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.

The haplotype ATA, which is known as a 'low interleukin-10 producer' is a putative risk indicator for generalized aggressive periodontitis.

HLA-A9 and -B15 seem to represent susceptibility factors for AP whereas HLA-A2 and -B5 are potential protective factors against periodontitis among Caucasians.

The present study elucidates the variety of HLA associations and therefore the difficulty to assign single HLA markers to periodontal disease. Susceptibility/resistance of both aggressive and chronic periodontitis may rather be influenced by particular HLA marker combinations. Associated HLA haplotypes may be of further importance for unknown gene loci representing a part of the genetic background for periodontitis. The different associations in aggressive and chronic periodontitis indicate different susceptibility/resistance factors for both diseases.

Based on modern DNA techniques the present study shows an association of HLA to both RPP and AP. Certain HLA alleles seem to be associated with susceptibility or resistance to periodontitis in general. However, before this knowledge can be used for differential diagnosis or prognosis, further investigations are necessary.

After adjustment for microbial plaque, JIA is not a risk factor for periodontitis.

The central Asian country Mongolia is home to more than 20 tribes and ethnic groups, some of which are related to neighboring Turkic populations. The main Mongolian people, Khalkha, live in central and eastern Mongolia while the Tsaatan minority lives in the north of the country. The Oold minority is from the western Altai mountain region and live in close proximity with Turkic people. We have typed the HLA-A, -B, -Cw, -DRB1 and -DQB1 loci by PCR-SSP in these three Mongolian populations as well as a sample of the German population. To examine their genetic relationships, a sample of the Turkish population already typed at the HLA-A, -B and -DRB1 loci were used. Altogether five populations were analyzed: Khalkha (n = 100), Tsaatan (n = 72), Oold (n = 52), German (n = 260) and (Anatolian) Turkish (n = 498). Nei's unbiased genetic identity (GI) and genetic distance (GD) were estimated from genotypes using PopGene v1.31, and dendrograms were constructed using phylip. The results suggested a close relationship of the Khalkha to the Tsaatan. The Turks and Germans were equally distant to all three Mongolian populations. These results confirmed the lack of strong genetic relationship between the Mongols and the Turks despite the close relationship of their languages (Altaic group) and shared historical neighborhood. This study has provided useful population data for genetic and anthropologic studies bridging eastern and western populations.

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