Polymorphisms in the TNF-alpha SNPs do not seem to be a more important genetic risk factor for psoriasis than the already known Cw*06 in Brazilian patients, but these markers may be related to clinical manifestations.

Human leukocyte antigen‐C (HLA‐C) is a classical HLA class I molecule that binds and presents peptides to cytotoxic T lymphocytes in the cell surface. HLA‐C has a dual function because it also interacts with Killer‐cell immunoglobulin‐like receptors (KIR) receptors expressed in natural killer and T cells, modulating their activity. The structure and diversity of the HLA‐C regulatory regions, as well as the relationship among variants along the HLA‐C locus, are poorly addressed, and few population‐based studies explored the HLA‐C variability in the entire gene in different population samples. Here we present a molecular and bioinformatics method to evaluate the entire HLA‐C diversity, including regulatory sequences. Then, we applied this method to survey the HLA‐C diversity in two population samples with different demographic histories, one highly admixed from Brazil with major European contribution, and one from Benin with major African contribution. The HLA‐C promoter and 3′UTR were very polymorphic with the presence of few, but highly divergent haplotypes. These segments also present conserved sequences that are shared among different primate species. Nucleotide diversity was higher in other segments rather than exons 2 and 3, particularly around exon 5 and the second half of the 3′UTR region. We detected evidence of balancing selection on the entire HLA‐C locus and positive selection in the HLA‐C leader peptide, for both populations. HLA‐C motifs previously associated with KIR interaction and expression regulation are similar between both populations. Each allele group is associated with specific regulatory sequences, reflecting the high linkage disequilibrium along the entire HLA‐C locus in both populations.

The strong association of HLA-C*06 allele with disease susceptibility, particularly in early onset psoriasis, indicates that younger ages could be considered to stratify psoriasis into early and late types. TNF -308 polymorphisms can be associated with psoriasis susceptibility and severity. Potential genetic markers of psoriasis in populations with a complex mixture of ethnicities should be investigated.

The HFE molecule controls iron uptake from gut, and defects in the molecule have been associated with iron overload, particularly in hereditary hemochromatosis. The HFE gene including both coding and boundary intronic regions were sequenced in 304 Brazilian individuals, encompassing healthy individuals and patients exhibiting hereditary or acquired iron overload. Six sites of variation were detected: (1) H63D C>G in exon 2, (2) IVS2 (+4) T>C in intron 2, (3) a C>G transversion in intron 3, (4) C282Y G>A in exon 4, (5) IVS4 (-44) T>C in intron 4, and (6) a new guanine deletion (G>del) in intron 5, which were used for haplotype inference. Nine HFE alleles were detected and six of these were officially named on the basis of the HLA Nomenclature, defined by the World Health Organization (WHO) Nomenclature Committee for Factors of the HLA System, and published via the IPD-IMGT/HLA website. Four alleles, HFE*001, *002, *003, and *004 exhibited variation within their exon sequences.

HLA Sequencing Based Typing is an accurate and flexible approach for high-resolution typing. Genotype ambiguities are resolved by allele separation, enabling determination of the cis-trans configuration of polymorphisms.We routinely apply Group Specific Sequencing Primers (GSSP) to selectively sequence one of the two alleles. This approach only needs additional sequencing reactions on the same PCR template, and therefore is easy and quick to apply. SBTengine® facilitates easy analysis of the combined generic and GSSP sequence results.The GSSPs are designed following the criteria that the polymorphic nucleotide positions necessary for allele identification are located upstream the GSSP primers. The resulting sequence determines the cis-trans relations of the critical ambiguous polymorphisms. This approach significantly reduces possibilities for errors, hence the discriminatory polymorphisms are included in the selective primers. In the final allele assignment to resolve the genotype ambiguity the primer sequence and specificity is thus not required.For the three class I loci, release IMGT 2.17.0, the number of pairs of ambiguous genotypes are 889 for HLA-A, 3483 for HLA-B, and 440 for HLA-C. More than 95% can be resolved using GSSPs.Following our criteria the number of GSSPs needed to resolve all these ambiguities are for HLA-A: 20, HLA-B:36, and for HLA-C: 16. This low number of GSSPs can easily be managed in a routine typing laboratory. In combination with the Dynamic Ambiguity Resolving Tool (DART™) feature of SBTengine®, which identifies the GSSPs required for resolving the ambiguity, ambiguities of any kind easily are resolved in daily routine typing practice.

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