A study of GJB2 and delGJB6-D13S1830 mutations in Brazilian non-syndromic deaf children from the Amazon region.

UNLABELLED: Hearing impairment affects about 1 in 1000 newborns. Mutations in the connexin 26 (GJB2) gene rank among the most frequent causes of non-syndromic deafness in different populations, while delGJB6-D13S1830 mutation located in the DFNB30 locus is known to cause sensorineural hearing loss. Despite the many studies on the involvement of GJB2 mutations in hearing impairment in different populations, there is little information on genetic deafness in Brazil, especially in the Amazon region. OBJECTIVE: To determine the prevalence of GJB2 mutations and delGJB6-D13S1830 in 77 sporadic non-syndromic deaf patients. METHOD: The coding region of the GJB2 gene was sequenced and polymerase chain reaction was performed to detect the delGJB6-D13S1830 mutation. RESULTS: Mutant allele 35delG was found in 9% of the patients (7/77). Mutations M34T and V95M were detected in two distinct heterozygous patients. Non-pathogenic mutation V27I was detected in 28.6% of the patients (22/77). None of the deaf patients carried the delGJB6-D13S1830 mutation. CONCLUSION: Mutant alleles on gene GJB2 were observed in 40% (31/77) of the subjects in the sample. Pathogenic variants were detected in only 12% (9/77) of the individuals. More studies are required to elucidate the genetic causes of hearing loss in miscegenated populations.

Estudo de mutações no gene GJB2 e deleção delGJB6-D13S1830 em indivíduos com surdez não sindrômica da região Amazônica / A study of GJB2 and delGJB6-D13S1830 mutations in Brazilian non-syndromic deaf children from the Amazon region

A deficiência auditiva afeta cerca de 1 em cada 1000 recém-nascidos. Mutações no gene da conexina 26 (GJB2) são as causas mais frequentes de surdez não sindrômica em diferentes populações e é sabido que a mutação delGJB6-D13S1830 em DFNB30 é causadora de surdez neurossensorial. Muitos estudos descrevem o envolvimento de mutações no gene GJB2 com a deficiência auditiva em diferentes populações. Entretanto, existe pouca informação sobre a surdez genética no Brasil, especialmente na região Amazônica. OBJETIVO: Determinar a prevalência de mutações no gene GJB2 e da mutação delGJB6-D13S1830 em 77 casos esporádicos de surdez não sindrômicas. MÉTODO: A região codificante do gene GJB2 foi sequenciada e a PCR foi realizada para detectar a mutação delGJB6-D13S1830. RESULTADOS: O alelo 35delG foi encontrado em 9% dos pacientes (7/77). As mutações M34T e V95M foram detectadas em dois distintos pacientes heterozigotos. A mutação não patogênica V27I foi detectada em 28,6% (22/77). Não foi detectada a mutação delGJB6-D13S1830 em nenhum paciente estudado. CONCLUSÃO: Alelos mutantes no gene GJB2 foram observados em 40% (31/77) da amostra. Variantes patogênicas foram detectadas em apenas 12% (9/77). Mais estudos são necessários para elucidar causas genéticas de deficiência auditiva em populações miscigenadas.

Hearing impairment affects about 1 in 1000 newborns. Mutations in the connexin 26 (GJB2) gene rank among the most frequent causes of non-syndromic deafness in different populations, while delGJB6-D13S1830 mutation located in the DFNB30 locus is known to cause sensorineural hearing loss. Despite the many studies on the involvement of GJB2 mutations in hearing impairment in different populations, there is little information on genetic deafness in Brazil, especially in the Amazon region. OBJECTIVE: To determine the prevalence of GJB2 mutations and delGJB6-D13S1830 in 77 sporadic non-syndromic deaf patients. METHOD: The coding region of the GJB2 gene was sequenced and polymerase chain reaction was performed to detect the delGJB6-D13S1830 mutation. RESULTS: Mutant allele 35delG was found in 9% of the patients (7/77). Mutations M34T and V95M were detected in two distinct heterozygous patients. Non-pathogenic mutation V27I was detected in 28.6% of the patients (22/77). None of the deaf patients carried the delGJB6-D13S1830 mutation. CONCLUSION: Mutant alleles on gene GJB2 were observed in 40% (31/77) of the subjects in the sample. Pathogenic variants were detected in only 12% (9/77) of the individuals. More studies are required to elucidate the genetic causes of hearing loss in miscegenated populations.

Insertion-deletion polymorphisms--utilization on forensic analysis.

Insertion-deletion (INDEL) markers are very frequent in the human genome and present several advantages for population and forensic studies, such as low mutation rates, easy interpretation, small amplicons, easy genotyping, and the possibility of using multiplex PCR. The great adaptability of INDELs for amplification of low copy number or degraded DNA allows its using as an interesting platform of genetic identity by DNA in forensic cases. In the present study, we tested the ability of 48 diallelic INDEL markers on genotyping forensic samples collected from different biological samples related to criminal cases. Moreover, we evaluated the lowest DNA concentration with which there was amplification of all markers from each one of three indel-plex panels. When comparing the performances obtained by the indel-plex panels described in this study with results obtained using Identifiler® kit (Applied Biosystems) related to forensic samples, as well as to control samples with different concentrations of DNA, we observed superior efficiency on samples with low copy number or in the presence of inhibitors.

Allelic frequencies and statistical data obtained from 12 codis STR loci in an admixed population of the Brazilian Amazon.

The allelic frequencies of 12 short tandem repeat loci were obtained from a sample of 307 unrelated individuals living in Macapá, a city in the northern Amazon region, Brazil. These loci are the most commonly used in forensics and paternity testing. Based on the allele frequency obtained for the population of Macapá, we estimated an interethnic admixture for the three parental groups (European, Native American and African) of, respectively, 46%, 35% and 19%. Comparing these allele frequencies with those of other Brazilian populations and of the Iberian Peninsula population, no significant distances were observed. The interpopulation genetic distances (F(ST) coefficients) to the present database ranged from F(ST) = 0.0016 between Macapá and Belém to F(ST) = 0.0036 between Macapá and the Iberian Peninsula.

Allelic frequencies and statistical data obtained from 12 codis STR loci in an admixed population of the Brazilian Amazon

The allelic frequencies of 12 short tandem repeat loci were obtained from a sample of 307 unrelated individuals living in Macapá, a city in the northern Amazon region, Brazil. These loci are the most commonly used in forensics and paternity testing. Based on the allele frequency obtained for the population of Macapá, we estimated an interethnic admixture for the three parental groups (European, Native American and African) of, respectively, 46 percent, 35 percent and 19 percent. Comparing these allele frequencies with those of other Brazilian populations and of the Iberian Peninsula population, no significant distances were observed. The interpopulation genetic distances (F ST coefficients) to the present database ranged from F ST = 0.0016 between Macapá and Belém to F ST = 0.0036 between Macapá and the Iberian Peninsula.

Estimates of interethnic admixture in the Brazilian population using a panel of 24 X-linked insertion/deletion markers.

OBJECTIVES: In this study, we aimed to identify ancestry informative haplotypes and make interethnic admixture estimates using X-chromosome markers. METHODS: A significant sample (461 individuals) of European, African, and Native American populations was analyzed, and four linkage groups were identified. The data obtained were used to describe the ancestral contribution of populations from four different geographical regions of Brazil (745 individuals). RESULTS: The global interethnic admixture estimates of the four mixed populations under investigation were calculated applying all the 24 insertion/deletion (INDEL) markers. In the North region, a larger Native Americans ancestry was observed (42%). The Northeast and Southeast regions had smaller Native American contribution (27% in both of them). In the South region, there was a large European contribution (46%). CONCLUSIONS: The estimates obtained are compatible with expectations for a colonization model with biased admixture between European men (one X chromosome) and Native American and African women (two X chromosomes), so the 24 X-INDEL panel described here can be a useful to make admixture interethnic estimates in Brazilian populations.

Y-STR haplotypes of Native American populations from the Brazilian Amazon region.

The allele and haplotype frequencies of nine Y-STRs (DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393, DYS385 I/II) were determined in a sample of six native tribes from the Brazilian Amazon (Tiriyó, Awa-Guajá, Waiãpi, Urubu-Kaapor, Zoé and Parakanã). Forty-eight different haplotypes were identified, 28 of which unique. Five haplotypes are very frequent and were shared by over 10 individuals. The estimated haplotype diversity (0.9114) was very low compared to other geographic groups, including Africans, Europeans and Asians.

Genetic data of twelve X-STRs in a Japanese immigrant population resident in Brazil.

In the last years, several works have been published on the variability of X-markers; however, few were on Asian populations. In this work, we present the genetic data of 12 X-STRs (DXS9895, DXS7132, DXS6800, DXS9898, DXS6789, DXS7133, GATA172D05, DXS7130, HPRTB, GATA31E08, DXS7423, DXS10011) obtained from a sample of 232 individuals of Japanese origin residing in Brazil. Most markers investigated present a high genetic diversity, with the exception of DXS6800. No deviations from Hardy-Weinberg equilibrium were observed, with the exception of DXS7133 locus. Linkage disequilibrium analysis did not reveal consistent evidence of association between the X-STRs used. The comparison of the Japanese immigrant population with other Asian populations (Japanese, Chinese, and Korean) demonstrates the inexistence of significant allelic frequency differences between these populations in most systems investigated.

An INDEL polymorphism at the X-STR GATA172D05 flanking region.

A new polymorphic INDEL was detected at the X-STR GATA172D05 flanking region, which corresponds to an 18-bp deletion, 141 bp upstream the TAGA repeat motif. This INDEL was found to be polymorphic in different population samples from Native Americans, Africans, and Europeans as well as in an admixed population from the Amazonia (Belém). Gene diversities varied between 37.5% in Native Americans and 49.9% in Africans. Comparison between human and chimpanzee sequences showed that the ancestral state corresponds to the presence of two copies of 18 bp, detected in both species; and the mutated allele has lost one of these two copies. The simultaneous analysis of the short tandem repeat (STR) and INDEL variation showed an association between the INDEL ancestral allele with the shorter STR alleles. High diversities were found in all population groups when combining the information provided by the INDEL and STR variation. Gene diversities varied between 76.7% in Native Americans and 80.6% in both Portugal and Belém.

Allele frequencies data and statistic parameters for 13 STR loci in a population of the Brazilian Amazon Region.

Allele frequencies for 13 short tandem repeat (D3S1358, vWA, D21S11, D18S51, D5S818, D13S317, D7S820, TH01, TPOX, D16S539, CSF1PO, D8S1179 and FGA) loci were determined in a sample of 325 unrelated individuals from the population of the Amazon of Belém, Brazil. These loci are the most commonly used in forensic and paternity testing. The forensic parameters investigated presented high values. The power of discrimination and the probability of exclusion for these 13 STRs are 99.999999999992% and 99.9998%, respectively. In conclusion, these 13 markers are suitable for forensic analysis and paternity tests of the Amazonian population.

Y-chromosomal STR haplotypes in a population from the Amazon region, Brazil.

Haplotype and allele frequencies of the nine Y-STR (DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393, DYS385 I/II) were determined in a population sample of 200 unrelated males from Belém, Brazil. The most common haplotypes are shared by 1.5% of the sample, while 186 haplotypes are unique. The haplotype diversity is 0.9995+/-0.0006. The data obtained were compared to those of other Brazilian populations. AMOVA indicates that 99.91% of all the haplotypical variation is found within geopolitical regions and only 0.09% is found among regions.