Epigenome-Wide Cross-Tissue Predictive Modeling and Comparison of Cord Blood and Placental Methylation in a Birth Cohort

References

• Barrero MJ , BoueS , Izpisua BelmonteJC . Epigenetic mechanisms that regulate cell identity . Cell Stem Cell7 ( 5 ), 565 – 570 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Cedar H , BergmanY . Programming of DNA methylation patterns . Annu. Rev. Biochem.81 , 97 – 117 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Kiefer JC . Epigenetics in development . Dev. Dyn.236 ( 4 ), 1144 – 1156 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Barault L , EllsworthRE , HarrisHR , ValenteAL , ShriverCD , MichelsKB . Leukocyte DNA as surrogate for the evaluation of imprinted Loci methylation in mammary tissue DNA . PLoS ONE8 ( 2 ), e55896 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Ursini G , BollatiV , FazioLet al. Stress-related methylation of the catechol-O-methyltransferase Val 158 allele predicts human prefrontal cognition and activity . J. Neurosci.31 ( 18 ), 6692 – 6698 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Byun HM , SiegmundKD , PanFet al. Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns . Hum. Mol. Genet.18 ( 24 ), 4808 – 4817 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Caliskan M , CusanovichDA , OberC , GiladY . The effects of EBV transformation on gene expression levels and methylation profiles . Hum. Mol. Genet.20 ( 8 ), 1643 – 1652 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Fan S , ZhangX . CpG island methylation pattern in different human tissues and its correlation with gene expression . Biochem. Biophys. Res. Commun.383 ( 4 ), 421 – 425 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Ma B , WilkerEH , Willis-OwenSAet al. Predicting DNA methylation level across human tissues . Nucleic Acids Res.42 ( 6 ), 3515 – 3528 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Vapnik VN . Statistical Learning Theory.Wiley , New York ( 1998 ).
   Google Scholar
• Janssen BG , ByunHM , GyselaersW , LefebvreW , BaccarelliAA , NawrotTS . Placental mitochondrial methylation and exposure to airborne particulate matter in the early life environment: an ENVIRONAGE birth cohort study . Epigenetics10 ( 6 ), 536 – 544 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Fortin JP , LabbeA , LemireMet al. Functional normalization of 450k methylation array data improves replication in large cancer studies . Genome Biol.15 ( 12 ), 503 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Buhule OD , MinsterRL , HawleyNLet al. Stratified randomization controls better for batch effects in 450K methylation analysis: a cautionary tale . Front. Genet.5 , 354 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Triche TJ Jr , WeisenbergerDJ , Van Den BergD , LairdPW , SiegmundKD . Low-level processing of Illumina Infinium DNA Methylation BeadArrays . Nucleic Acids Res.41 ( 7 ), e90 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Teschendorff AE , MarabitaF , LechnerMet al. A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data . Bioinformatics29 ( 2 ), 189 – 196 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Pidsley R , CcYW , VoltaM , LunnonK , MillJ , SchalkwykLC . A data-driven approach to preprocessing Illumina 450k methylation array data . BMC Genomics14 , 293 ( 2013 ).
   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
• Butcher L . Illumina450ProbeVariants.db: Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes. R package version 1.6.0 ( 2013 ). https://bioc.ism.ac.jp/packages/3.2/data/experiment/html/Illumina450ProbeVariants.db.html
   Google Scholar
• Sofer T , SchifanoED , HoppinJA , HouL , BaccarelliAA . A-clustering: a novel method for the detection of co-regulated methylation regions, and regions associated with exposure . Bioinformatics29 ( 22 ), 2884 – 2891 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Hastie TT , FriedmanJ . The Elements of Statistical Learning. Data Mining, Inference, and Prediction (2nd Edition).Springer-Verlag , NY, USA ( 2009 ).
   Google Scholar
• Kuhn M . caret: Classification and Regression Training. R package version 6.0–71 . https://CRAN.R-project.org/package=caret
   Google Scholar
• Illumina . http://support.illumina.com/array/array_kits/infinium_humanmethylation450_beadchip_kit/downloads.html
   Google Scholar
• Court F , TayamaC , RomanelliVet al. Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment . Genome Res.24 ( 4 ), 554 – 569 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• R Core Team . R: a language and environment for statistical computing . www.R-project.org/
   Google Scholar
• Phipson B , MaksimovicJ , OshlackA . missMethyl: an R package for analyzing data from Illumina’s HumanMethylation450 platform . Bioinformatics32 ( 2 ), 286 – 288 ( 2016 ).
   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
• Reinius LE , AcevedoN , JoerinkMet al. Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility . PLoS ONE7 ( 7 ), e41361 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Jones PA . Functions of DNA methylation: islands, start sites, gene bodies and beyond . Nat. Rev. Genet.13 ( 7 ), 484 – 492 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Hwang W , OliverVF , MerbsSL , ZhuH , QianJ . Prediction of promoters and enhancers using multiple DNA methylation-associated features . BMC Genomics16 ( Suppl. 7 ), S11 ( 2015 ).
   PubMedGoogle Scholar