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      Protocol for CARES–HAPIN: an ambidirectional cohort study on exposure to environmental tobacco smoke and risk of early childhood caries

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          Abstract

          Introduction

          Prenatal and postnatal exposure to environmental tobacco smoke (ETS) has been linked with early childhood caries (ECC), but the specific molecular mechanisms and pathways remain largely unknown. The Caries Risk from exposure to Environmental tobacco Smoke (CARES) within the Household Air Pollution Intervention Network (HAPIN) study aims to establish the association between ETS and ECC by employing epidemiological and novel biomarker-based approaches. Here, we outline the overall design and rationale of the project.

          Methods and analysis

          We will leverage the infrastructure and data from the HAPIN trial (India) to mount the CARES study. In this ambidirectional cohort study, children (n=735, aged: 3–5 years) will undergo ECC examination by a trained dentist using standard criteria and calibrated methods. Structured questionnaires will be used to gather information on sociodemographic variables, dietary habits, oral hygiene, oral health-related quality of life and current exposure to ETS. We will collect non-invasive or minimally invasive biospecimens (i.e., saliva, buccal cells, dried blood spots and urine) from a subset of HAPIN children (n=120) to assess a battery of biomarkers indicative of exposure to ETS, early biological effect and epigenetic modifications. Both self-reported and objective measures of ETS exposure collected longitudinally during in utero and early postnatal periods will be accessed from the HAPIN database. We will apply current science data techniques to assess the association and interrelationships between ETS, ECC, and multiple biomarkers.

          Ethics and dissemination

          Information gathered in this research will be published in peer-reviewed journals and summaries will be shared with the key stakeholders as well as patients and their parents/guardians involved in this study. Sri Ramachandra Institute of Higher Education and Research Ethics Board has approved the study protocol (IEC-NI22/JUL/83/82).

          Trial registration number

          NCT02944682.

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          Most cited references64

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          Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.

          The recently released Infinium HumanMethylation450 array (the '450k' array) provides a high-throughput assay to quantify DNA methylation (DNAm) at ∼450 000 loci across a range of genomic features. Although less comprehensive than high-throughput sequencing-based techniques, this product is more cost-effective and promises to be the most widely used DNAm high-throughput measurement technology over the next several years. Here we describe a suite of computational tools that incorporate state-of-the-art statistical techniques for the analysis of DNAm data. The software is structured to easily adapt to future versions of the technology. We include methods for preprocessing, quality assessment and detection of differentially methylated regions from the kilobase to the megabase scale. We show how our software provides a powerful and flexible development platform for future methods. We also illustrate how our methods empower the technology to make discoveries previously thought to be possible only with sequencing-based methods. http://bioconductor.org/packages/release/bioc/html/minfi.html. khansen@jhsph.edu; rafa@jimmy.harvard.edu Supplementary data are available at Bioinformatics online.
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            Hierarchical Grouping to Optimize an Objective Function

            Joe Ward (1963)
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              Orchestrating high-throughput genomic analysis with Bioconductor.

              Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors.
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                Author and article information

                Journal
                BMJ Open
                BMJ Open
                bmjopen
                bmjopen
                BMJ Open
                BMJ Publishing Group (BMA House, Tavistock Square, London, WC1H 9JR )
                2044-6055
                2024
                15 May 2024
                : 14
                : 5
                : e083874
                Affiliations
                [1 ] departmentDepartment of Environmental Health Engineering, Faculty of Public Health , Ringgold_204733Sri Ramachandra Institute of Higher Education and Research (Deemed to be University) , Chennai, Tamil Nadu, India
                [2 ] departmentDepartment of Pediatric and Preventive Dentistry , Dr. D.Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth , Pune, Maharashtra, India
                [3 ] departmentDepartment of Epidemiology and Population Health , Stanford University , Stanford, California, USA
                [4 ] departmentGangarosa Department of Environmental Health , Rollins School of Public Health, Emory University , Atlanta, Georgia, USA
                [5 ] departmentDepartment of Biostatistics , St John's Medical College , Bengaluru, Karnataka, India
                Author notes
                [Correspondence to ] Dr Naveen Puttaswamy; naveen@ 123456ehe.org.in
                Author information
                http://orcid.org/0000-0001-6698-2711
                http://orcid.org/0000-0002-8221-1682
                http://orcid.org/0000-0002-5566-2138
                Article
                bmjopen-2024-083874
                10.1136/bmjopen-2024-083874
                11097839
                38749682
                f860c6e3-cf55-467e-9d82-f9a005ef63c9
                © Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY. Published by BMJ.

                This is an open access article distributed in accordance with the Creative Commons Attribution 4.0 Unported (CC BY 4.0) license, which permits others to copy, redistribute, remix, transform and build upon this work for any purpose, provided the original work is properly cited, a link to the licence is given, and indication of whether changes were made. See: https://creativecommons.org/licenses/by/4.0/.

                History
                : 02 January 2024
                : 09 April 2024
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000865, Bill and Melinda Gates Foundation;
                Award ID: OPP1131279
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: D43TW010540
                Award ID: cooperative agreement 1UM1HL134590
                Categories
                Dentistry and Oral Medicine
                1506
                1686
                Protocol
                Custom metadata
                unlocked

                Medicine
                public health,community child health,epidemiologic studies
                Medicine
                public health, community child health, epidemiologic studies

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