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Recombinant structures expand and contract inter and intragenic diversification at the KIR locus

Chul-Woo Pyo1, Ruihan Wang1, Quyen Vu1, Nezih Cereb2, Soo Young Yang2, Fuh-Mei Duh3, Steven Wolinsky4, Maureen P Martin3, Mary Carrington3 and Daniel E Geraghty1*

Author affiliations

1 Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA

2 Histogenetics LLC, Ossining, NY, USA

3 Cancer and Inflammation Program, Laboratory of Experimental Immunology, Frederick National Laboratory for Cancer Research, Frederick, MD, USA

4 Division of Infectious Diseases, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA

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Citation and License

BMC Genomics 2013, 14:89  doi:10.1186/1471-2164-14-89

Published: 8 February 2013



The human KIR genes are arranged in at least six major gene-content haplotypes, all of which are combinations of four centromeric and two telomeric motifs. Several less frequent or minor haplotypes also exist, including insertions, deletions, and hybridization of KIR genes derived from the major haplotypes. These haplotype structures and their concomitant linkage disequilibrium among KIR genes suggest that more meaningful correlative data from studies of KIR genetics and complex disease may be achieved by measuring haplotypes of the KIR region in total.


Towards that end, we developed a KIR haplotyping method that reports unambiguous combinations of KIR gene-content haplotypes, including both phase and copy number for each KIR. A total of 37 different gene content haplotypes were detected from 4,512 individuals and new sequence data was derived from haplotypes where the detailed structure was not previously available.


These new structures suggest a number of specific recombinant events during the course of KIR evolution, and add to an expanding diversity of potential new KIR haplotypes derived from gene duplication, deletion, and hybridization.

Natural killer cells; Human; KIR; Recombinant structures