Linkage disequilibrium organization of the human KIR superlocus: implications for KIR data analyses

Pierre-Antoine Gourraud 0 2 3 Ashley Meenagh 0 2 3 Anne Cambon-Thomsen 0 2 3 Derek Middleton 0 2 3 0 Contributions Ashley Meenagh performed the genotyping. Pierre- Antoine Gourraud set up the analytical strategy. Anne Cambon- Thomsen contributed to the discussion and the manuscript. Derek Middleton and Pierre-Antoine Gourraud conceived the research and wrote the paper 1 ) Department of Neurology, University of California , 513 Parnassus Avenue, San Francisco, CA 94143, USA 2 D. Middleton Division of Immunology, School of Infection and Host Defense, University of Liverpool, Transplant Immunology, Royal Liverpool University Hospital , Liverpool, UK 3 A. Meenagh Northern Ireland Histocompatibility and Immunogenetics Laboratory, City Hospital , Blood Transfusion Building, Belfast, UK An extensive family-based study of linkage disequilibrium (LD) in the killer cell immunoglobulin-like receptors (KIR) cluster was performed. We aimed to describe the LD structure in the KIR gene cluster using a sample of 418 founder haplotypes identified by segregation in a group of 106 families from Northern Ireland. The LD was studied at two levels of polymorphism: the structural level (presence or absence of KIR genes) and the allelic level (between alleles of KIR genes). LD was further assessed using the predictive value of one KIR polymorphism for another one in order to provide an interpretative framework for the LD effect in association studies. In line with previous research, distinct patterns of KIR genetic diversity within the genomic region centromeric to KIR2DL4 (excluding KIR2DL4) and within the telomeric region including KIR2DL4 were found. In a comprehensive PPV/NPV-based LD analysis within the KIR cluster, robust tag markers were found that can be used to identify which genes are concomitantly present or absent and to further identify groups of associated KIR alleles. Several extended KIR haplotypes in the study population w e r e i d e n t i f i e d ( K I R 2 D S 2 * P O S - K I R 2 D L 2 * 0 0 1 - KIR2DL5B*002-KIR2DS3*00103-KIR2DL1*00401; K I R 2 D L 4 * 0 11 - K I R 3 D L 1 / S 1 * 0 0 5 - K I R 2 D S 4 * 0 0 3 - KIR3DL2*003; KIR2DL4*00802-KIR3DL1/S1*004K I R 2 D S 4 *0 0 6 - K I R 3D L 2* 0 0 5; K I R 2 D L 4* 0 0 80 1KIR3DL1/S1*00101-KIR2DS4*003-KIR3DL2*001; KIR2DL4*00103-KIR3DL1/S1*008-KIR2DS4*003KIR3DL2*009; KIR2DL4*00102-KIR3DL1/S1*01502/ *002-KIR2DS4*00101-KIR3DL2*002; KIR2DL4*00501KIR3DL1/S1*013-KIR2DL5A*001-KIR2DS5*002KIR2DS1*002-KIR3DL2*007). The present study provides a rationale for analyzing associations of KIR polymorphisms by taking into account the complex LD structure of the KIR region. - Natural killer (NK) cells are key components of the innate immune response. According to the missing-self model, NK cells integrate activating and inhibitory signals and modulate the targeting of MHC Class I-deficient cells, in particular virus-infected and transformed malignant cells (Bashirova et al. 2006). NK cells maintain wide-ranging interactions with other immune cells, such as macrophages and dendritic cells, resulting in numerous effects on the immune response as a whole through the stimulation of cytokine production and induction of cytotoxicity (Carrington and Martin 2006). NK cells may provide benefit or act to the detriment of to the host: They play a central role not only in viral clearance (Khakoo et al. 2004; Martin et al. 2007), cancer (Middleton et al. 2009; Verheyden and Demanet 2008), and hematopoietic stem cell transplantation (Velardi 2008) but also in the development of autoimmune disorders (Lowe et al. 2009; Ploski et al. 2006) and less common conditions such as pre-eclampsia (Hiby et al. 2008). The NK cell receptors consist of two distinct families, Ctype lectin-like group (CD94/NKG2) mapping to chromosome 12q1.3-13.4 and the immunoglobulin-like super family consisting of the killer cell immunoglobulin-like receptors (KIR), leukocyte immunoglobulin-like receptors, and the leukocyte-associated immunoglobulin-like receptors mapping to chromosome 19q13.4 (Bashirova et al. 2006; Carrington and Martin 2006). The KIR gene cluster has generated great interest due to its complex genetic variability (Bashirova et al. 2006; Carrington and Martin 2006; Middleton et al. 2007; Parham 2005). KIR genes may be either present or absent, leading to substantial variation in gene content across individuals and populations. The deletion and/or duplication of KIR genes occur frequently, creating great structural variation and generating a variable number of copies of KIR genes relative to a reference sequence (i.e., the most frequent one; Hsu et al. 2002). When present, individual KIR genes show high allelic polymorphisms. Their frequencies vary across populations, some being common, others rare. The patterns of gene presence or absence and allelic polymorphism combine to generate a high degree of KIR heterogeneity between individuals (Middleton and Gonzelez 2010). The polymorphism of genes in the KIR cluster may be assessed at two levels: the structural variation (also known as copy number variation, CNV) of genes and the allelic variation of each gene. Linkage disequilibrium (LD) is the nonrandom association of alleles at two or more neighboring loci. Furthermore, because KIR genes are arrayed in tandem over more than 150 kb (Uhrberg et al. 1997), extensive LD implicates both gene content and allelic variation (Shilling et al. 2002). Such complex LD patterns, already complicated in pedigree analyses, may lead to ambiguous interpretation in population association studies because nonindependent associations between KIR genes or alleles may result in potential synergistic or antagonist functional effects. This complexity may explain the difficulty encountered in replication of disease CNV genetic association studies. The KIR cluster can be considered as a model region for CNV genomics, because it is the most important region outside the MHC establishing the functional role for variation in the number of genes. The complexity of KIR genetics increases the risk for false-positive findings and misinterpretation of genetic associations, particularly in studies with small sample size, requiring the development of improved analytical methods and better characterization of control populations. In the present study using predictive values, we provide a statistical description of LD that aids in the interpretation of associations between KIR polymorphisms. The LD tagging approach identifies a single genetic position that marks a block of positions in LD with one another (Gu et al. 2008; Johnson et al. 2001). This approach helps to deal with the complexity of the haplotype structure by measuring whether the different polymorphisms (genes and/or alleles) carry different or redundant information. The tagging concept applies LD between KIR genes in order to help understand the complex associations observed in KIR haplotypes. LD studies require haplotype frequency data. To sup (...truncated)