Rodrigo S. Moura-Neto

Color and genomic ancestry in Brazilians: a study with forensic microsatellites.

The population of Brazil, formed by extensive admixture between Amerindians, Europeans and Africans, is one of the most variable in the world. We have recently published a study that used ancestry-informative markers to conclude that in Brazil, at an individual level, color, as determined by physical evaluation, was a poor predictor of genomic ancestry, estimated by molecular markers. To corroborate these findings we undertook the present investigation based on data from 12 commercially available forensic microsatellites that were utilized to estimate the personal genomic origin for each of 752 individuals from the city of São Paulo, belonging to different Brazilian color categories (275 Whites, 192 Intermediates and 285 Blacks). The genotypes permitted the calculation of a personal likelihood-ratio estimator of African or European ancestry. Although the 12 marker set proved capable of discriminating between European and African individuals, we observed very significant overlaps among the three color categories of Brazilians. This was confirmed quantitatively using a Bayesian analysis of population structure that did not demonstrate significant genetic differentiation between the three color groups. These results corroborate and validate our previous conclusions using ancestry-informative markers that in Brazil at the individual level there is significant dissociation of color and genomic ancestry.

DGGE analysis as a tool to identify point mutations, de novo mutations and carriers of the dystrophin gene

Approximately 30% of Duchenne muscular dystrophy patients have undefined mutations in the dystrophin gene and it is difficult to identify single nucleotide variations in genomic DNA using current diagnostic techniques. This represents a great obstacle in genetic analysis of these patients and genetic counselling of their families. In this work we performed denaturing gradient gel electrophoresis analysis to search for Duchenne muscular dystrophy mutations. We screened the whole dystrophin gene in 20 Brazilian Duchenne muscular dystrophy patients without a detectable deletion or duplication, and their mothers. The disease causing mutations, all of which have not been described before, were identified, and we could determine the carrier status of the mothers in all analyzed families. We concluded that denaturing gradient gel electrophoresis is very efficient in identifying small mutations and de novo mutations and in determining the carrier status of the mothers in these 30% of Duchenne muscular dystrophy patients. Denaturing gradient gel electrophoresis showed a high mutation detection rate (100%) for Duchenne muscular dystrophy and can be used as a current diagnostic procedure.

Genetic data on 12 STRs (F13A01, F13B, FESFPS, LPL, CSF1PO, TPOX, TH01, vWA, D16S539, D7S820, D13S317, D5S818) from four ethnic groups of São Paulo, Brazil

Allelic frequencies for 12 short tandem repeats (STRs) (F13A01, F13B, FESFPS, LPL, CSF1PO, TPOX, TH01, vWA, D16S539, D7S820, D13S317 and D5S818) were estimated, also as forensic parameters, from a sample of 916 unrelated Brazilian subjects classified into four ethnic groups: European-derived, African-derived, Brazilian Mulattos and Asian-derived.

Análise combinada de fatores genéticos e ambientais na hipertensão essencial em um município da região Amazônica

OBJECTIVE In the present study, we evaluated the contribution of six genetic polymorphisms of the Renin-Angiotensis-Aldosterone system (RAAS) and clinical risk factors in the development of essential hypertension in a Brazilian rural population in the Amazon region. METHODS Eighty-two hypertensive patients and seventy-eight normotensive individuals were evaluated. Genotyping for renin (REN G1051A), angiotensinogen (AGT) M235T, insertion/deletion of angiotensin-converting enzyme (ACE I/D), angiotensin II type 1 receptor (AGTR1) A1166C and aldosterone synthase (CYP11B2) C344T polymorphisms were performed using polymerase chain reaction, with further restriction analysis when required. The influence of genetic polymorphisms and clinical risk factors on blood pressure variation was assessed by stepwise linear regression. RESULTS We report the co-occurrence of clinical risk factors and angiotensin-converting enzyme (ACE) gene polymorphism in a Brazilian rural population in the Amazon region. Our results indicate that increase of systolic blood pressure (SBP) is favored by ACE I/D- D allele and advanced age, while alcohol consumption and aging are associated with high diastolic blood pressure (DBP). CONCLUSION These findings suggest that in the Santa Isabel do Rio Negro population, the residents that carry ACE-D allele or have an alcohol consumption habit present higher values of SBP and DBP, respectively, with the passing of years.

Control of tubulin gene expression during metacyclogenesis of Trypanosoma cruzi

During differentiation of the dividing epimastigote to the non‐dividing metacyclic trypomastigote form of the parasitic protozoan Trypanosoma cruzi there is a marked reduction in the rate of synthesis of the major proteins α‐ and β‐tubulin. Our results indicate that the control of synthesis of these proteins during the differentiation event is exerted at the level of α‐ and β‐tubulin mRNA accumulation.

Population genetic analyses of the AmpFlSTR ® NGM™ in Brazil

Population data of 15 short tandem repeat loci of the AmpFlSTR® next generation multiplex (NGM)™ were obtained from a sample of 835 individuals. The loci are the ten short tandem repeats (STRs) in the SGM Plus® Kit plus the EDNAP- and ENSFI-recommended STRs D10S1248, D22S1045, D2S441, D1S1656, and D12S391. Allele frequency and other forensically relevant statistics data were generated for the NGM loci into five current country macroregions of Brazil (North, Northeast, Central West, Southeast, and South). All the analyzed loci meet Hardy–Weinberg equilibrium expectations and no linkage disequilibrium in all pairs of loci. The observed and expected heterozygosity, power of discrimination, polymorphic information content, and the other population–genetic indices were calculated. The overall power of discrimination was greater than 0.99999999999999999996 and the combined power of exclusion was greater than 0.9999998 in all Brazilian populations. Comparative analysis between populations from different Brazilian macroregions as well as between Brazil and Caucasian, African Americans, and Hispanic US populations are presented.

Genetic data on 15 STR autosomal loci for a sample population of the Northern Region of the State of Rio de Janeiro, Brazil

Allele frequencies data, paternity and forensic parameters for 15 autosomal short tandem repeat (STR) autosomal markers (D8S1179, D21S11, D7S820, CSF1PO, D5S818, D3S1358, TH01, D13S317, D16S539, D2S1338, TPOX, D19S433, vWA, D18S51, FGA) were determined for a sample of 494 unrelated individuals undergoing kinship analysis and molecular cytogenetic testing from the population of the city of Campos dos Goytacazes, Northern State of Rio de Janeiro, Brazil. The loci with the highest polymorphism information content were D18S51 (0.874), D2S1338 (0.853), FGA (0.852), D21S11 (0.838). The combined power of discrimination and the combined power of exclusion were 0.999999999999999 and 0.999526684, respectively. At the available common loci CSF1PO, TH01, TPOX, vWA, D16S539, D7S820 and D13S317, allele frequencies were compared with population databases from State of Alagoas, State of Amazonas, State of São Paulo (Brazilian mulattoes, descendants of Europeans, Africans or Asians), State of Mato Grosso do Sul and State of Rio de Janeiro. No significant distances were observed. The interpopulation genetic distance (Fst coefficients) to the present database, ranged 0.0022 (p=0.446) (Northern State Rio de Janeiro-State of São Paulo European-descendants) to 0.0138 (p=0.993) (Northern State Rio de Janeiro-State of São Paulo Asian-descendants). The Asian-descendants Brazilians are the least admixed. All other groups are admixed as one unique population.

Malignant peripheral nerve sheath tumors: clinicopathological aspects, expression of p53 and survival

Malignant peripheral nerve sheath tumors (MPNSTs) arerare and highly aggressive neoplasms, representing only 5%of soft tissue sarcomas (1,2). Approximately half of MPNSTcases occur in association with neurofibromatosis type 1(NF1) (3). MPNSTs may appear de novo or develop from themalignant transformation of a benign neural neoplasm,generally a plexiform neurofibroma (1). Solitary (unasso-ciated with NF1) and localized (or discrete; multiple in NF1)neurofibromas do not have malignant transformationpotential (1,3). NF1 loss of heterozygosity (LOH) has beendemonstrated in NF1-associated and sporadic MPNSTs.Although NF1 LOH is believed to be sufficient for neu-rofibroma development, MPNST pathogenesis has beensuggested to be a multistage process that includes othermolecular alterations (4,5). TP53 mutations have been foundin a subgroup of MPNSTs, indicating that a p53-mediatedpathway is involved in their development (5,6).Some clinicopathological features (e.g., the presence ofNF1,high histologicalgrade,necrosis,andrhabdomyoblasticdifferentiation) have been indicated to be important factorsforlower survival in MPNST cases in some studies butnotinothers (2,7–10). The clinical significance of p53 expression inMPNSTs is also a controversial issue. We aimed to study p53expression in MPNSTs and investigate its impact, as well astheimpactsoftheclinicopathologicalfeaturesofMPNSTs,onthe survival rates. We also compared p53 expression inMPNSTswith theirclinicopathological features and with p53expression in neurofibromas.

Selection of highly informative SNP markers for population affiliation of major US populations

Ancestry informative markers (AIMs) can be used to detect and adjust for population stratification and predict the ancestry of the source of an evidence sample. Autosomal single nucleotide polymorphisms (SNPs) are the best candidates for AIMs. It is essential to identify the most informative AIM SNPs across relevant populations. Several informativeness measures for ancestry estimation have been used for AIMs selection: absolute allele frequency differences (δ), F statistics (FST), and informativeness for assignment measure (In). However, their efficacy has not been compared objectively, particularly for determining affiliations of major US populations. In this study, these three measures were directly compared for AIMs selection among four major US populations, i.e., African American, Caucasian, East Asian, and Hispanic American. The results showed that the FST panel performed slightly better for population resolution based on principal component analysis (PCA) clustering than did the δ panel and both performed better than the In panel. Therefore, the 23 AIMs selected by the FST measure were used to characterize the four major American populations. Genotype data of nine sample populations were used to evaluate the efficiency of the 23-AIMs panel. The results indicated that individuals could be correctly assigned to the major population categories. Our AIMs panel could contribute to the candidate pool of AIMs for potential forensic identification purposes.

Epidermal growth factor receptor gene polymorphisms are associated with prognostic features of breast cancer

BackgroundThe epidermal growth factor receptor (EGFR) is differently expressed in breast cancer, and its presence may favor cancer progression. We hypothesized that two EGFR functional polymorphisms, a (CA)n repeat in intron 1, and a single nucleotide polymorphism, R497K, may affect EGFR expression and breast cancer clinical profile.MethodsThe study population consisted of 508 Brazilian women with unilateral breast cancer, and no distant metastases. Patients were genotyped for the (CA)n and R497K polymorphisms, and the associations between (CA)n polymorphism and EGFR transcript levels (n = 129), or between either polymorphism and histopathological features (n = 505) were evaluated. The REMARK criteria of tumor marker evaluation were followed.Results(CA)n lengths ranged from 14 to 24 repeats, comprehending 11 alleles and 37 genotypes. The most frequent allele was (CA)16 (0.43; 95% CI = 0.40–0.46), which was set as the cut-off length to define the Short allele. Variant (CA)n genotypes had no significant effect in tumoral EGFR mRNA levels, but patients with two (CA)n Long alleles showed lower chances of being negative for progesterone receptor (ORadjusted = 0.42; 95% CI = 0.19–0.91). The evaluation of R497K polymorphism indicated a frequency of 0.21 (95% CI = 0.19 – 0.24) for the variant (Lys) allele. Patients with variant R497K genotypes presented lower proportion of worse lymph node status (pN2 or pN3) when compared to the reference genotype Arg/Arg (ORadjusted = 0.32; 95% CI = 0.17–0.59), which resulted in lower tumor staging (ORadjusted = 0.34; 95% CI = 0.19-0.63), and lower estimated recurrence risk (OR = 0.50; 95% CI = 0.30-0.81). The combined presence of both EGFR polymorphisms (Lys allele of R497K and Long/Long (CA)n) resulted in lower TNM status (ORadjusted = 0.22; 95% CI = 0.07-0.75) and lower ERR (OR = 0.25; 95% CI = 0.09-0.71). When tumors were stratified according to biological classification, the favorable effects of variant EGFR polymorphisms were preserved for luminal A tumors, but not for other subtypes.ConclusionsThe data suggest that the presence of the variant forms of EGFR polymorphisms may lead to better prognosis in breast cancer, especially in patients with luminal A tumors.