Development of Methodologies for Prospection and Imputation of SNP Markers Based on Data from Resequencing of Complex Genomes

• Grant number: 12/05002-9
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: September 01, 2012
• End date: January 31, 2015
• Field of knowledge: Biological Sciences - Genetics - Molecular Genetics and Genetics of Microorganisms
• Principal Investigator: Michel Eduardo Beleza Yamagishi
• Grantee: Joaquim Manoel da Silva
• Host Institution: Instituto de Biologia (IB). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil

Abstract

In recent years, important advances have been made in Genome-Wide Association Study (GWAS), yielding a large number of associations between genotypes and complex human diseases. Genotype imputation has proved to be an important tool that can be used in GWAS, able to boost its power and facilitate the combination of results from different studies by means of meta-analysis. This piece of research aims at developing methodologies for the prospection of Single Nucleotide Polymorphism (SNP) markers and the imputation of genotypes in GWAS based on data from resequencing of complex genomes. Different statistical methods for prospection and imputation will be reviewed and assessed, discussing factors that influence performance of imputation and association of tests in imputed SNPs. Genotype imputation addressed in this study adds to other efforts undertaken by the Animal Genomics Network Project of Brazilian Agricultural Research Corporation (Embrapa) to identify genes responsible for variations in economically relevant characteristics.

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

DA SILVA, JOAQUIM MANOEL; GIACHETTO, POLIANA FERNANDA; CAMPOS DA SILVA, LUIZ OTAVIO; CINTRA, LEANDRO CARRIJO; PAIVA, SAMUEL REZENDE; CAETANO, ALEXANDRE RODRIGUES; BELEZA YAMAGISHI, MICHEL EDUARDO. Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle. PLoS One, v. 10, n. 8, AUG 25 2015. (12/05002-9)

DA SILVA, JOAQUIM MANOEL; GIACHETTO, POLIANA FERNANDA; DA SILVA, LUIZ OTAVIO; CINTRA, LEANDRO CARRIJO; PAIVA, SAMUEL REZENDE; BELEZA YAMAGISHI, MICHEL EDUARDO; CAETANO, ALEXANDRE RODRIGUES. Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits. BMC Genomics, v. 17, JUN 13 2016. (12/05002-9)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

SILVA, Joaquim Manoel da. Detection of genomic variations in nelore-breed cattle using genotyping and resequenced data. 2015. Doctoral Thesis - Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia Campinas, SP.