Common genetic variants associated with urinary phthalate levels in children: a genome-wide study

Introduction Phthalates, or dieters of phthalic acid, are a ubiquitous type of plasticizer used in a variety of common consumer and industrial products. They act as endocrine disruptors and are associated with increased risk for several diseases. Once in the body, phthalates are metabolized through partially known mechanisms, involving phase I and phase II enzymes. Objective In this study we aimed to identify common single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) associated with the metabolism of phthalate compounds in children through genome-wide association studies (GWAS). Methods The study used data from 1,044 children with European ancestry from the Human Early Life Exposome (HELIX) cohort. Ten phthalate metabolites were assessed in a two-void urine pool collected at the mean age of 8 years. Six ratios between secondary and primary phthalate metabolites were calculated. Genome-wide genotyping was done with the Infinium Global Screening Array (GSA) and imputation with the Haplotype Reference Consortium (HRC) panel. PennCNV was used to estimate copy number variants (CNVs) and CNVRanger to identify consensus regions. GWAS of SNPs and CNVs were conducted using PLINK and SNPassoc, respectively. Subsequently, functional annotation of suggestive SNPs (p-value <1E-05) was done with the FUMA web-tool. Results We identified four genome-wide significant (p-value <5E-08) loci at chromosome (chr) 3 ( FECHP1 for oxo-MiNP\_oh-MiNP ratio), chr6 ( SLC17A1 for MECPP\_MEHPP ratio), chr9 ( RAPGEF1 for MBzP), and chr10 ( CYP2C9 for MECPP_MEHPP ratio). Moreover, 113 additional loci were found at suggestive significance (p-value <1E-05). Two CNVs located at chr11 ( MRGPRX1 for oh-MiNP and SLC35F2 for MEP) were also identified. Functional annotation pointed to genes involved in phase I and phase II detoxification, molecular transfer across membranes, and renal excretion. Conclusion Through genome-wide screenings we identified known and novel loci implicated in phthalate metabolism in children. Genes annotated to these loci participate in detoxification and renal excretion. ![Figure][1] Highlights ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement The study has received funding from the European Community's Seventh Framework Programme (FP7/2007-206) under grant agreement no 308333 (HELIX project) and the H2020-EU.3.1.2. - Preventing Disease Programme under grant agreement no 874583 (ATHLETE project). The genotyping was supported by the project PI17/01225 and PI17/01935, funded by the Instituto de Salud Carlos III and co-funded by European Union (ERDF, "A way to make Europe") and the Centro Nacional de Genotipado-CEGEN (PRB2-ISCIII). BiB received core infrastructure funding from the Wellcome Trust (WT101597MA) and a joint grant from the UK Medical Research Council (MRC) and Economic and Social Science Research Council (ESRC) (MR/N024397/1), and National Institute for Health Research Applied Research Collaboration Yorkshire and Humber (NIHR200166). The views expressed are those of the author(s), and not necessarily those of the NHS, the NIHR or the Department of Health and Social Care. INMA data collections were supported by grants from the Instituto de Salud Carlos III, CIBERESP, and the Generalitat de Catalunya-CIRIT. KANC was funded by the grant of the Lithuanian Agency for Science Innovation and Technology (6-04-2014_31V-66). The Norwegian Mother, Father and Child Cohort Study is supported by the Norwegian Ministry of Health and Care Services and the Ministry of Education and Research. The Rhea project was financially supported by European projects (EU FP6-2003-Food-3-NewGeneris, EU FP6. STREP Hiwate, EU FP7 ENV.2007.1.2.2.2. Project No 211250 Escape, EU FP7-2008-ENV-1.2.1.4 Envirogenomarkers, EU FP7-HEALTH-2009- single stage CHICOS, EU FP7 ENV.2008.1.2.1.6. Proposal No 226285 ENRIECO, EU- FP7- HEALTH-2012 Proposal No 308333 HELIX), and the Greek Ministry of Health (Program of Prevention of obesity and neurodevelopmental disorders in preschool children, in Heraklion district, Crete, Greece: 2011-2014; "Rhea Plus": Primary Prevention Program of Environmental Risk Factors for Reproductive Health, and Child Health: 2012-15). ISGlobal acknowledges support from the Spanish Ministry of Science and Innovation through the "Centro de Excelencia Severo Ochoa 2019-2023" Program (CEX2018-000806-S), and support from the Generalitat de Catalunya through the CERCA Program. CRG acknowledge the support of the Spanish Ministry of Science, Innovation, and Universities to the EMBL partnership, the Centro de Excelencia Severo Ochoa, and the CERCA Programme/Generalitat de Catalunya. LM is funded by a Juan de la Cierva-Incorporación fellowship (IJC2018-035394-I) awarded by the Spanish Ministerio de Economía, Industria y Competitividad. MC holds a Miguel Servet fellowship (MS16/00128) funded by Instituto de Salud Carlos III and co-funded by European Social Fund "Investing in your future". ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics committee of Parc de Salut MAR, Barcelona, Spain, gave ethical approval for this work (REF: 2005/2106/I and 2013/5414/I). Regional Ethical Committee for Medical and Health Research (Regionale komiteer for medisinsk og helsefaglig forskningsetikk), Norway, gave ethical approval for this work (REF: 2013/1628 REK sør-øst B). Ethical Committee of the general university hospital of Heraklion, Crete, Greece, gave ethical approval for this work (REF: 14694/5-11-2013). Ethical Committee for people protection (Comite de Protection des personnes), Grenoble, France, gave ethical approval for this work (REF: 2013-A01491-44). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The raw data supporting the current study are available from the corresponding author on request subject to ethical and legislative review. The "HELIX Data External Data Request Procedures" are available with the data inventory in this website: http://www.projecthelix.eu/data-inventory. * ABC : ATP-binding cassette BBP : butylbenzyl phthalate chr : chromosome CNV : copy number variant CYP : Cytochrome P450 monooxygenase DBzP : dibenzyl phthalate DEP : diethyl phthalate DEHP : bis(2-ethylhexyl) phthalate DiBP : diisobutyl phthalate DINCH : 2-cyclohexane dicarboxylic acid, diisononyl ester DnBP : di-n-butyl-phthalate EDCs : endocrine disrupting chemicals GSA : Infinium Global Screening Array GWAS : genome-wide association study HELIX : Human Early Life Exposome project HMW : high-molecular-weight HRC : haplotype reference consortium LD : linkage disequilibrium LMW : low-molecular-weight MBzP : mono benzyl phthalate MECPP : mono-2-ethyl-5-carboxypentyl phthalate MECPP_MEHP : ratio between MECPP and MEHP MECPP_MEHHP : ratio between MECPP and MEHHP MEHHP : mono-2-ethyl-5-hydroxyhexyl phthalate MEHHP_MEHP : ratio between MEHHP and MEHP MEHP : mono-2-ethylhexyl phthalate MEOHP : mono-2-ethyl-5-oxohexyl phthalate MEOHP_MEHP : ratio between MEOHP and MEHP MEOPP_MEHHP : ratio between MEOPP and MEHHP MEP : monoethyl phthalate MiBP : mono-iso-butyl phthalate MnBP : mono-n-butyl phthalate oh-MiNP : mono-4-methyl-7-hydroxyoctyl phthalate oxo-MiNP : mono-4-methyl-7-oxooctyl phthalate oxo-MiNP_oh-MiNP : ratio between oxo-MiNP and oh-MiNP PVC : polyvinyl chloride QQ : quantile-quantile SCL : Solute carrier SNP : single nucleotide polymorphism SULT : Sulfotransferase UGT : UDP-glucuronosyltransferase [1]: pending:yes