Aplicação de microssatélites (STR) de bovinos em animais de raças zebuínas

O gado zebu (Bos indicus) é predominante em todo o mundo. Atualmente, no Brasil, o rebanho de bovinos e zebuínos é composto por aproximadamente 170 milhões de indivíduos, no qual, 80% são zebuínos ou animais de raças cruzadas com zebu. O principal objetivo deste estudo foi determinar a possibilidade da utilização de marcadores moleculares de bovinos na identificação genética de zebuínos. A confirmação desta possibilidade seria de extrema valia, já que a quantidade de informações sobre o genoma zebuíno é limitada e metodologias específicas de identificação de marcadores genéticos para raças zebuínas são raras. Assim, o DNA de 65 zebus, de 4 raças diferentes (Gir, Tabapuã, Nelore e Brahman), foi extraído a partir de sangue aplicado em papel filtro, utilizando o “kit” DNA IQTM SYSTEM (Promega®). Após a extração de DNA, foi feito um PCR Multiplex utilizando o “kit” StockMarks® (Applied Biosystems®), o qual amplifica um total de 11 loci (BM1824, BM2113, ETH10, ETH225, ETH3, INRA023, SPS115, TGLA122, TGLA126, TGLA227 e TGLA53). Os fragmentos gerados pela PCR foram analisados por eletroforese capilar utilizando o analisador genético ABI Prism 3100 (Applied Biosystems®) e o programa GeneScan® v.3.7 (Applied Biosystems®). A freqüência dos marcadores e os índices de variabilidade genética foram calculados utilizando o programa Microsatellite Toolkit v.3.1 e o equilíbrio de Hardy-Weinberg foi determinado através do programa GENEPOP v.3.4. Através destas técnicas foi possível demonstrar que os marcadores moleculares utilizados para identificação genética de bovinos podem também ser utilizados para a realização da técnica de identificação genética de zebuínos Além disso, foi possível demonstrar a freqüência alélica na população de zebuínos analisada como um todo, assim como foi determinada a freqüência alélica para os diferentes marcadores moleculares dentro das 4 raças estudas. Considerando o total de 100 diferentes alelos identificados entre os 11 STR (Short Tandem Repeats) analisados, foi possível observar que a heterozigosidade esperada (He) foi relativamente alta na população analisada, assim como na análise por raça. Estes dados indicam alto grau de diversidade genética nas diferentes raças. Neste sentido, a raça Brahman apresentou a menor diversidade (0,60) e a raça Tabapuã, a maior (0,69). Contudo, estudos complementares são necessários, a fim de confirmar as freqüências alélicas estabelecidas, uma vez que os resultados encontrados no presente trabalho referem-se a um número relativamente pequeno de zebuínos, quando comparados com o total de zebus encontrados no rebanho brasileiro.

Análise da frequência alélica de 15 LOCI STR na população do Rio Grande do Norte

Human population have a significant number of polymorphic loci, whose use and applications range from construction of linkage maps, to study the evolution of populations, through the determination of paternity, forensic medicine and migration. Currently, STRs (Short Tanden Repeats) markers are considered the major markers for human identification, mainly due to its abundance and high variability because of the fact that they are easily amplifiable by PCR (Polymerase Chain Reaction), work with low amounts of DNA and be capable of automation processes involving fluorescence detection. The creation of regional databases containing allele frequencies of population provide subsidies to increase the reliability of the results of determining the genetic link. This paper aims to obtain a database of allele frequencies of 15 polymorphic molecular loci (D8S1179, D21S11, D7S820, CSF1PO, D19S433, vWA, TPOX, D18S51, D3S1358, TH01, D13S317, D16S539, D2S1338, D5S818 e FGA) in a population classifies as born in the State of Rio Grande do Norte, Brazil, totaling 1100 unrelated individuals. To evaluate the frequency, DNA samples were submitted to PCR amplification, followed by capilarry electrophoresis genetic sequencer. The frequencies identified in this study were compared with brazilian population in general and other states in Brazil. Except for the loci D21S11, D19S433 and D2D1338, the genotypes found were in Hardy-Weinberg equilibrium and no significant differences among the frequencies were found in the populations studied. The most informative loci was D2S1338 and D18S51, and the less informative is the locus TPOX

X-chromosome genetic variation in São Paulo State (Brazil) population

As data on X-chromosomal short tandem repeats (X-STRs) for the Brazilian population are scarse, the aim of this study was to determine the allele frequencies of five X-STRs (DXS6854, DXS7424, DXS101, DXS6808 and DXS7132) in the São Paulo State, Brazil. No deviations from the Hardy-Weinberg equilibrium were observed, with the exception of DXS101. The forensic efficiency parameters demonstrated that DXS101 was the most informative marker. Population comparisons revealed that the X-STR profile sampled in the state of São Paulo was more similar to European and African populations than Asiatic populations reported in this work.

Polymorphisms in the AR and PSA Genes as Markers of Susceptibility and Aggressiveness in Prostate Cancer

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Genetic profile characterization of 10 X-STRs in four populations of the southeastern region of Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genetic data of 15 autosomal STR loci: an analysis of the Araraquara population colonization (São Paulo, Brazil)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genetic population data of 12 STR loci of the PowerPlex (R) Y system in the state of São Paulo population (Southeast of Brazil)

Allele frequency distributions and population data for 12 Y-chromosomal short tandem repeats (STRs) included in the PowerPlex (R) Y Systems (Promega) were obtained for a sample of 200 healthy unrelated males living in S (a) over tildeo Paulo State (Southeast of Brazil). A total of 192 haplotypes were identified, of which 184 were unique and 8 were found in 2 individuals. The average gene diversity of the 12 Y-STR was 0.6746 and the haplotype diversity was 0.9996. Pairwise analysis confirmed that our population is more similar with the Italy, North Portugal and Spain, being more distant of the Japan. (c) 2007 Elsevier B.V. All rights reserved.

A GEP-ISFG collaborative study on the optimization of an X-STR decaplex: data on 15 Iberian and Latin American populations

In a collaborative work carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG), a polymerase chain reaction multiplex was optimized in order to type ten X-chromosome short tandem repeats (STRs) in a single reaction, including: DXS8378, DXS9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7133, GATA172D05, GATA31E08, and DXS7423. Using this X-decaplex, each 17 of the participating laboratories typed a population sample of approximately 200 unrelated individuals (100 males and 100 females). In this work, we report the allele frequencies for the ten X-STRs in 15 samples from Argentina (Buenos Aires, CA(3)rdoba, Rio Negro, Entre Rios, and Misiones), Brazil (SA o pound Paulo, Rio de Janeiro, Parana, and Mato Grosso do Sul), Colombia (Antioquia), Costa Rica, Portugal (Northern and Central regions), and Spain (Galicia and Cantabria). Gene diversities were calculated for the ten markers in each population and all values were above 56%. The average diversity per locus varied between 66%, for DXS7133, and 82%, for DXS6809. For this set of STRs, a high discrimination power was obtained in all populations, both in males (a parts per thousand yen1 in 5 A- 10(5)) and females (a parts per thousand yen1 in 3 A- 10(9)), as well as high mean exclusion chance in father/daughter duos (a parts per thousand yen99.953%) and in father/mother/daughter trios (a parts per thousand yen99.999%). Genetic distance analysis showed no significant differences between northern and central Portugal or between the two Spanish samples from Galicia and Cantabria. Inside Brazil, significant differences were found between Rio de Janeiro and the other three populations, as well as between SA o pound Paulo and Parana. For the five Argentinean samples, significant distances were only observed when comparing Misiones with Entre Rios and with Rio Negro, the only two samples that do not differ significantly from Costa Rica. Antioquia differed from all other samples, except the one from Rio Negro.

Estudo de frequências alélicas de STRs do cromossomo X na população brasileira de Araraquara-SP

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudo de polimorfismo do cromossomo x na população da região sudeste do Brasil

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Brazilian genetic database of chromosome X

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Análise de 15 STRS autossômicos na população de Araraquara (São Paulo, Brasil)

Os marcadores genéticos mais utilizados para fins de identificação humana são regiões autossômicas de repetições consecutivas curtas (Short Tandem Repeats - STRs) e para interpretar a análise de DNA, os resultados de um caso necessitam ser comparados com os dados de uma pertinente população. O objetivo do trabalho, portanto, foi caracterizar o perfil genético da população de Araraquara, (São Paulo, Brasil) pela análise de 15 STRs autossômicos (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, VWA, D8S1179, TPOX and FGA) inclusos no kit PowerPlex 16 (Promega) e correlacionar esses dados com a história de formação da população. Não foram observados desvio do equilíbrio de Hardy - Weinberg após correção de Bonferroni. Parâmetros forenses apresentaram valores elevados, sendo os marcadores mais polimórficos o Penta E, D18S51 e FGA. A árvore UPGMA (Unweighted Pair- Group Method with Arithmetic Mean) baseada na medida de distância genética mostrou a população de Araraquara agrupada com as populações da região sudeste do Brasil, próxima do grupo europeu e distante das populações Africana e Ameríndia. Estimativas de mistura revelaram que a contribuição parental para a população de Araraquara foi 76% européia, 18% africana e 6% ameríndia

Cloning and characterisation of a novel chromosome end repeat enriched with homopolymeric (dA)/(dT) DNA in Rhynchosciara americana (Diptera: Sciaridae)

Short tandem DNA repeats and telomerase compose the telomere structure in the vast majority of eukaryotic organisms. However, such a conserved organisation has not been found in dipterans. While telomeric DNA in Drosophila is composed of specific retrotransposons, complex terminal tandem repeats are present in chromosomes of Anopheles and chironomid species. In the sciarid Rhynchosciara americana, short repeats (16 and 22 bp long) tandemly arrayed seem to reach chromosome ends. Moreover, in situ hybridisation data using homopolymeric RNA probes suggested in this species the existence of a third putative chromosome end repeat enriched with (dA).(dT) homopolymers. In this work, chromosome micro-dissection and PCR primed by homopolymeric primers were employed to clone these repeats. Named T-14 and 93 % AT-rich, the repetitive unit is 14 bp long and appears organised in tandem arrays. It is localised in five non-centromeric ends and in four interstitial bands of R. americana chromosomes. To date, T-14 is the shortest repeat that has been characterised in chromosome ends of dipterans. As observed for short tandem repeats identified previously in chromosome ends of R. americana, the T-14 probe hybridised to bridges connecting non-homologous polytene chromosome ends, indicative of close association of T-14 repeats with the very end of the chromosomes. The results of this work suggest that R. americana represents an additional example of organism provided with more than one DNA sequence that is able to reach chromosome termini.

DNA typing in thirty seconds with a microfabricated device

We report the development of a practical ultrafast allelic profiling assay for the analysis of short tandem repeats (STRs) by using a highly optimized microfluidic electrophoresis device. We have achieved baseline-resolved electrophoretic separations of single-locus STR samples in 30 sec. Analyses of PCR samples containing the four loci CSF1PO, TPOX, THO1, and vWA (abbreviated as CTTv) were performed in less than 2 min. This constitutes a 10- to 100-fold improvement in speed relative to capillary or slab gel systems. The separation device consists of a microfabricated channel 45 μm × 100 μm in cross section and 26 mm in length, filled with a replaceable polyacrylamide matrix operated under denaturing conditions at 50°C. A fluorescently labeled STR ladder was used as an internal standard for allele identification. Samples were prepared by standard procedures and only 4 μl was required for each analysis. The device is capable of repetitive operation and is suitable for automated high-speed and high-throughput applications.

Sequence variation in the Fanconi anemia gene FAA

Fanconi anemia (FA) is a genetically heterogeneous autosomal recessive syndrome associated with chromosomal instability, hypersensitivity to DNA crosslinking agents, and predisposition to malignancy. The gene for FA complementation group A (FAA) recently has been cloned. The cDNA is predicted to encode a polypeptide of 1,455 amino acids, with no homologies to any known protein that might suggest a function for FAA. We have used single-strand conformational polymorphism analysis to screen genomic DNA from a panel of 97 racially and ethnically diverse FA patients from the International Fanconi Anemia Registry for mutations in the FAA gene. A total of 85 variant bands were detected. Forty-five of the variants are probably benign polymorphisms, of which nine are common and can be used for various applications, including mapping studies for other genes in this region of chromosome 16q. Amplification refractory mutation system assays were developed to simplify their detection. Forty variants are likely to be pathogenic mutations. Seventeen of these are microdeletions/microinsertions associated with short direct repeats or homonucleotide tracts, a type of mutation thought to be generated by a mechanism of slipped-strand mispairing during DNA replication. A screening of 350 FA probands from the International Fanconi Anemia Registry for two of these deletions (1115–1118del and 3788–3790del) revealed that they are carried on about 2% and 5% of the FA alleles, respectively. 3788–3790del appears in a variety of ethnic groups and is found on at least two different haplotypes. We suggest that FAA is hypermutable, and that slipped-strand mispairing, a mutational mechanism recognized as important for the generation of germ-line and somatic mutations in a variety of cancer-related genes, including p53, APC, RB1, WT1, and BRCA1, may be a major mechanism for FAA mutagenesis.