DNA Methylation Abundantly Associates with Fetal Alcohol Spectrum Disorder and its Subphenotypes

References

• Popova S , LangeS , ProbstC , GmelG , RehmJ . Estimation of national, regional, and global prevalence of alcohol use during pregnancy and fetal alcohol syndrome: a systematic review and meta-analysis . Lancet. Glob. Health5 ( 3 ), e290 – e299 ( 2017 ).
   PubMed Web of Science ®Google Scholar
• May PA , BaeteA , RussoJet al. Prevalence and characteristics of fetal alcohol spectrum disorders . Pediatrics134 ( 5 ), 855 – 866 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• May PA , ChambersCD , KalbergWOet al. Prevalence of fetal alcohol spectrum disorders in 4 US communities . JAMA319 ( 5 ), 474 – 482 ( 2018 ).
   PubMed Web of Science ®Google Scholar
• Lange S , RehmJ , PopovaS . Implications of higher than expected prevalence of fetal alcohol spectrum disorders . JAMA319 ( 5 ), 448 – 449 ( 2018 ).
   PubMed Web of Science ®Google Scholar
• Coles CD , GaileyAR , MulleJG , KableJA , LynchME , JonesKL . A comparison among 5 methods for the clinical diagnosis of fetal alcohol spectrum disorders . Alcohol Clin. Exp. Res.40 ( 5 ), 1000 – 1009 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Astley SJ . Validation of the fetal alcohol spectrum disorder (FASD) 4-digit diagnostic code . J. Popul. Ther. Clin. Pharmacol.20 ( 3 ), e416 – e467 ( 2013 ).
   PubMedGoogle Scholar
• Hoyme HE , MayPA , KalbergWOet al. A practical clinical approach to diagnosis of fetal alcohol spectrum disorders: clarification of the 1996 institute of medicine criteria . Pediatrics115 ( 1 ), 39 – 47 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Hoyme HE , KalbergWO , ElliottAJet al. Updated clinical guidelines for diagnosing fetal alcohol spectrum disorders . Pediatrics138 ( 2 ), pii: e20154256 ( 2016 ).
   Web of Science ®Google Scholar
• Chasnoff IJ , WellsAM , KingL . Misdiagnosis and missed diagnoses in foster and adopted children with prenatal alcohol exposure . Pediatrics135 ( 2 ), 264 – 270 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Caprara DL , NashK , GreenbaumR , RovetJ , KorenG . Novel approaches to the diagnosis of fetal alcohol spectrum disorder . Neurosci. Biobehav. Rev.31 ( 2 ), 254 – 260 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Eberhart JK , ParnellSE . The genetics of fetal alcohol spectrum disorders . Alcohol Clin. Exp. Res.40 ( 6 ), 1154 – 1165 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Julian CG . Epigenomics and human adaptation to high altitude . J. Appl. Physiol. (1985)   123 ( 5 ), 1362 – 1370 ( 2017 ).
   PubMed Web of Science ®Google Scholar
• Liu L , LiY , TollefsbolTO . Gene–environment interactions and epigenetic basis of human diseases . Curr. Issues Mol. Biol.10 ( 1–2 ), 25 – 36 ( 2008 ).
   PubMedGoogle Scholar
• Waterland RA , TravisanoM , TahilianiKG , RachedMT , MirzaS . Methyl donor supplementation prevents transgenerational amplification of obesity . Int. J. Obes. (Lond.)32 ( 9 ), 1373 – 1379 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Nemoda Z , SzyfM . Epigenetic alterations and prenatal maternal depression . Birth Defects Res.109 ( 12 ), 888 – 897 ( 2017 ).
   PubMedGoogle Scholar
• Joubert BR , FelixJF , YousefiPet al. DNA methylation in newborns and maternal smoking in pregnancy: genome-wide consortium meta-analysis . Am. J. Hum. Genet.98 ( 4 ), 680 – 696 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Tobi EW , GoemanJJ , MonajemiRet al. DNA methylation signatures link prenatal famine exposure to growth and metabolism . Nat. Commun.5 , 5592 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Liu Y , BalaramanY , WangG , NephewKP , ZhouFC . Alcohol exposure alters DNA methylation profiles in mouse embryos at early neurulation . Epigenetics4 ( 7 ), 500 – 511 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Laufer BI , DiehlEJ , SinghSM . Neurodevelopmental epigenetic etiologies: insights from studies on mouse models of fetal alcohol spectrum disorders . Epigenomics5 ( 5 ), 465 – 468 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Laufer BI , ManthaK , KleiberML , DiehlEJ , AddisonSM , SinghSM . Long-lasting alterations to DNA methylation and ncRNAs could underlie the effects of fetal alcohol exposure in mice . Dis. Model Mech.6 ( 4 ), 977 – 992 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Laufer BI , KapalangaJ , CastellaniCA , DiehlEJ , YanL , SinghSM . Associative DNA methylation changes in children with prenatal alcohol exposure . Epigenomics7 ( 8 ), 1259 – 1274 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Manolio TA , CollinsFS , CoxNJet al. Finding the missing heritability of complex diseases . Nature461 ( 7265 ), 747 – 753 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Dirks RA , StunnenbergHG , MarksH . Genome-wide epigenomic profiling for biomarker discovery . Clin. Epigenetics8 , 122 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Abdelmalik N , Van HaelstM , ManciniGet al. Diagnostic outcomes of 27 children referred by pediatricians to a genetics clinic in The Netherlands with suspicion of fetal alcohol spectrum disorders . Am. J. Med. Genet. A.161A ( 2 ), 254 – 260 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Touleimat N , TostJ . Complete pipeline for Infinium((R)) Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation . Epigenomics4 ( 3 ), 325 – 341 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Chen YA , LemireM , ChoufaniSet al. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray . Epigenetics8 ( 2 ), 203 – 209 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Houseman EA , AccomandoWP , KoestlerDCet al. DNA methylation arrays as surrogate measures of cell mixture distribution . BMC Bioinformatics13 , 86 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Mistry M , GillisJ , PavlidisP . Genome-wide expression profiling of schizophrenia using a large combined cohort . Mol. Psychiatry18 ( 2 ), 215 – 225 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Aryee MJ , JaffeAE , Corrada-BravoHet al. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays . Bioinformatics30 ( 10 ), 1363 – 1369 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Tsai PC , BellJT . Power and sample size estimation for epigenome-wide association scans to detect differential DNA methylation . Int. J. Epidemiol.44 ( 4 ), 1429 – 1441 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Lin X , BartonS , HolbrookJD . How to make DNA methylome wide association studies more powerful . Epigenomics8 ( 8 ), 1117 – 1129 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Gauthier TW . Prenatal alcohol exposure and the developing immune system . Alcohol Res.37 ( 2 ), 279 – 285 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Lussier AA , BodnarTS , MingayMet al. Prenatal alcohol exposure: profiling developmental DNA methylation patterns in central and peripheral tissues . Front. Genet.9 , 610 ( 2018 ).
   PubMed Web of Science ®Google Scholar
• Bacalini MG , GentiliniD , BoattiniAet al. Identification of a DNA methylation signature in blood cells from persons with down syndrome . Aging (Albany NY)7 ( 2 ), 82 – 96 ( 2015 ).
   PubMedGoogle Scholar
• Starnawska A , HansenCS , SparsoTet al. Differential DNA methylation at birth associated with mental disorder in individuals with 22q11.2 deletion syndrome . Transl. Psychiatry7 ( 8 ), e1221 ( 2017 ).
   PubMed Web of Science ®Google Scholar
• Whittaker S . Global patterns of methylation in sezary syndrome provide insight into the role of epigenetics in cutaneous T-Cell lymphoma . J. Invest. Dermatol.136 ( 9 ), 1753 – 1754 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Portales-Casamar E , LussierAA , JonesMJet al. DNA methylation signature of human fetal alcohol spectrum disorder . Epigenetics Chromatin9 , 25 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Lussier AA , MorinAM , MacisaacJLet al. DNA methylation as a predictor of fetal alcohol spectrum disorder . Clin. Epigenetics10 , 5 ( 2018 ).
   PubMed Web of Science ®Google Scholar
• Sharp GC , ArathimosR , ReeseSEet al. Maternal alcohol consumption and offspring DNA methylation: findings from six general population-based birth cohorts . Epigenomics10 ( 1 ), 27 – 42 ( 2018 ).
   PubMed Web of Science ®Google Scholar
• Breton CV , MarsitCJ , FaustmanEet al. Small-magnitude effect sizes in epigenetic end points are important in children’s environmental health studies: The Children’s Environmental Health and Disease Prevention Research Center’s Epigenetics Working Group . Environ. Health Perspect.125 ( 4 ), 511 – 526 ( 2017 ).
   PubMed Web of Science ®Google Scholar
• Michels KB , BinderAM , DedeurwaerderSet al. Recommendations for the design and analysis of epigenome-wide association studies . Nat. Methods10 ( 10 ), 949 – 955 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Lee K , KunkeawN , JeonSHet al. Precursor miR-886, a novel noncoding RNA repressed in cancer, associates with PKR and modulates its activity . RNA17 ( 6 ), 1076 – 1089 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Minina VI , SobolevaOA , GlushkovANet al. Polymorphisms of GSTM1, GSTT1, GSTP1 genes and chromosomal aberrations in lung cancer patients . J. Cancer Res. Clin. Oncol.143 ( 11 ), 2235 – 2243 ( 2017 ).
   PubMed Web of Science ®Google Scholar
• Rahbar MH , Samms-VaughanM , MaJet al. Interaction between GSTT1 and GSTP1 allele variants as a risk modulating-factor for autism spectrum disorders . Res. Autism Spectr. Disord.12 , 1 – 9 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Fish EW , MurdaughLB , SulikKK , WilliamsKP , ParnellSE . Genetic vulnerabilities to prenatal alcohol exposure: limb defects in Sonic Hedgehog and GLI2 heterozygous mice . Birth Defects Res.109 ( 11 ), 860 – 865 ( 2017 ).
   PubMedGoogle Scholar
• Flemming GM , KlammtJ , AmblerGet al. Functional characterization of a heterozygous GLI2 missense mutation in patients with multiple pituitary hormone deficiency . J. Clin. Endocrinol. Metab.98 ( 3 ), E567 – E575 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Cartwright MM , SmithSM . Stage-dependent effects of ethanol on cranial neural crest cell development: partial basis for the phenotypic variations observed in fetal alcohol syndrome . Alcohol Clin. Exp. Res.19 ( 6 ), 1454 – 1462 ( 1995 ).
   PubMed Web of Science ®Google Scholar
• Cartwright MM , SmithSM . Increased cell death and reduced neural crest cell numbers in ethanol-exposed embryos: partial basis for the fetal alcohol syndrome phenotype . Alcohol Clin. Exp. Res.19 ( 2 ), 378 – 386 ( 1995 ).
   PubMed Web of Science ®Google Scholar
• Tolosa EJ , Fernandez-ZapicoME , BattiatoNL , RovasioRA . Sonic Hedgehog is a chemotactic neural crest cell guide that is perturbed by ethanol exposure . Eur. J. Cell Biol.95 ( 3–5 ), 136 – 152 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Pispa J , PummilaM , BarkerPA , ThesleffI , MikkolaML . Edar and Troy signalling pathways act redundantly to regulate initiation of hair follicle development . Hum. Mol. Genet.17 ( 21 ), 3380 – 3391 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Hisaoka T , MorikawaY , KomoriT , SugiyamaT , KitamuraT , SenbaE . Characterization of TROY-expressing cells in the developing and postnatal CNS: the possible role in neuronal and glial cell development . Eur. J. Neurosci.23 ( 12 ), 3149 – 3160 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Zlotina A , NikulinaT , YanyNet al. Ring chromosome 18 in combination with 18q12.1 (DTNA) interstitial microdeletion in a patient with multiple congenital defects . Mol. Cytogenet.9 , 18 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Finsterer J . Cardiogenetics, neurogenetics, and pathogenetics of left ventricular hypertrabeculation/noncompaction . Pediatr. Cardiol.30 ( 5 ), 659 – 681 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Moric-Janiszewska E , Markiewicz-LoskotG . Genetic heterogeneity of left-ventricular noncompaction cardiomyopathy . Clin. Cardiol.31 ( 5 ), 201 – 204 ( 2008 ).
   PubMed Web of Science ®Google Scholar