Polymethylation scores for prenatal maternal smoke exposure persist until age 15 and are detected in saliva in the Fragile Families and Child Wellbeing cohort

References

• U.S. Department of Health and Human Services (2020) Smoking cessation. A report of the surgeon general. Atlanta, GA: U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, National Center for Chronic Disease Prevention and Health Promotion, Office on Smoking and Health
   Google Scholar
• Avşar TS, McLeod H, Jackson L. Health outcomes of smoking during pregnancy and the postpartum period: an umbrella review. BMC Pregnancy Childbirth. 2021. DOI:10.1186/s12884-021-03729-1
   Google Scholar
• Banderali G, Martelli A, Landi M, et al. Short and long term health effects of parental tobacco smoking during pregnancy and lactation: a descriptive review. J Transl Med. 2015;13:327.
   Google Scholar
• U.S. Department of Health and Human services, Substance Abuse and Mental Health Services Administration, Center for Behavioral Health Statistics and Quality. (2019. Accessed10 05 2022). National survey on drug use and health 2018. retrieved from: https://www.samhsa.gov/data/report/2018-nsduh-detailed-tables
   Google Scholar
• Kvalvik LG, Nilsen RM, Skjærven R, et al. Self-reported smoking status and plasma cotinine concentrations among pregnant women in the Norwegian mother and child cohort study. Pediatr Res. 2012;72:101–107.
   Google Scholar
• Dietz PM, Homa D, England LJ, et al. Estimates of nondisclosure of cigarette smoking among pregnant and nonpregnant women of reproductive age in the United States. Am J Epidemiol. 2011;173:355–359.
   Google Scholar
• Dempsey D, Jacob P 3rd, Benowitz NL. Accelerated metabolism of nicotine and cotinine in pregnant smokers. J Pharmacol Exp Ther. 2002;301:594–598.
   Google Scholar
• Rousseaux S, Seyve E, Chuffart F, et al. Immediate and durable effects of maternal tobacco consumption alter placental DNA methylation in enhancer and imprinted gene-containing regions. BMC Med. 2020;18. DOI:10.1186/s12916-020-01736-1.
   Google Scholar
• Joubert BR, Felix JF, Yousefi P, et al. DNA methylation in newborns and maternal smoking in pregnancy: genome-wide consortium meta-analysis. Am J Hum Genet. 2016;98:680–696.
   Google Scholar
• Everson TM, Vives-Usano M, Seyve E, et al. Placental DNA methylation signatures of maternal smoking during pregnancy and potential impacts on fetal growth. Nat Commun. 2021;12:5095.
   Google Scholar
• Cardenas A, Lutz SM, Everson TM, et al. Mediation by placental DNA methylation of the association of prenatal maternal smoking and birth weight. Am J Epidemiol. 2019;188:1878–1886.
   Google Scholar
• Richmond RC, Suderman M, Langdon R, et al. DNA methylation as a marker for prenatal smoke exposure in adults. Int J Epidemiol. 2018;47:1120–1130.
   Google Scholar
• Tehranifar P, Wu H-C, McDonald JA, et al. Maternal cigarette smoking during pregnancy and offspring DNA methylation in midlife. Epigenetics. 2018;13:129–134.
   Google Scholar
• Langie SAS, Moisse M, Declerck K, et al. Salivary DNA methylation profiling: aspects to consider for biomarker identification. Basic Clin Pharmacol Toxicol. 2017;121:93–101.
   Google Scholar
• Bakulski KM, Halladay A, Hu VW, et al. Epigenetic research in neuropsychiatric disorders: the “Tissue issue.” Curr Behav Neurosci Rep 2016;3:264–274.
   Google Scholar
• Ladd-Acosta C, Shu C, Lee BK, et al. Presence of an epigenetic signature of prenatal cigarette smoke exposure in childhood. Environ Res. 2016;144:139–148.
   Google Scholar
• Zhang B, Hong X, Ji H, et al. Maternal smoking during pregnancy and cord blood DNA methylation: new insight on sex differences and effect modification by maternal folate levels. Epigenetics. 2018;13:505–518.
   Google Scholar
• Gonseth S, de Smith AJ, Roy R, et al. Genetic contribution to variation in DNA methylation at maternal smoking-sensitive loci in exposed neonates. Epigenetics. 2016;11:664–673.
   Google Scholar
• Neophytou AM, Oh SS, Hu D, et al. In utero tobacco smoke exposure, DNA methylation, and asthma in latino children. Environ Epidemiol. 2019;3. DOI:10.1097/EE9.0000000000000048
   Google Scholar
• Philibert RA, Beach SRH, Lei M-K, et al. Changes in DNA methylation at the aryl hydrocarbon receptor repressor may be a new biomarker for smoking. Clin Epigenetics. 2013. DOI:10.1186/1868-7083-5-19
   Google Scholar
• Chen J, Zang Z, Braun U, et al. Association of a reproducible epigenetic risk profile for schizophrenia with brain methylation and function. JAMA Psychiatry. 2020;77:628.
   Google Scholar
• Bakulski KM, Fisher JD, Dou JF, et al. Prenatal particulate matter exposure is associated with saliva DNA methylation at age 15: applying cumulative DNA methylation scores as an exposure biomarker. Toxics. 2021;9:262.
   Google Scholar
• Reese SE, Zhao S, Wu MC, et al. DNA methylation score as a biomarker in newborns for sustained maternal smoking during pregnancy. Environ Health Perspect. 2017;125:760–766.
   Google Scholar
• Philibert R, Dogan M, Beach SRH, et al. AHRR methylation predicts smoking status and smoking intensity in both saliva and blood DNA. Am J Med Genet B Neuropsychiatr Genet. 2020;183(1):51–60.
   Google Scholar
• Reichman NE, Teitler JO, Garfinkel I, et al. Fragile families: sample and design. Child Youth Services Rev. 2001;23:303–326.
   Google Scholar
• Gard AM, Maxwell AM, Shaw DS, et al. Beyond family-level adversities: exploring the developmental timing of neighborhood disadvantage effects on the brain. Dev Sci. 2020. DOI:10.1111/desc.12985
   Google Scholar
• Ware EB, Fisher J, Schneper L, et al. FFCWS polygenic scores - release 1. Michigan, New Jersey: Institute for Social Research, University of Michigan; Department of Molecular Biology, Princeton University; 2021. Accessed 10 05 2022. Survey Research Center.
   Google Scholar
• Sandoval J, Heyn H, Moran S, et al. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics. 2011;6:692–702.
   Google Scholar
• Xu Z, Niu L, Taylor JA. The ENmix DNA methylation analysis pipeline for Illumina beadchip and comparisons with seven other preprocessing pipelines. Clin Epigenetics. 2021;13. DOI:10.1186/s13148-021-01207-1.
   Google Scholar
• Heiss JA, Just, Just AC, AC. Identifying mislabeled and contaminated DNA methylation microarray data: an extended quality control toolset with examples from GEO. Clin Epigenetics. 2018;10. 10.1186/s13148-018-0504-1.
   Google Scholar
• Chen Y, Lemire M, Choufani S, et al. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina infinium humanmethylation450 microarray. Epigenetics. 2013;8:203–209.
   Google Scholar
• Middleton LYM, Dou J, Fisher J, et al. Saliva cell type DNA methylation reference panel for epidemiological studies in children. Epigenetics. 2021 17 2 ;161–177.
   Google Scholar
• Rauschert S, Melton PE, Heiskala A, et al. Machine learning-based DNA methylation score for fetal exposure to maternal smoking: development and validation in samples collected from adolescents and adults. Environ Health Perspect. 2020;128:097003.
   Google Scholar
• Rauschert S. DNAsmokeR: DNA methylation based score for in utero exposure to maternal smoking. 2019.
   Google Scholar
• Wiklund P, Karhunen V, Richmond RC, et al. DNA methylation links prenatal smoking exposure to later life health outcomes in offspring. Clin Epigenetics. 2019;11. DOI:10.1186/s13148-019-0683-4.
   Google Scholar
• McEwen LM, O’Donnell KJ, McGill MG, et al. (2019) The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells. Proc Natl Acad Sci U S A. 117;38:23329–23335. doi:10.1073/pnas.1820843116.
   Google Scholar
• Lu AT, Quach A, Wilson JG, et al. DNA methylation GrimAge strongly predicts lifespan and healthspan. Aging (Albany NY). 2019;11:303–327.
   Google Scholar
• Jt L, WE J, HS P, et al. Sva: surrogate variable analysis. 2021.
   Google Scholar
• Robin X, Turck N, Hainard A, et al. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics. 2011;12. DOI:10.1186/1471-2105-12-77.
   Google Scholar
• Langie SAS, Szarc Vel Szic K, Declerck K, et al. Whole-genome saliva and blood DNA methylation profiling in individuals with a respiratory allergy. PLOS ONE. 2016;11:e0151109.
   Google Scholar
• Martin AR, Kanai M, Kamatani Y, et al. Clinical use of current polygenic risk scores may exacerbate health disparities. Nat Genet. 2019;51:584–591.
   Google Scholar
• Hüls A, Czamara D. Methodological challenges in constructing DNA methylation risk scores. Epigenetics. 2019;15:1–11.
   Google Scholar
• Xu R, Hong X, Zhang B, et al. DNA methylation mediates the effect of maternal smoking on offspring birthweight: a birth cohort study of multi-ethnic US mothernewborn pairs. Clin Epigenetics. 2021;13. DOI:10.1186/s13148-021-01032-6.
   Google Scholar
• Borrell LN, Elhawary JR, Fuentes-Afflick E, et al. Race and genetic ancestry in medicinea time for reckoning with racism. N Engl J Med. 2021;384:474–480.
   Google Scholar
• Okazaki S, Otsuka I, Shinko Y, et al. Epigenetic clock analysis in children with fetal alcohol spectrum disorder. Alcohol Clin Exp Res. 2021;45:329–337.
   Google Scholar
• Pineles BL, Park E, Samet JM. Systematic review and meta-analysis of miscarriage and maternal exposure to tobacco smoke during pregnancy. Am J Epidemiol. 2014;179:807–823.
   Google Scholar
• Leung M, Kioumourtzoglou M-A, Raz R, et al. Bias due to selection on live births in studies of environmental exposures during pregnancy: a simulation study. Environ Health Perspect. 2021;129. DOI:10.1289/ehp7961.
   Google Scholar
• Liew Z, Olsen J, Cui X, et al. Bias from conditioning on live birth in pregnancy cohorts: an illustration based on neurodevelopment in children after prenatal exposure to organic pollutants. Int J Epidemiol. 2015;44:345–354.
   Google Scholar
• Liu C, Marioni RE, Hedman ÅK, et al. A DNA methylation biomarker of alcohol consumption. Mol Psychiatry. 2016;23:422–433.
   Google Scholar
• Ligthart S, Marzi C, Aslibekyan S, et al. DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases. Genome Biol. 2016;17. DOI:10.1186/s13059-016-1119-5.
   Google Scholar
• Sayols-Baixeras S, Subirana I, Fernández-Sanlés A, et al. DNA methylation and obesity traits: an epigenome-wide association study. The REGICOR study. Epigenetics. 2017;12:909–916.
   Google Scholar
• Wahl S, Drong A, Lehne B, et al. Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity. Nature. 2016;541:81–86.
   Google Scholar
• Sirugo G, Williams SM, Tishkoff SA. The missing diversity in human genetic studies. Cell. 2019;177:26–31.
   Google Scholar
• Bentley AR, Callier S, Rotimi CN. Diversity and inclusion in genomic research: why the uneven progress? J Community Genet. 2017;8:255–266.
   Google Scholar