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Bioinformatics analysis for variants identification in patients with Molar Incisor Hypomineralization (MIH)

Grant number: 19/26920-5
Support type:Scholarships abroad - Research Internship - Post-doctor
Effective date (Start): February 29, 2020
Effective date (End): July 28, 2020
Field of knowledge:Health Sciences - Dentistry - Pediatric Dentistry
Principal Investigator:Raquel Mantuaneli Scarel Caminaga
Grantee:Diego Girotto Bussaneli
Supervisor abroad: Hakon Hakonarson
Home Institution: Faculdade de Odontologia (FOAr). Universidade Estadual Paulista (UNESP). Campus de Araraquara. Araraquara , SP, Brazil
Local de pesquisa : Children's Hospital of Philadelphia (CHOP), United States  
Associated to the scholarship:17/22252-2 - Whole-exome sequencing for investigation of genetic variants associated with molar-incisor HIPOMINERALIZATION, BP.PD

Abstract

Molar-Incisor Hypomineralization (MIH) is an enamel defect of systemic origin that affects one or more permanent primary molars, and may or may not be associated with the permanent incisors. From the etiological point of view, this condition may be considered multifactorial and complex. Recently, genetic variants such as polymorphisms and some genes related for enamel formation were associated with MIH. However, considering that the human genome contains millions of genetic variants (mutations and polymorphisms), the genetic etiology of MIH needs to be investigated more extensively, the aim of this study is to identify genetic alterations, by means of investigating the expanded exome of patients with MIH, with the purpose of gaining better understanding of the genetic component as an etiological factor of this condition. The methodology of the whole exome sequencing is also known as New Generation Sequencing, or NGS (Next Generation Sequencing), which is the most modern genetic screening methodology. Since 2008, we have organized a DNA Sample Bank, which at present contains 104 families that have at least one child affected by MIH. Each patient has a complete history of medical and dental characteristics, and we also have retrospective information about the gestational period of the children. Saliva was collected from 402 patients (coming from 104 families), whose DNA was extracted and quantified. An aliquot of this DNA will be used for extensive investigation of the genetic variants by means of expanded exome, which will be performed as outsourced services provided by a specialized company. The final number of families included will be the maximum number that the value financed by FAPESP (US$ 30.000,00) will allow; that is to say, considering these values, it will be possible to sequence the exome of approximately 30 families (100 patients). As soon as the files containing the sequences are made available, we will perform the complex bioinformatic and statistical analyses. Initially, we intend comparing the sequencing among the members of each family, discarding the common variants between the affected and non-affected genitor, as well as the variants in common with the non-affected child. Subsequently, only the variants in common with the affected child will be selected. The same filtering of variants methodology will be applied to each family, until the sequences of the affected individuals have been compared, seeking to identify the variants in common between them, which may be considered associated with MIH. The selected variants will be validated by means of Sanger sequencing. For prospecting the function of the validated variants, Bioinformatics analyses will be performed such as construction of a protein-protein interaction (PPI) network and silico analysis to identify the impact of each variant on the protein structure of the respective gene. Lastly, we intend to correlate these genetic variants with the clinical characteristics of the patients and severity of MIH.