1. ¹Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
2. ²Interbranch HLA Laboratory, Martin Luther University Medical School, Halle, Germany
3. ³Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
4. ⁴Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea

Correspondence: Dr MT Dorak, Newcastle University, School of Clinical Medical Sciences (Child Health), Sir James Spence Institute, Royal Victoria Infirmary, Newcastle NE1 4LP, UK. E-mail: dorak@openlink.org

Received 28 April 2006; Accepted 3 May 2006; Published online 22 June 2006.

Abstract

Since the complete sequencing of a human major histocompatibility complex (MHC) haplotype, interest in non-human leucocyte antigen (HLA) genes encoded in the MHC has been growing. Non-HLA genes, which outnumber the HLA genes, may contribute to or account for HLA and disease associations. Most information on non-HLA genes has been obtained in separate studies of individual loci. To comprehensively address polymorphisms of relevant non-HLA genes in 'conserved extended haplotypes' (CEH), we investigated 101 International Histocompatibility Workshop reference cell lines and nine additional anonymous samples representing all 37 unambiguously characterized CEHs at MICA, NFKBIL1, LTA, NCR3, AIF1, HSPA1A, HSPA1B, BF, NOTCH4 and a single nucleotide polymorphism (SNP) at HLA-DQA1 as well as MICA, NOTCH4, HSPA1B and all five tumour necrosis factor short tandem repeat (STR) polymorphisms. This work (1) provides an extensive catalogue of MHC polymorphisms in all CEHs, (2) unravels interrelationships between HLA and non-HLA haplotypical lineages, (3) resolves reported typing ambiguities and (4) describes haplospecific markers for a number of CEHs. Analysis also identified a DQA1 SNP and segments containing MHC class III polymorphisms that corresponded with class II (DRB3 and DRB4) lineages. These results portray the MHC where lineages containing non-HLA and HLA variants in linkage disequilibrium may operate in concert and can guide more thorough design and interpretation of HLA–disease relationships.