Investigation of genetic variations susceptibility to chronic periodontitis by OpenArray®: Biostatistics, Bioinformatics and Functional Analysis

• Grant number: 16/18313-3
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• Start date: December 01, 2016
• End date: November 30, 2017
• Field of knowledge: Health Sciences - Dentistry - Periodontology
• Principal Investigator: Raquel Mantuaneli Scarel Caminaga
• Grantee: Rafael Nepomuceno Oliveira
• Supervisor: Silvana Pereira Barros
• Host Institution: Faculdade de Odontologia (FOAr). Universidade Estadual Paulista (UNESP). Campus de Araraquara. Araraquara , SP, Brazil
• Institution abroad: University of North Carolina at Chapel Hill (UNC), United States
• Associated to the scholarship: 14/13295-1 - Investigation of the association of genetic variation regarding susceptibility to chronic periodontal disease by OpenArray, BP.DR

Abstract

Many studies around the world have investigated genetic polymorphisms associated with susceptibility to periodontal disease (PD), but more studies are need to know risk factors to chronic periodontitis (CP) in the Brazilian population, mainly because its miscegenation. Moreover, there are few studies focused on identifying biological functionality of polymorphisms in the context of PD. This present BEPE proposal aims to complement the PhD project (supported by FAPESP) in the University of North Carolina at Chapel Hill (UNC). The PhD project in development in Brazil aims to investigate single nucleotide polymorphism (SNPs) in candidate genes that potentially could influence susceptibility to CP in a Brazilian population. A total of 712 patients were selected and divided as: (i) Group A (n = 356) patients with moderate or severe CP; Group B (n = 356): patients with mild CP and healthy patients. Genotyping data will be obtained from 64 SNP in candidate genes, by Real-Time PCR (Polymerase Chain Reaction) reactions using the OpenArrayTM system (Applied Biosystems). After doing this part in Brazil, we propose to execute in UNC a deeper and complex biostatistical and bioinformatics analyses of the genotypes data. Principal component analysis (PCA) of these genotyped SNPs will be made to explore the sample relationship. After doing the complete logistic regression for single SNPs and covariates, further test interactions between two SNPs and covariates and functional genomics analyses will be executed. Moreover, we aimed to do functional analysis of a selected SNP, investigating its potential transcriptional/ translational influence on the gene that resides, as well other genes biologically related with it, as other genes in the same signaling cascade.

Scientific publications

(9)

(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)

NEPOMUCENO, RAFAEL; PIGOSSI, SUZANE C.; FINOTI, LIVIA S.; ORRICO, SILVANA R. P.; CIRELLI, JONI A.; BARROS, SILVANA P.; OFFENBACHER, STEVEN; SCAREL-CAMINAGA, RAQUEL M.. Serum lipid levels in patients with periodontal disease: A meta-analysis and meta-regression. JOURNAL OF CLINICAL PERIODONTOLOGY, v. 44, n. 12, p. 1192-1207, DEC 2017. (16/18313-3, 14/13295-1)

DA SILVA, BARBARA ROQUE; CIRELLI, THAMIRIS; NEPOMUCENO, RAFAEL; THEODORO, LETICIA HELENA; ORRICO, SILVANA R. P.; CIRELLI, JONI A.; BARROS, SILVANA P.; SCAREL-CAMINAGA, RAQUEL M.. Functional haplotype in the Interleukin8 (CXCL8) gene is associated with type 2 Diabetes Mellitus and Periodontitis in Brazilian population. DIABETES & METABOLIC SYNDROME-CLINICAL RESEARCH & REVIEWS, v. 14, n. 6, p. 1665-1672, NOV-DEC 2020. (14/13295-1, 16/03753-8, 16/18313-3, 16/25418-6, 18/26367-1, 16/08070-6)

CIRELLI, THAMIRIS; NEPOMUCENO, RAFAEL; ORRICO, SILVANA R. P.; ROSSA, JR., CARLOS; CIRELLI, JONI A.; NORTH, KARI E.; GRAFF, MARIAELISA; BARROS, SILVANA P.; SCAREL-CAMINAGA, RAQUEL M.. Validation in a Brazilian population of gene markers of periodontitis previously investigated by GWAS and bioinformatic studies. Journal of Periodontology, v. 92, n. 5, p. 689-703, MAY 2021. (16/03753-8, 16/18313-3, 14/13295-1)

CIRELLI, THAMIRIS; NEPOMUCENO, RAFAEL; RIOS, ANA CLAUDIA S.; ORRICO, SILVANA R. P.; CIRELLI, JONI A.; THEODORO, LETICIA H.; BARROS, SILVANA P.; SCAREL-CAMINAGA, RAQUEL M.. Genetic polymorphisms in theInterleukins IL1B, IL4,andIL6are associated with concomitant periodontitis and type 2 diabetes mellitus in Brazilian patients. JOURNAL OF PERIODONTAL RESEARCH, v. 55, n. 6, p. 13-pg., 2020-07-09. (16/08070-6, 14/13295-1, 16/03753-8, 16/18313-3)

RIMACHI HIDALGO, MARCO A.; CIRELLI, THAMIRIS; DA SILVA, BARBARA ROQUE; NICCHIO, INGRA GAGNO; NEPOMUCENO, RAFAEL; ORRICO, SILVANA R. P.; CIRELLI, JONI A.; THEODORO, LETICIA HELENA; BARROS, SILVANA P.; SCAREL-CAMINAGA, RAQUEL M.. Polymorphisms and haplotypes in the Interleukin 17 Alfa gene: potential effect of smoking habits in the association with periodontitis and type 2 diabetes mellitus. MOLECULAR BIOLOGY REPORTS, v. 48, n. 2, FEB 2021. (18/26367-1, 16/03753-8, 16/08070-6, 16/18313-3, 14/13295-1)

SILVA, ARLES NAISA AMARAL; NICCHIO, INGRA GAGNO; DA SILVA, BARBARA ROQUE; MARTELLI, MAURICIO GANDINI GIANI; HIDALGO, MARCO A. RIMACHI; NEPOMUCENO, RAFAEL; THEODORO, LETICIA H.; CIRELLI, JONI A.; ORRICO, SILVANA R. P.; CIRELLI, THAMIRIS; et al. Polymorphisms in risk genes of type 2 diabetes mellitus could be also markers of susceptibility to periodontitis. ARCHIVES OF ORAL BIOLOGY, v. 143, p. 12-pg., 2022-09-01. (16/18313-3, 16/08070-6, 14/13295-1)

CIRELLI, THAMIRIS; NICCHIO, INGRA G.; BUSSANELI, DIEGO G.; SILVA, BARBARA R.; NEPOMUCENO, RAFAEL; ORRICO, SILVANA R. P.; CIRELLI, JONI A.; THEODORO, LETICIA H.; BARROS, SILVANA P.; SCAREL-CAMINAGA, RAQUEL M.. Evidence Linking PPARG Genetic Variants with Periodontitis and Type 2 Diabetes Mellitus in a Brazilian Population. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, v. 24, n. 7, p. 17-pg., 2023-04-01. (16/08070-6, 16/03753-8, 14/13295-1, 16/18313-3, 18/26367-1)

CIRELLI, THAMIRIS; NEPOMUCENO, RAFAEL; RIOS, ANA CLAUDIA S.; ORRICO, SILVANA R. P.; CIRELLI, JONI A.; THEODORO, LETICIA H.; BARROS, SILVANA P.; SCAREL-CAMINAGA, RAQUEL M.. Genetic polymorphisms in theInterleukins IL1B, IL4,andIL6are associated with concomitant periodontitis and type 2 diabetes mellitus in Brazilian patients. JOURNAL OF PERIODONTAL RESEARCH, v. 55, n. 6, JUL 2020. (14/13295-1, 16/18313-3, 16/03753-8, 16/08070-6)

CIRELLI, THAMIRIS; NEPOMUCENO, RAFAEL; GOVEIA, JESSICA MARINA; ORRICO, SILVANA R. P.; CIRELLI, JONI A.; THEODORO, LETICIA HELENA; BARROS, SILVANA P.; SCAREL-CAMINAGA, RAQUEL M.. Association of type 2 diabetes mellitus and periodontal disease susceptibility with genome-wide association-identified risk variants in a Southeastern Brazilian population. CLINICAL ORAL INVESTIGATIONS, v. 25, n. 6, JAN 2021. (18/26367-1, 14/13295-1, 16/18313-3, 16/08070-6, 16/03753-8)