Mitochondrial DNA control region diversity in a population from Parana state-increasing the Brazilian forensic database.

The entire mitochondrial DNA (mtDNA) control region (nucleotide position 16024-576) sequences were obtained through Sanger sequencing method for 122 individuals from Parana state, South of Brazil. We observed a total of 108 different haplotypes of which 97 were unique and 11 were shared by more than one individual. The haplogroups were classified according to the updated mtDNA phylogeny, by EMMA (estimating mitochondrial haplogroups using a maximum likelihood approach). Our results revealed the predominance of Amerindian haplogroups with a frequency of 49.2% of the population sample, followed by European lineages with 38.5% and 12.3% of African lineages. Parana population sample set presented a high haplotype diversity (0.9976) and the random match probability was 0.0106. The phylogenetical findings and the diversity indices confirm the high genetic heterogeneity of this population and suggest a high informativeness of mtDNA analyses in forensic cases. The population data will contribute to increase the Brazilian mtDNA database for forensic purposes and it is available through EMPOP (European DNA Profiling Group mitochondrial DNA population database) under the accession number EMP00714.

HLA-G 5' URR SNPs and 3' UTR 14-bp insertion/deletion polymorphism in an Afro-Brazilian population from Paraná State.

The present study investigated 23 SNPs in the 5'URR promoter region and the 14 bp ins/del polymorphism at the 3'UTR region of the HLA-G gene in 150 individuals with Afro-Brazilian ancestry. Three haplotypes were found to be the most frequent. Comparing these polymorphisms in other samples, our data suggest that Afro-Brazilians are more similar to the Euro-Brazilians than to Hutterite population.

Identification of a new HLA-DRB1*11 variant, HLA-DRB1*11:130, by sequence-based typing in a Brazilian individual.

HLA-DRB1*11:130, detected in a Euro-Brazilian female, presents a point mutation at codon 59.3 (GAG→GAC).

HLA class II polymorphisms and recurrent spontaneous abortion in a Southern Brazilian cohort.

A high proportion of human recurrent spontaneous abortions (RSA) remain unexplained. The possible association between RSA and different genetic polymorphisms within the human leucocyte antigen system (HLA system, the human major histocompatibility complex) has been investigated with conflicting results since many decades. Here, we describe a case-control study with 136 Southern Brazilian women of predominantly European ancestry (75 control and 61 cases with unexplained RSA). We investigated the relationship between unexplained RSA and alleles and genotypes from two classical loci of the HLA: HLA-DRB1 and HLA-DQB1, as well as three loci related to cytokine production and their serum levels: TNFA (-308G>A), IL10 (-1082G>A, -819T>C, -592A>C) and IFNG (+874A>T). Genotyping was performed by an allele-specific PCR method. While all results concerning cytokine-related genes turned out to be negative, we found the genotype HLA-DQB1*02:02, 03:01 to be significantly decreased and the allele HLA-DRB1*11:04 to be significantly increased among patients.

HLA-B*18:35, a new HLA-B*18 allele identified by sequence-based typing in a Brazilian volunteer bone marrow donor.

A novel human leukocyte antigen-B allele named B*18:35 was identified in a Brazilian volunteer bone marrow donor.

A new allele, HLA-B*4212, identified in a Brazilian volunteer bone marrow donors by sequence-based typing.

Here we report the discovery of a novel HLA-B allele, named B*4212 in a Brazilian volunteer bone marrow donor. The new sequence has nucleotide variation at position 496 (T→G) as compared with B*4201. This variation results in a conservative amino acid substitution from valine to glycine at codon 165 of exon 3.

A bioinformatics approach to ascertaining the rarity of HLA alleles.

A project of the 15th International Histocompatibility Workshop examined the rarity of human leukocyte antigen (HLA) alleles. A section was constructed in the website, www.allelefrequencies.net to contain this data from different sources. A mechanism to search the data was implemented for use by any individual.

MHC microsatellites in a Southern Brazilian population.

Microsatellites are short tandem repeats of 1-6 bp DNA fragments, which are found throughout the genome. Due to their high levels of polymorphism, many of them are used as markers for population studies. Here we report an investigation on four microsatellites (D6S273, D6S2792, STR_MICA and D6S2810) located within the major histocompatibility complex in a sample of 281 Southern Brazilians of European ancestry. Allelic and haplotypic frequencies are described, as well as linkage disequilibrium (LD) between alleles of these microsatellites and alleles of three HLA genes: HLA-B, HLA-DRB1 and HLA-DQB1. The most polymorphic microsatellite was D6S2810, located close to the HLA-B locus. Strong LD was observed between alleles of microsatellites and HLA genes. The strongest associations occurred among STR_MICA*A5.1-HLA-B*13, STR_MICA*A6-HLA-B*49, STR_MICA*A9-HLA-B*39, STR_MICA*A9-HLAB*57, D6S2810*334-HLA-B*14, D6S2810*334-HLA-B*38, STR_MICA*A5.1-HLA-DRB1*1501-HLA-DQB1*0602 and D6S2810*344-HLA-DRB1*0411-HLA-DQB1*0302. This study contributes with important information on HLA haplotypes, and is potentially useful in resolving cases of low resolution HLA genotyping ambiguities.

High frequencies of alleles MICA*020 and MICA*027 in Amerindians and evidence of positive selection on exon 3.

MICA is a nonclassical polymorphic MHC molecule. We investigated MICA allelic frequencies and MICA-HLA-B-HLA-C haplotypes in Brazilian Amerindians to describe the polymorphism and to extract information about the evolution of MICA gene. Kaingang is the first population described to have a high frequency of MICA*020, found associated with HLA-B*3505-HLA-Cw*0401. Allele MICA*020 probably originated de novo in South America. The Guarani population had high frequencies of MICA*027. Allele MICA*00801 is common worldwide but rare among Amerindians, occurring only because of gene flow. The analysis of the 64 described MICA alleles revealed that in exons 2 and 4, synonymous substitutions are in excess, a result compatible with purifying selection. The opposite was observed for exons 3 and 6 and the excess of nonsynonymous substitutions was significant for exon 3, indicating positive selection. Few of the alleles described so far had exon 6 sequenced, impeding conclusions for the corresponding portion of the molecule. The analysis of the entire gene is required for a better understanding of the evolution of MICA's polymorphism and its functional consequences. This knowledge is of prime importance in view of the increasing awareness of the functional and medical implications of MICA gene variability.

Major histocompatibility complex class I chain-related gene A polymorphism and linkage disequilibrium with HLA-B alleles in Euro-Brazilians.

Major histocompatibility complex class I chain-related gene A (MICA) was identified within the human leukocyte antigen (HLA) class I region and was located 46 kb centromeric from HLA-B locus. It functions as a ligand for human gammadelta T, CD8 T and natural killer (NK) cells by binding the NKG2D receptor. The aims of the present study were to determine the distribution of MICA alleles and MICA-HLA-B haplotypes in a sample of Euro-Brazilians. Through the combination of three typing methods, polymerase chain reaction (PCR)-sequence-specific oligonucleotide probe, PCR-sequence-specific primer and PCR-restriction fragment length polymorphism, 19 alleles were detected besides a MICA gene deletion in a sample composed by 204 unrelated Euro-Brazilians. The most commonly observed alleles were: MICA*00801 (25.3%), MICA*00201 (17.7%) and MICA*00901 (13.7%). The GCT repeat polymorphism variant A6 was the most commonly found. The most frequent haplotype found in this study was MICA*00901-B*51 (8.1%), followed by haplotypes MICA*00201-B*35 (6.1%) and MICA*00801-B*07 (6.1%). MICA*00801 truncated product, and its low affinity for NKG2D receptor may work as an inhibitor in its putative soluble form. It may also be that selective forces may favor MICA*00801 heterozygosity with NKG2D high affinity MICA alleles enabling activation and inhibition of cytotoxic activity of cells expressing the NKG2D receptor. The possibility of selective neutrality or of balancing selection still provides no explanation for MICA gene polymorphisms. Is it maintained by genetic drift or by the influence of migratory waves? Are there favored alleles while others present the same adaptive value?

CYP1A1 and GSTP1 polymorphisms in an oral cancer case-control study.

CYP1A1 and GSTP1 polymorphisms have been associated with a higher risk to develop several cancers, including oral squamous cell carcinoma (OSCC), which is closely related to tobacco and alcohol consumption. Both genes code for enzymes that have an important role in activating or detoxifying carcinogenic elements found in tobacco and other compounds, and polymorphic variants of these genes may result in alterations of the enzymatic activity. The CYP1A1 gene codes for the enzyme aryl hydrocarbon hydroxylase, which is responsible for the metabolism of polycyclic aromatic hydrocarbons. The investigated polymorphism, Ile/Val, seems to increase the activity of the enzyme in homozygous individuals, leading to an accumulation of carcinogens. The Ile/Val polymorphism occurs because of an A->G transition at exon 7, resulting in the CYP1A1*2B allele. The GSTP1*B variant shows an A->G transition at exon 5, changing the amino acid Ile to Val, with a reduced catalytic activity of the enzyme. Due to this reduction, the carriers of mutant alleles lost the capability to metabolize carcinogens, which could be responsible for a higher susceptibility to cancer. We conducted a case-control study in a group of 72 cases with newly diagnosed OSCC and 60 healthy controls matched for age, gender, smoking habits, and ethnicity. We used PCR methods to identify the allelic variants CYP1A1*2B and GSTP1*B. The data obtained showed no statistically significant association of allelic or genotypic variants of CYP1A1*2B (OR = 1.06; 95% CI = 0.49-2.29) and GSTP1*B (OR = 1.40; 95% CI = 0.70-2.79) with OSCC.

Frequencies at three polymorphic sites of interleukin-10 gene promoter in Brazilian renal recipients.

We genotyped by PCR-RFLP 141 renal patients (77 men and 64 women with ages between 12 and 58, predominantly Caucasians) for allelic variants of three polymorphic sites of the interleukin-10 gene promoter, previously showed to be associated with different production of IL-10 cytokine: -1082 (G/A), -819 (C/T), and -592 (C/A). These polymorphisms may confer flexibility in the common immune responses and influence the outcome of allo-responses after transplantation. Our aim was to determine the frequencies of three functional polymorphic sites -1082, -819, and -592 of the interleukin-10 gene promoter in renal recipients of Curitiba, Paraná. Paraná State is located in southern Brazil, and its capital is Curitiba with approximately 1.5 million inhabitants. Genotypes were classified as follows: "low" IL-10 producer genotypes (ATA/ATA, ACC/ATA, ACC/ACC), "intermediate" genotypes (GCC/ACC, GCC/ATA), and "high" IL-10 producer genotype (GCC/GCC). In our population we observed linkage disequilibrium between alleles -819C and -592C and this haplotypic combination was more frequent (65%) than -819T and -592A. We found significantly reduced frequency of the genotype and haplotype responsible for high production of interleukin-10, maybe because we have a selected group (only renal patients) or maybe because Brazilian people are very heterogeneous (miscegenational), which may differ from other groups.

CYP1A1 and GSTP1 polymorphisms in an oral cancer case-control study

CYP1A1 and GSTP1 polymorphisms have been associated with a higher risk to develop several cancers, including oral squamous cell carcinoma (OSCC), which is closely related to tobacco and alcohol consumption. Both genes code for enzymes that have an important role in activating or detoxifying carcinogenic elements found in tobacco and other compounds, and polymorphic variants of these genes may result in alterations of the enzymatic activity. The CYP1A1 gene codes for the enzyme aryl hydrocarbon hydroxylase, which is responsible for the metabolism of polycyclic aromatic hydrocarbons. The investigated polymorphism, Ile/Val, seems to increase the activity of the enzyme in homozygous individuals, leading to an accumulation of carcinogens. The Ile/Val polymorphism occurs because of an A->G transition at exon 7, resulting in the CYP1A1*2B allele. The GSTP1*B variant shows an A->G transition at exon 5, changing the amino acid Ile to Val, with a reduced catalytic activity of the enzyme. Due to this reduction, the carriers of mutant alleles lost the capability to metabolize carcinogens, which could be responsible for a higher susceptibility to cancer. We conducted a case-control study in a group of 72 cases with newly diagnosed OSCC and 60 healthy controls matched for age, gender, smoking habits, and ethnicity. We used PCR methods to identify the allelic variants CYP1A1*2B and GSTP1*B. The data obtained showed no statistically significant association of allelic or genotypic variants of CYP1A1*2B (OR = 1.06; 95 percent CI = 0.49-2.29) and GSTP1*B (OR = 1.40; 95 percent CI = 0.70-2.79) with OSCC.