x.
  • Toneva M, Lepage V, Lafay G, Dulphy N, Busson M, Lester S, Vu-Trien A, Michaylova A, Naumova E, McCluskey J, et al. Genomic diversity of natural killer cell receptor genes in three populations. Tissue Antigens. 2001;57(4):358–362. doi:10.1034/j.1399-0039.2001.057004358.x.
  • Velickovic M, Velickovic Z, Panigoro R, Dunckley H. Diversity of killer cell immunoglobulin-like receptor genes in Indonesian populations of Java, Kalimantan, Timor and Irian Jaya. Tissue Antigens. 2009;73(1):9–16. doi:10.1111/j.1399-0039.2008.01149.xTAN1149 [pii].
  • Conesa A, Fernández-Mestre M, Padrón D, Toro F, Silva N, Tassinari P, Blanca I, Martin MP, Carrington M, Layrisse Z, et al. Distribution of killer cell immunoglobulin-like receptor genes in the mestizo population from Venezuela. Tissue Antigens. 2010;75(6):724–729. doi:10.1111/j.1399-0039.2010.01446.x.
  • Wu G-Q, Zhao Y-M, Lai X-Y, Yang K-L, Zhu F-M, Zhang W, Wang W, Luo Y, Tan Y-M, Wang Y-J, et al. distribution of killer-cell immunoglobulin-like receptor genes in Eastern mainland Chinese Han and Taiwanese Han populations. Tissue Antigens. 2009;74(6):499–507. doi:10.1111/j.1399-0039.2009.01366.x.
  • Ozturk O, Gun F, Oncology GP-M. 2012. Killer cell immunoglobulin-like receptor genes in patients with breast cancer. Springer. . [ accessed 2021 Jan 3]. https://link.springer.com/content/pdf/10.1007/s12032-011-9932-x.pdf.
  • Djulejic E, Petlichkovski A, Trajkov D, Hristomanova S, Middleton D, Spiroski M. Distribution of killer cell immunoglobulinlike receptors in the Macedonian population. Hum Immunol. 2010;71(3):281–288. doi:10.1016/j.humimm.2009.12.001S0198-8859(09)00655-7 [pii].
  • Kulkarni S, Single RM, Martin MP, Rajalingam R, Badwe R, Joshi N, Carrington M. comparison of the rapidly evolving KIR locus in Parsis and natives of India. Immunogenetics. 2008;60(3–4):121–129. doi:10.1007/s00251-008-0279-1.
  • Tajik N, Shahsavar F, Mousavi T, Radjabzadeh MF. Distribution of KIR genes in the Iranian population. Tissue Antigens. 2009;74(1):22–31. doi:10.1111/j.1399-0039.2009.01263.x [pii].
  • Ozturk OG, Polat G, Atik U. Determination of KIR gene frequencies in Mersin district of Turkey and comparison with selected world populations. Tissue Antigens. 2009;73(5):385–523. doi:10.1111/j.1399-0039.2009.01255.x.
  • Hiby SE, Ashrafian-Bonab M, Farrell L, Single RM, Balloux F, Carrington M, Moffett A. distribution of killer cell immunoglobulin-like receptors (KIR) and their HLA-C ligands in two Iranian populations. Immunogenetics. 2010;62(2):65–73. doi:10.1007/s00251-009-0408-5.
  • Witt CS, Christopher D, Sayer David C, Marcus U, Peter P, Christiansen Frank T. Population frequencies and putative haplotypes of the killer cell immunoglobulin-like receptor sequences and evidence for recombination. Transplantation. 1999;68(11):1784–1789. doi:10.1097/00007890-199912150-00024.
  • Momot T, Koch S, Hunzelmann N, Krieg T, Ulbricht K, Schmidt RE, Witte T. Association of killer cell immunoglobulin-like receptors with scleroderma. Arthritis Rheum. 2004;50(5):1561–1565. doi:10.1002/art.20216.
  • Deng Z, Zhao J, Cai S, Qi Y, Yu Q, Martin MP, Gao X, Chen R, Zhuo J, Zhen J, et al. Natural killer cells offer differential protection from leukemia in Chinese southern han. Front Immunol. 2019;10(JULY). doi:10.3389/fimmu.2019.01646
  • Market M, Angka L, Martel AB, Bastin D, Olanubi O, Tennakoon G, Boucher DM, Ng J, Ardolino M, Auer RC, et al. Flattening the COVID-19 curve with natural killer cell based immunotherapies. Front Immunol. 2020;11:1512. doi:10.3389/fimmu.2020.01512.
  • Santin I, De Nanclares GP, Calvo B, Gaafar A, Castaño L, Bilbao JR. Killer cell immunoglobulin-like receptor (KIR) genes in the basque population: association study of KIR gene contents with Type 1 diabetes mellitus. Hum Immunol. 2006;67(1–2):118–124. doi:10.1016/j.humimm.2006.02.036.
  • Díaz-Peña R, Vidal-Castiñeira JR, Moro-García MA, Alonso-Arias R, Castro-Santos P. Significant association of the KIR2DL3/HLA-C1 genotype with susceptibility to Crohn’s disease. Hum Immunol. 2016;77(1):104–109. doi:10.1016/j.humimm.2015.10.020.
  • Campillo JA, Legaz I, López-Álvarez MR, Bolarín JM, Las Heras B, Muro M, Minguela A, Moya-Quiles MR, Blanco-García R, Martínez-Banaclocha H, et al. KIR gene variability in cutaneous malignant melanoma: influence of KIR2D/HLA-C pairings on disease susceptibility and prognosis. Immunogenetics. 2013;65(5):333–343. doi:10.1007/s00251-013-0682-0.
  • Wu GQ, Zhao YM, Lai XY, Yang K-L, Zhu F-M, Zhang W, Wang W, Luo Y, Tan Y-M, Wang Y-J, et al. distribution of killer-cell immunoglobulin-like receptor genes in Eastern mainland Chinese Han and Taiwanese Han populations. Tissue Antigens. 2009;74(6):499–507. doi:10.1111/j.1399-0039.2009.01366.x [pii]
  • Petlichkovski A, Djulejic E, Trajkov D, et al. distribution of killer cell immunoglobulin-like receptor genes in Roma from Republic of Macedonia. Int J Immunogenet. 2011;38(6):493–500. doi:10.1111/j.1744-313X.2011.01039.x.
  • Norman P, Carrington C, Byng M, LM-G&#x0026. Natural killer cell immunoglobulin-like receptor (KIR) locus profiles in African and South Asian populations. nature.com; 2002. [ accessed 2021 Jan 8]. https://www.nature.com/articles/6363836/.
  • Whang D, Park H, Yoon J, Immunology MP-H. Haplotype analysis of killer cell immunoglobulin-like receptor genes in 77 Korean families. Elsevier; 2005 [ accessed 2021 Jan 4]. https://www.sciencedirect.com/science/article/pii/S0198885904006585?casa_token=eNOHzbsXIQoAAAAA:9hAh5raDyNTBcNTpBrdN8MC-kZZKp2-pDJ86iOSdR_TQJNPZN4ORB_P23iJoVIrbEnGr2eui.
  • Shilling HG, Guethlein LA, Cheng NW, Gardiner CM, Rodriguez R, Tyan D, Parham P. Allelic polymorphism synergizes with variable gene content to individualize human KIR genotype. J Immunol. 2002;168(5):2307–2315. doi:10.4049/jimmunol.168.5.2307.
  • Williams F, duToit ED, Middleton D. KIR allele frequencies in a Xhosa population from South Africa. Hum Immunol. 2004;65(9–10):1084–1085. doi:10.1016/j.humimm.2004.08.120.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.