Navegando por Autor "Ribeiro-dos-Santos, Ândrea"

Agora exibindo 1 - 6 de 6

Exome sequencing of native populations from the Amazon reveals patterns on the peopling of South America
(Frontiers Media SA, 2020-10-29) Ribeiro-dos-Santos, André M.; Vidal, Amanda Ferreira; Vinasco-Sandoval, Tatiana; Guerreiro, João; Santos, Sidney; Ribeiro-dos-Santos, Ândrea; Souza, Sandro José de
Studies on the peopling of South America have been limited by the paucity of sequence data from Native Americans, especially from the east part of the Amazon region. Here, we investigate the whole exome variation from 58 Native American individuals (eight different populations) from the Amazon region and draw insights into the peopling of South America. By using the sequence data generated here together with data from the public domain, we confirmed a strong genetic distinction between Andean and Amazonian populations. By testing distinct demographic models, our analysis supports a scenario of South America occupation that involves migrations along the Pacific and Atlantic coasts. Occupation of the southeast part of South America would involve migrations from the north, rather than from the west of the continent
High-Throughput Sequencing of a South American Amerindian
(2013-12-30) Ribeiro-dos-Santos, André M.; Souza, Jorge Estefano Santana de; Almeida, Renan; Alencar, Dayse O.; Barbosa, Maria Silvanira; Gusmão, Leonor; Silva Jr., Wilson A.; Souza, Sandro José de; Silva, Artur; Ribeiro-dos-Santos, Ândrea; Darnet, Sylvain; Santos, Sidney
The emergence of next-generation sequencing technologies allowed access to the vast amounts of information that are contained in the human genome. This information has contributed to the understanding of individual and population-based variability and improved the understanding of the evolutionary history of different human groups. However, the genome of a representative of the Amerindian populations had not been previously sequenced. Thus, the genome of an individual from a South American tribe was completely sequenced to further the understanding of the genetic variability of Amerindians. A total of 36.8 giga base pairs (Gbp) were sequenced and aligned with the human genome. These Gbp corresponded to 95.92% of the human genome with an estimated miscall rate of 0.0035 per sequenced bp. The data obtained from the alignment were used for SNP (single-nucleotide) and INDEL (insertion-deletion) calling, which resulted in the identification of 502,017 polymorphisms, of which 32,275 were potentially new high-confidence SNPs and 33,795 new INDELs, specific of South Native American populations. The authenticity of the sample as a member of the South Native American populations was confirmed through the analysis of the uniparental (maternal and paternal) lineages. The autosomal comparison distinguished the investigated sample from others continental populations and revealed a close relation to the Eastern Asian populations and Aboriginal Australian. Although, the findings did not discard the classical model of America settlement; it brought new insides to the understanding of the human population history. The present study indicates a remarkable genetic variability in human populations that must still be identified and contributes to the understanding of the genetic variability of South Native American populations and of the human populations history.
Identification of NUDT15 gene variants in Amazonian Amerindians and admixed individuals from northern Brazil
(2020-04-15) Rodrigues, Juliana Carla Gomes; Souza, Tatiane Piedade de; Pastana, Lucas Favacho; Santos, André Maurício Ribeiro dos; Fernandes, Marianne Rodrigues; Pinto, Pablo; Wanderley, Alayde Vieira; Souza, Sandro José de; Kroll, José Eduardo; Pereira, Adenilson Leão; Magalhães, Leandro; Mercês, Laís Reis das; Vidal, Amanda Ferreira; Vinasco-Sandoval, Tatiana; Cavalcante, Giovanna Chaves; Guerreiro, João Farias; Assumpção, Paulo Pimentel de; Ribeiro-dos-Santos, Ândrea; Santos, Sidney; Santos, Ney Pereira Carneiro dos
Introduction The nudix hydrolase 15 (NUDT15) gene acts in the metabolism of thiopurine, by catabolizing its active metabolite thioguanosine triphosphate into its inactivated form, thioguanosine monophosphate. The frequency of alternative NUDT15 alleles, in particular those that cause a drastic loss of gene function, varies widely among geographically distinct populations. In the general population of northern Brazilian, high toxicity rates (65%) have been recorded in patients treated with the standard protocol for acute lymphoblastic leukemia, which involves thiopurine-based drugs. The present study characterized the molecular profile of the coding region of the NUDT15 gene in two groups, non-admixed Amerindians and admixed individuals from the Amazon region of northern Brazil. Methods The entire NUDT15 gene was sequenced in 64 Amerindians from 12 Amazonian groups and 82 admixed individuals from northern Brazil. The DNA was extracted using phenol-chloroform. The exome libraries were prepared using the Nextera Rapid Capture Exome (Illumina) and SureSelect Human All Exon V6 (Agilent) kits. The allelic variants were annotated in the ViVa® (Viewer of Variants) software. Results Four NUDT15 variants were identified: rs374594155, rs1272632214, rs147390019, andrs116855232. The variants rs1272632214 and rs116855232 were in complete linkage disequilibrium, and were assigned to the NUDT15*2 genotype. These variants had high frequencies in both our study populations in comparison with other populations catalogued in the 1000 Genomes database. We also identified the NUDT15*4 haplotype in our study populations, at frequencies similar to those reported in other populations from around the world. Conclusion Our findings indicate that Amerindian and admixed populations from northern Brazil have high frequencies of the NUDT15 haplotypes that alter the metabolism profile of thiopurines.
Identification of variants (rs11571707, rs144848, and rs11571769) in the BRCA2 gene associated with hereditary breast cancer in indigenous populations of the brazilian Amazon
(MDPI AG, 2021-01-22) Dobbin, Elizabeth Ayres Fragoso; Medeiros, Jéssyca Amanda Gomes; Costa, Marta Solange Camarinha Ramos; Rodrigues, Juliana Carla Gomes; Guerreiro, João Farias; Kroll, José Eduardo; Souza, Sandro José de; Assumpção, Paulo Pimentel de; Ribeiro-dos-Santos, Ândrea; Santos, Sidney Emanuel Batista dos; Burbano, Rommel Mario Rodríguez; Fernandes, Marianne Rodrigues; Santos, Ney Pereira Carneiro dos
Estimates show that 5–10% of breast cancer cases are hereditary, caused by genetic variants in autosomal dominant genes; of these, 16% are due to germline mutations in the BRCA1 and BRCA2 genes. The comprehension of the mutation profile of these genes in the Brazilian population, particularly in Amazonian Amerindian groups, is scarce. We investigated fifteen polymorphisms in the BRCA1 and BRCA2 genes in Amazonian Amerindians and compared the results with the findings of global populations publicly available in the 1000 Genomes Project database. Our study shows that three variants (rs11571769, rs144848, and rs11571707) of the BRCA2 gene, commonly associated with hereditary breast cancer, had a significantly higher allele frequency in the Amazonian Amerindian individuals in comparison with the African, American, European, and Asian groups analyzed. These data outline the singular genetic profiles of the indigenous population from the Brazilian Amazon region. The knowledge about BRCA1 and BRCA2 variants is critical to establish public policies for hereditary breast cancer screening in Amerindian groups and populations admixed with them, such as the Brazilian population
Pharmacogenomic Profile of Amazonian Amerindians
(MDPI AG, 2022-06-10) Rodrigues, Juliana Carla Gomes; Fernandes, Marianne Rodrigues; Ribeiro-dos-Santos, André Maurício; Araújo, Gilderlanio Santana de; Souza, Sandro José de; Guerreiro, João Farias; Ribeiro-dos-Santos, Ândrea; Assumpção, Paulo Pimentel de; Santos, Ney Pereira Carneiro dos; Santos, Sidney
Given the role of pharmacogenomics in the large variability observed in drug efficacy/safety, an assessment about the pharmacogenomic profile of patients prior to drug prescription or dose adjustment is paramount to improve adherence to treatment and prevent adverse drug reaction events. A population commonly underrepresented in pharmacogenomic studies is the Native American populations, which have a unique genetic profile due to a long process of geographic isolation and other genetic and evolutionary processes. Here, we describe the pharmacogenetic variability of Native American populations regarding 160 pharmacogenes involved in absorption, distribution, metabolism, and excretion processes and biological pathways of different therapies. Data were obtained through complete exome sequencing of individuals from 12 different Amerindian groups of the Brazilian Amazon. The study reports a total of 3311 variants; of this, 167 are exclusive to Amerindian populations, and 1183 are located in coding regions. Among these new variants, we found non-synonymous coding variants in the DPYD and the IFNL4 genes and variants with high allelic frequencies in intronic regions of the MTHFR, TYMS, GSTT1, and CYP2D6 genes. Additionally, 332 variants with either high or moderate (disruptive or non-disruptive impact in protein effectiveness, respectively) significance were found with a minimum of 1% frequency in the Amazonian Amerindian population. The data reported here serve as scientific basis for future design of specific treatment protocols for Amazonian Amerindian populations as well as for populations admixed with them, such as the Northern Brazilian population
Whole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades
(2018-07-05) Vialle, Ricardo Assunção; Souza, Jorge Estefano Santana de; Lopes, Katia de Paiva; Teixeira, Diego Gomes; Alves Sobrinho, Pitágoras de Azevedo; Ribeiro-dos-Santos, André M.; Furtado, Carolina; Sakamoto, Tetsu; Silva, Fábio Augusto Oliveira; Oliveira, Edivaldo Herculano Corrêa de; Hamoy, Igor Guerreiro; Assumpção, Paulo Pimentel; Ribeiro-dos-Santos, Ândrea; Lima, João Paulo Matos Santos; Seuánez, Héctor N.; Souza, Sandro José de; Santos, Sidney
The Pirarucu (Arapaima gigas) is one of the world's largest freshwater fishes and member of the superorder Osteoglossomorpha (bonytongues), one of the oldest lineages of ray-finned fishes. This species is an obligate air-breather found in the basin of the Amazon River with an attractive potential for aquaculture. Its phylogenetic position among bony fishes makes the Pirarucu a relevant subject for evolutionary studies of early teleost diversification. Here, we present, for the first time, a draft genome version of the A. gigas genome, providing useful information for further functional and evolutionary studies. The A. gigas genome was assembled with 103 Gb raw reads sequenced in an Illumina platform. The final draft genome assembly was approximately 661 Mb, with a contig N50 equal to 51.23 kb and scaffold N50 of 668 kb. Repeat sequences accounted for 21.69% of the whole genome, and a total of 24,655 protein-coding genes were predicted from the genome assembly, with an average of 9 exons per gene. Phylogenomic analysis based on 24 fish species supported the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons and bonefishes) are sister groups, both forming a sister lineage with respect to Clupeocephala (remaining teleosts). Divergence time estimations suggested that Osteoglossomorpha and Elopomorpha lineages emerged independently in a period of approximately 30 million years in the Jurassic. The draft genome of A. gigas provides a valuable genetic resource for further investigations of evolutionary studies and may also offer a valuable data for economic applications.

SIGAA

Navegando por Autor "Ribeiro-dos-Santos, Ândrea"