Training a Model for Estimating Leukocyte Composition using Whole-Blood DNA Methylation and Cell Counts as Reference

References

• Zhang Y , YangR , BurwinkelB , BreitlingLP , BrennerH . F2RL3 methylation as a biomarker of current and lifetime smoking exposures . Environ. Health Perspect.122 ( 2 ), 131 – 137 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Chambers JC , LohM , LehneBet al. Epigenome-wide association of DNA methylation markers in peripheral blood from Indian Asians and Europeans with incident Type 2 diabetes: a nested case–control study . Lancet Diabetes Endocrinol.3 ( 7 ), 526 – 534 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Zhang Y , SchöttkerB , FlorathIet al. Smoking-associated DNA methylation biomarkers and their predictive value for all-cause and cardiovascular mortality . Environ. Health Perspect.124 ( 1 ), 67 – 74 ( 2015 ).
   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
• Langevin SM , HousemanEA , AccomandoWPet al. Leukocyte-adjusted epigenome-wide association studies of blood from solid tumor patients . Epigenetics9 ( 6 ), 884 – 895 ( 2014 ).
   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
• Jaffe AE , IrizarryRA . Accounting for cellular heterogeneity is critical in epigenome-wide association studies . Genome Biol.15 ( 2 ), R31 ( 2014 ).
   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
• Koestler DC , JonesMJ , UssetJet al. Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL) . BMC Bioinformatics17 , 120 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Küpers LK , XuX , JankipersadsingSAet al. DNA methylation mediates the effect of maternal smoking during pregnancy on birthweight of the offspring . Int. J. Epidemiol.44 ( 4 ), 1224 – 1237 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Sharp GC , LawlorDA , RichmondRCet al. Maternal pre-pregnancy BMI and gestational weight gain, offspring DNA methylation and later offspring adiposity: findings from the Avon Longitudinal Study of Parents and Children . Int. J. Epidemiol.44 ( 4 ), 1288 – 1304 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Koestler DC , ChristensenB , KaragasMRet al. Blood-based profiles of DNA methylation predict the underlying distribution of cell types: a validation analysis . Epigenetics8 ( 8 ), 816 – 826 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Lehne B , DrongAW , LohMet al. A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies . Genome Biol.16 , 37 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Yousefi P , HuenK , QuachHet al. Estimation of blood cellular heterogeneity in newborns and children for epigenome-wide association studies . Environ. Mol. Mutagen.56 ( 9 ), 751 – 758 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Waite LL , WeaverB , DayKet al. Estimation of cell-type composition including T and B cell subtypes for whole blood methylation microarray data . Front. Genet. doi:10.3389/fgene.2016.00023 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Zhang Q-L , BrennerH , KoenigW , RothenbacherD . Prognostic value of chronic kidney disease in patients with coronary heart disease: role of estimating equations . Atherosclerosis211 ( 1 ), 342 – 347 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Heiss JA , BrennerH . Between-array normalization for 450K data . Front. Genet. doi:10.3389/fgene.2015.00092 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Aitchison J . The statistical analysis of compositional data . Blackburn Press , NJ, USA ( 2003 ).
   Google Scholar
• Schwender H . Siggenes: multiple testing using SAM and Efron’s empirical Bayes approaches. R package version 1.46.40 ( 2012 ). https://www.bioconductor.org/packages/siggenes/ .
   Google Scholar
• Storey JD , TibshiraniR . Statistical significance for genomewide studies . Proc. Natl Acad. Sci. USA100 ( 16 ), 9440 – 9445 ( 2003 ).
   PubMed Web of Science ®Google Scholar
• Accomando WP , WienckeJK , HousemanE , NelsonHH , KelseyKT . Quantitative reconstruction of leukocyte subsets using DNA methylation . Genome Biol.15 ( 3 ), R50 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Bakulski KM , FeinbergJI , AndrewsSVet al. DNA methylation of cord blood cell types: applications for mixed cell birth studies . Epigenetics11 ( 5 ), 354 – 362 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Park BG , ParkC-J , KimSet al. Comparison of the Cytodiff flow cytometric leucocyte differential count system with the Sysmex XE-2100 and Beckman Coulter UniCel DxH 800 . Int. J. Lab. Hematol.34 ( 6 ), 584 – 593 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Tsuda I , HinoM , TakuboTet al. First basic performance evaluation of the XE-2100 haematology analyser . J. Auto. Meth. Manage. Chem.21 ( 4 ), 127 – 133 ( 1999 ).
   PubMedGoogle Scholar
• Maciel TES , ComarSR , BeltrameMP . Performance evaluation of the Sysmex® XE-2100D automated hematology analyzer . J. Bras. Patol. Med. Lab.50 ( 1 ), 26 – 35 ( 2014 ).
   Google Scholar
• Imeri F , HerklotzR , RischLet al. Stability of hematological analytes depends on the hematology analyser used: a stability study with Bayer Advia 120, Beckman Coulter LH 750 and Sysmex XE 2100 . Clin. Chim. Acta397 ( 1–2 ), 68 – 71 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Houseman EA , KelseyKT , WienckeJK , MarsitCJ . Cell-composition effects in the analysis of DNA methylation array data: a mathematical perspective . BMC Bioinformatics16 , 95 ( 2015 ).
   PubMed Web of Science ®Google Scholar