Posters
Category 'L'- Population Genetics Variation and Evolution' |
Poster - L01 |
APPLICATION OF A PROBABILISTIC METHOD TO CHARACTERIZE THE GENETIC DIVERSITY OF HUMAN PAPILLOMAVIRUS IN NORTHEASTERN BRAZIL |
Edilaine Araújo, Universidade Federal de Sergipe, Brazil |
Gerlane Barros, Universidade Federal de Sergipe, Brazil Maíra Arruda-Lima, FIOCRUZ, Recife, Brazil Marcus Batista, Universidade Federal de Sergipe, Brazil Norma Silva, FIOCRUZ, Recife, Brazil Renan Gomes, FIOCRUZ, Recife, Brazil |
Short Abstract: Assessment of genetic diversity of HPV in northeastern Brazil, using a probabilistic method for phylogenetic reconstruction. Maximum likelihood (ML) tree was constructed with the evolutionary model that best fit the data using the PhyML program. Phylogenetic trees showed that different strains of HPV are infecting women in this same location. |
Poster - L02 |
Corynebacterium pseudotuberculosis may be under anagenesis and biovar equi is forming biovar ovis: a phylogenic inference from sequence and structural analysis |
Alberto Oliveira Junior, Universidade Federal de Minas Gerais, Brazil |
Pammella Teixeira, Universidade Federal de Minas Gerais, Brazil Marcela Azevedo, Universidade Federal de Minas Gerais, Brazil Vasco Azevedo, Universidade Federal de Minas Gerais, Brazil |
Short Abstract: Corynebacterium pseudotuberculosis can be classified into two biovars. Using evolutionarily conserved genes (rpoB, gapA, fusA, and rsmE) and their corresponding nucleotides sequences we analyzed the phylogenetic relationship among fifteen strains of Cp. belonging to both biovars. Taken together the results suggest that biovar equi is forming the biovar ovis. |
Poster - L03 |
Brazilian population structure inferred by X-chromosome data |
Hanaisa Sant'Anna, Universidade Federal de Minas Gerais, Brazil |
Hanaisa Sant Anna, Universidade Federal de Minas Gerais, Brazil Mateus Gouveia, Universidade Federal de Minas Gerais, Brazil Eduardo Tarazona-Santos, Universidade Federal de Minas Gerais, Brazil Fernanda Kehdy, Universidade Federal de Minas Gerais, Brazil The Brazilian EPIGEN consortium The Brazilian EPIGEN consortium, UFMG, FMUSP, UFBA, UFPel, Fiocruz, Brazil |
Short Abstract: The Brazilian population, one of the most heterogeneous in the world, is a result of mixture between Africans, Amerindian and Europeans. Little is known about how those interethnic crosses are revealed by the Brazilian X-chromosome. In this study, the sex-biased gene flow among Native American, European and African in the recent admixture population of Brazil was evaluated in 4,192 females’ samples genotyped with the Illumina’s HumanOmni2.5-8v1 and HumanOmni5-4v1 arrays. The autosomal and X-chromosome ancestry composition was estimated using principal component analysis (PCA) and ADMIXTURE with a SNPs dataset of 331,790 in autosomes and 5,792 in the X-chromosome. To compare those results, we performed a Wilcoxon Signed-Rank Test. We observed that: (i) The distributions in PCA space of each individual obtained from PC 1 and 2, the only informative clustering pattern for X-chromosome, as well as for autosomes, suggest differences in the evolutionary history of males and females. For all cohorts, we observed that compared with autosomal data, a larger number of females X-chromosome cluster near the Native American and African parental populations. This is consistent with the lower effective recombination rate of the X-chromosome that result in a larger number of X-chromosomes with a unique continental ancestry. This differential pattern between X-chromosome and autosomal markers is not evident for European ancestry because it is the predominant continental ancestry in our sample, and therefore there is a high number of individuals with both high autosomal and X-chromosome European ancestry. (ii) Both PCA and ADMIXTURE analyses show that compared with autosomal data, the X-chromosome evidences a larger Native American and African contribution to extant Brazilian genomic diversity than at genome wide level. This is due to a historical pattern of sex-biased preferential mating between males with predominant European ancestry with women with predominant African or Native American ancestry. (iii) On average, the sex-bias in admixture was larger in Salvador, and lower in Bambuí and Pelotas, and it was higher for Native American ancestry than for African ancestry. Overall, our results suggest a significantly higher contribution from Native American and African ancestors into the composition of the X chromosome of Brazilian women, supporting the presence of sex-biased gene flow during the process of admixture. |
Poster - L04 |
Transcriptome analyses of Bothrops neuwiedi venom gland and evolutionary studies of snake venom metalloproteinases (SVMPs) |
Valéria G. Alvarenga, FUNED, Brazil |
Fabiano Pais FIOCRUZ/Minas, Brazil Valéria G. Alvarenga, FUNED, Brazil Fabiano S. Pais, FIOCRUZ/Minas, Brazil Larissa L. S. Scholte, FIOCRUZ/Minas, Brazil Laila A. Nahum, FIOCRUZ/Minas, Brazil Flávio M. G. Araújo, FIOCRUZ/Minas, Brazil Anna C. M. Salim, FIOCRUZ/Minas, Brazil Eladio F. Sanchez, FUNED, Maria Inácia Estevão-Costa, FUNED, Guilherme Oliveira, FIOCRUZ/Minas, |
Short Abstract: We describe the de novo assembly, mapping and transcript annotation of the venom-gland transcriptome of a widely distributed Brazilian pit viper: Bothrops neuwiedi. In addition, we performed phylogenetic analyzes of SVMP homologs to better understand the molecular biodiversity of these proteins, as well as the evolutionary mechanisms underlying their evolution. |
Poster - L05 |
Finding the unexpected, RNA-seq and Potyvirus in plants. |
Giovanni de Castro, Universidade Estadual de Campinas, Brazil |
Leonardo Boiteux, Embrapa Hortaliças, Brazil Maria Fonseca, Embrapa Hortaliças, Brazil Francisco Lobo, Embrapa Informática Agropecuária, Brazil Elibio Rech, EMBRAPA, Brazil Felipe Silva, Embrapa Informática Agropecuária, Brazil |
Short Abstract: It was found millions sequences of a virus in cDNA library from a sample of Fevillea cordifolia by using the RNA-seq method. This plant isn't described as a host for this virus, and no other sequence of the virus had such high coverage to allow an observation of its quasispecies. |
Poster - L06 |
MASSA (Multi-Agent System for Snp Annotation) uses at genomic population studies |
Giordano Soares-Souza, Universidade Federal de Minas Gerais, Brazil |
Short Abstract: Genetic diversity is associated with the phenotypic differentiation found among human populations. While most part of this diversity occurs among individuals of the same population and the interaction with the environment is crucial to determine the phenotype, the study of variants that are genetically structured in the human population is essential in two important fields of biology: evolution and medicine. In the present work, we describe the database integration tool MASSA (Multi-Agent System for SNP Annotation) and in the genomic scope, the identification of 69891 polymorphisms (SNPs) highly differentiated in Native American populations in respect to the West Africa, Europe and East Asia populations. These genetic variants were annotated using MASSA. Through the enrichment analysis performed by MASSA on database attributes of GO, HGNC, OMIM, PGKB and Reactome, we identified enriched terms of these databases in the annotation of differentiated genes in Native American. These analyzes confirmed previous knowledge on the genetic structure of natives, such as: high diversity in polymorphisms associated with type 2 diabetes and evidence of positive selection in genes involved in immune response and nervous system activity. And also was possible to identify new insights at Natives as groups of differentiated genes involved in the production of ionotropic membrane receptors related to the efficacy of treatment and severity of cognitive phenotypes; and nucleoporines associated with viral infection and carbohydrate transport. |
Poster - L07 |
A GENOME-WIDE SCAN FOR SIGNATURE OF ADAPTATION IN MAIZE LANDRACES |
LAURA GONZALEZ, UNIVERSIDAD DE LOS ANDES, Colombia |
SARAH HEARNE, International Maize and Wheat Improvement Center, Mexico CHARLES CHEN, International Maize and Wheat Improvement Center, Mexico MARTHA WILLCOX, International Maize and Wheat Improvement Center, Mexico NATALIA PALACIOS, International Maize and Wheat Improvement Center, Mexico |
Short Abstract: Landraces are the maize material with the highest genetic variation and they contain the best adaptation to the natural environment. In this study we explore the genetic diversity of landraces to understand the allelic variation, assess directional selection and functional enrichment between samples for different environments and races. |
Poster - L08 |
Resampling individuals through Kinship coefficient by using a node selection algorithm in Guzerá breed |
Pablo Fonseca, Universidade Federal de Minas Gerais, Brazil |
Fernanda Caroline dos Santos, Universidade Federal de Minas Gerais, Brazil Mateus Henrique Gouveia, Universidade Federal de Minas Gerais, Brazil Thiago Peixoto Leal, Universidade Federal de Minas Gerais, Brazil Izinara da Cruz Rosse, Universidade Federal de Minas Gerais, Brazil Maria Gabriela Campolina Diniz Peixoto, EMBRAPA Gado de Leite , Brazil Eduardo Martins-Tarazona , Universidade Federal de Minas Gerais, Brazil Maria Raquel dos Santos Carvalho, Universidade Federal de Minas Gerais, Brazil |
Short Abstract: BACKGROUND Phylogenetic, phylogeographic and particularly genome-wide association studies can be seriously impacted by population genetic structure induced by endogamy. This problem is particularly serious in the cattle, produced by current intensive selection processes as well as by the strong bottlenecks generally associated with the establishment of each one of the breeds. Therefore, the development of strategies for reducing the relatedness level in a sample is a crucial step for genetic studies. Some tools based on the estimation of identical by descendent (IBD) probabilities for alleles or haplotypes have already developed to help to ascertain population genetic structure as well as in the identification of the individuals who should be kept out of the sample, in order to reduce effects of population genetic structure induced by consanguinity on the studies. However, such tools may exclude a large number of individuals from the sample, and consequently its power. Here, we describe the applicability of a node selection algorithm based on a network’s degree centrality statistic for livestock samples. This approach was chosen in order to reduce the level of family structure of our data without eliminating all families, and by eliminating the smallest possible number of individuals. This statistic was calculated using the last version of NetworkX2 Software. This methodology (centrality sampling) was compared with a simple, but widely used methodology in which all individuals who share a Kinship coefficient >0.1 with any other individual in the sample are removed from it (IBD sampling). For this comparison, a sample of 1036 cows of the indicine Guzerá breed were genotyped using the BovineSNP50 v2 DNA Analysis BeadChip. The pattern of genetic structure in the sample was evaluated using the Admixture software. Moreover, the pattern of linkage disequilibrium (LD) and the distribution of runs of homozygosity (ROH) genome were analyzed using the SNP and variation Suite 7 (Golden Helix, Inc.). RESULTS After the resampling, from an initial sample of 1.036 animals, 210 animals were retained in the sample using the centrality strategy and 158 animals in the IBD sampling. The 210 subsample obtained using the centrality algorithm presented a lower mean LD and the double of ROH when compared with the IBD sampling strategy. This can be explained due to the higher number of individuals in the final sample, the more homogeneous distribution of Kinship coefficient and better genetic representativeness of the original sample retained using the centrality algorithm. Additionally, the elimination of only the central nodes in the Kinship coefficient based network allows the IBD segments of DNA, shared with other nodes in the network, to remain in the final sample. CONCLUSIONS The node selection algorithm based on a network’s degree centrality statistic enabled the efficient reduction of the relatedness in the sample, with the loss of as few individuals as possible. The strategy was proven efficient and fully applicable for reducing structure produced by the artificial selection process in livestock samples. |
Poster - L09 |
Leptospira's Species Classication based on Data Mining |
Timóteo Rico, Federal University of Rio Grande, Brazil |
Marcus Eslabão, Federal University of Pelotas, Brazil Frederico Kremer, Federal University of Pelotas, Brazil Pedro Almeida da Silva, Federal University of Rio Grande, Brazil Eduardo Borges, Federal University of Rio Grande, Brazil Luciano Pinto, Federal University of Pelotas, Brazil Odir Dellagostin, Federal University of Pelotas, Brazil Karina Machado, Federal University of Rio Grande, Brazil |
Short Abstract: The present work aims the application of a classic machine learning tool in the analysis of molecular biology data. Thus, this work presents an example of application of data mining tool in real world biological data. |
Poster - L10 |
Revisiting molecular serotyping of Streptococcus pneumoniae |
Roney Coimbra, FIOCRUZ, Brazil |
Dhian Camargo, FUNED, Brazil Fabiano Pais, FIOCRUZ, Brazil Ângela Volpini, FIOCRUZ, Brazil Marluce Oliveira, FUNED, Brazil Roney Coimbra, FIOCRUZ, Brazil |
Short Abstract: None On File |
Poster - L11 |
HIV-1 Tropism determines different mutation profiles in proviral DNA |
Mário Janini, Universidade Federal de São Paulo, Brazil |
Sieberth Nascimento-Brito, UFRRJ, Brazil Jean Paulo Zukurov, UNIFESP, Brazil Juliana Maricato, UNIFESP , Brazil Angela Volpini, FIOCRUZ , Brazil Anna Christina Salim , FIOCRUZ , Brazil Flavio Araujo , FIOCRUZ , Brazil Roney Coimbra , FIOCRUZ , Brazil Guilherme Oliveira , FIOCRUZ , Brazil Fernando Antoneli, UNIFESP, |
Short Abstract: None On File |
Poster - L12 |
THE FINE-SCALE GENETICS OF BRAZILIANS: A POPULATION-BASED APPROACH |
Mateus Gouveia, Universidade Federal de Minas Gerais, Brazil |
Short Abstract: Here we present results of the EPIGEN-Brazil Initiative (Genomic Epidemiology of Complex Diseases in Population-based Brazilian Cohorts, http://epigen.grude.ufmg.br). We performed a population-based genome-wide analysis of nearly 2.2 million SNPs (Omni2.5M-Illumina) from the three most populated regions of Brazil: Salvador-Bahia (n=1309), Bambui (n=1442) and Pelotas (n=3736) from Northeast, Southeast and Southern Brazil respectively. While Amerindian ancestry was low (5-7% at population level, with no individual with > 30% of this ancestry), the three populations showed individuals with all possible combinations of African and European ancestry. At population level, African ancestry ranged from 14-15% in Pelotas and Bambui to 51% in Salvador. The EPIGEN cohorts also exemplify how kinship and inbreeding coefficients may be differently structured in small (Bambuí), medium-size (Pelotas) and large (Salvador) admixed Latin American populations. Model-based ADMIXTURE analysis revealed an unknown cluster of African ancestry, likely Bantu or Eastern Africa-associated more common in Southern Brazil that in any other Latin America population, probably related with slave trade from regions such as Mozambique. Genetic diversity of European origin in Brazil recapitulates a considerable portion of the whole diversity of this continent, not being restricted to the Iberian Peninsula. At a local ancestry level, the distribution of chromosomal segments of distinct ancestry do show evidence of very recent European admixture into the South East and Southern Brazil but not in the Salvador cohort (NE), while African admixture into admixed populations fits a model of continuous gene flow across the three cohorts. In conclusion, the inferred genetic structure of Brazilian populations has implications for the design of genetic association studies in these and other admixed populations. First, assortative mating by ancestry implies that when performing association studies in admixed populations, Hardy-Weinberg disequilibrium is actual and relevant, and filtering SNPs in Hardy-Weinberg disequilibrium in quality-control analyses conceals real aspects of the genetic structure of these populations. Second, we identified relevant components of genetic structure at subcontinental level, both for European and African ancestry. This implies that when mapping the genetic basis of diseases in Brazilians, spurious association may arise if the genetic structure within continents is not accounted for. Interestingly, the two within-African ancestry clusters in the Brazilian populations (characterized by an average FST between them of 0.02) are characterized by a set of 3318 SNPs (the 10% of total SNPs with the highest FST [>0.06], which include 38 SNPs that are GWAS hits. |
Posters
Poster Presentation List & Schedule
Odd numbers:
Poster set up: Day 1 - all day long
Take down: Day 2 after Poster Session
Size: Up to 90cm width x 120 cm height
Even Numbers:
Poster set up: Day 2 after Poster session and Day 3 until the first coffee break
Take Down: Day 3 after Poster Session
Size: Up to 90cm width x 120 cm height
View Posters By Category |
- A) Bioinformatics of Disease and Treatment
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- E) Education
- F) Epigenetics
- G) Functional Genomics
- H) Genome Organization and Annotation
- I) Genetic Variation Analysis
- J) Metagenomics
- K) Pathogen informatics
- L) Population Genetics Variation and Evolution
- M) Protein Structure and Function Prediction and Analysis
- N) Proteomics
- O) Sequence Analysis
- P) Systems Biology and Networks
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