Estimation of blood cellular heterogeneity in newborns and children for epigenome-wide association studies

Environmental and Molecular Mutagenesis

Volumn 56, Issue 9, 2015, Pages 751-758

  Yousefi, Paul ^a   Huen, Karen ^a   Quach, Hong ^a   Motwani, Girish ^a   Hubbard, Alan ^a   Eskenazi, Brenda ^a   Holland, Nina ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

450K; Birth cohort; Differential cell count; Epigenetics; Minfi

Indexed keywords

ENVIRONMENTAL CHEMICAL; PESTICIDE;

ALGORITHM; ARTICLE; B LYMPHOCYTE; BASOPHIL; CD4+ T LYMPHOCYTE; CD8+ T LYMPHOCYTE; CELL COMPOSITION; CELL HETEROGENEITY; CHILD; COHORT ANALYSIS; EOSINOPHIL; EPIGENETICS; EXPOSURE; FEMALE; GENETIC ASSOCIATION; GRANULOCYTE; HUMAN; LEUKOCYTE; LEUKOCYTE COUNT; LEUKOCYTE DIFFERENTIAL COUNT; LYMPHOCYTE; MAJOR CLINICAL STUDY; MALE; MONOCYTE; NATURAL KILLER CELL; NEUTROPHIL; NEWBORN; AGE; BLOOD CELL; BLOOD CELL COUNT; COMPARATIVE STUDY; CYTOLOGY; DNA METHYLATION; GENETIC EPIGENESIS; GENOME-WIDE ASSOCIATION STUDY; LONGITUDINAL STUDY; PHYSIOLOGY; PROCEDURES; REFERENCE VALUE;

AGE FACTORS; BLOOD CELL COUNT; BLOOD CELLS; CHILD; COHORT STUDIES; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; INFANT, NEWBORN; LEUKOCYTE COUNT; LONGITUDINAL STUDIES; MALE; REFERENCE VALUES;

EID: 84946495535     PISSN: 08936692     EISSN: 10982280     Source Type: Journal    
DOI: 10.1002/em.21966     Document Type: Article

References (41)

1. Adkins RM, Krushkal J, Tylavsky FA, Thomas F. 2011. Racial differences in gene-specific DNA methylation levels are present at birth. Birth Defects Res A Clin Mol Teratol 91:728-736.
2. Armstrong DA, Lesseur C, Conradt E, Lester BM, Marsit CJ. 2014. Global and gene-specific DNA methylation across multiple tissues in early infancy: Implications for children's health research. FASEB J 28:2088-2097.
3. Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA. 2014. Minfi: A flexible and comprehensive bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics 30:1363-1369.
4. Babenko O, Kovalchuk I, Metz GA. 2014. Stress-induced perinatal and transgenerational epigenetic programming of brain development and mental health. Neurosci Biobehav Rev 48C:70-91.
5. Barker DJ. 1998. In utero programming of chronic disease. Clin Sci (Lond) 95:115-128.
6. Bibikova M, Le J, Barnes B, Saedinia-Melnyk S, Zhou L, Shen R, Gunderson KL. 2009. Genome-wide DNA methylation profiling using Infinium® assay. Epigenomics 1:177-200.
7. Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, Delano D, Zhang L, Schroth GP, Gunderson KL, et al. 2011. High density DNA methylation array with single CpG site resolution. Genomics 98:288-295.
8. Chadwick LH, Sawa A, Yang I, Baccarelli A, Breakefield X, Deng H, Dolinoy DC, Fallin MD, Holland N, Houseman EA, et al. 2015. New insights and updated guidelines for epigenome-wide association studies. Neuroepigenetics 1:14-19.
9. Cheng CK-W, Chan J, Cembrowski GS, van Assendelft OW. 2004. Complete blood count reference interval diagrams derived from NHANES III: Stratification by age, sex, and race. Lab Hematol Off Publ Int Soc Lab Hematol 10:42-53.
10. Dallman PR. 1977. Blood and blood-forming tissues. In: Rudolph A, editor. Paediatrics. New York: Appleton-Century-Crofts. pp 1109-1112.
11. Eskenazi B, Bradman A, Gladstone E, Jaramillo S, Birch K, Holland N. 2003. CHAMACOS, a longitudinal birth cohort study: Lessons from the fields. J Childrens Healt 1:3-27.
12. Eskenazi B, Harley K, Bradman A, Weltzien E, Jewell NP, Barr DB, Furlong CE, Holland NT. 2004. Association of in utero organophosphate pesticide exposure and fetal growth and length of gestation in an agricultural population. Environ Health Perspect 112:1116-1124.
13. Essex MJ, Boyce WT, Hertzman C, Lam LL, Armstrong JM, Neumann SM, Kobor MS. 2013. Epigenetic vestiges of early developmental adversity: Childhood stress exposure and DNA methylation in adolescence. Child Dev 84:58-75.
14. Foley DL, Craig JM, Morley R, Olsson CJ, Dwyer T, Smith K, Saffery R. 2009. Prospects for epigenetic epidemiology. Am J Epidemiol 169:389-400.
15. Guo H, Zhu P, Yan L, Li R, Hu B, Lian Y, Yan J, Ren X, Lin S, Li J, et al. 2014. The DNA methylation landscape of human early embryos. Nature 511:606-610.
16. Harris RA, Nagy-Szakal D, Kellermayer R. 2013. Human metastable epiallele candidates link to common disorders. Epigenetics 8:157-163.
17. Holland N, Furlong C, Bastaki M, Richter R, Bradman A, Huen K, Beckman K, Eskenazi B. 2006. Paraoxonase polymorphisms, haplotypes, and enzyme activity in Latino mothers and newborns. Environ Health Perspect 114:985-991.
18. Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, Nelson HH, Wiencke JK, Kelsey KT. 2012. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinform 13:86.
19. Hsieh MM, Everhart JE, Byrd-Holt DD, Tisdale JF, Rodgers GP. 2007. Prevalence of neutropenia in the US population: Age, sex, smoking status, and ethnic differences. Ann Intern Med 146:486-492.
20. Hughes V. 2014. Epigenetics: The sins of the father. Nature 507:22-24.
21. Jaffe AE. FlowSorted.Blood.450k: Illumina HumanMethylation data on sorted blood cell populations. R package version 1.2.0. http://bioconductor.org/packages/release/data/experiment/html/FlowSorted.Blood.450k.html.
22. Jaffe AE, Irizarry RA. 2014. Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol 15:R31.
23. Joubert BR, Håberg SE, Nilsen RM, Wang X, Vollset SE, Murphy SK, Huang Z, Hoyo C, Midttun Ø Cupul-Uicab LA, et al. 2012. 450K Epigenome-wide scan identifies differential DNA methylation in newborns related to maternal smoking during pregnancy. Environm Health Perspect 120:1425-1431.
24. Koestler DC, Avissar-Whiting M, Houseman EA, Karagas MR, Marsit CJ. 2013. Differential DNA methylation in umbilical cord blood of infants exposed to low levels of arsenic in utero. Environ Health Perspect 121:971-977.
25. Laird PW. 2010. Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 11:191-203.
26. Liang L, Cookson WOC. 2014. Grasping nettles: Cellular heterogeneity and other confounders in epigenome-wide association studies. Hum Mol Genet 23:ddu284-R88.
27. Lim EM, Cembrowski G, Cembrowski M, Clarke G. 2010. Race-specific WBC and neutrophil count reference intervals. Int J Lab Hematol 32:590-597.
28. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, et al. 2009. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315-322.
29. Liu Y, Aryee MJ, Padyukov L, Fallin MD, Hesselberg E, Runarsson A, Reinius L, Acevedo N, Taub M, Ronninger M, others. 2013. Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis. Nat Biotechnol 31:142-147.
30. Lowe R, Rakyan VK. 2014. Correcting for cell-type composition bias in epigenome-wide association studies. Genome Med 6:1-2.
31. McCarthy NS, Melton PE, Cadby G, Yazar S, Franchina M, Moses EK, Mackey DA, Hewitt AW. 2014. Meta-analysis of human methylation data for evidence of sex-specific autosomal patterns. BMC Genom 15:981.
32. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C Jaffe DB, et al. 2008. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454:766-770.
33. Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, Houseman EA, Izzi B, Kelsey KT Meissner A, et al. 2013. Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods 10:949-955.
34. Nathan DG, Oski FA. 1981. Hematology of Infancy and Childhood, 2nd ed., Philadelphia: Saunders, pp 1552-1574.
35. Reinius LE, Acevedo N, Joerink M, Pershagen G, Dahlen SE, Greco D, Soderhall C, Scheynius A, Kere J. 2012. Differential DNA methylation in purified human blood cells: Implications for cell lineage and studies on disease susceptibility. PLoS One 7:e41361.
36. Sandoval J, Heyn H, Moran S, Serra-Musach J, Pujana MA, Bibikova M, Esteller M. 2011. Validation of a DNA methylation microarray for 450, 000 CpG sites in the human genome. Epigenetics 6:692-702.
37. Smith ZD, Chan MM, Humm KC, Karnik R, Mekhoubad S, Regev A, Eggan K, Meissner A. 2014. DNA methylation dynamics of the human preimplantation embryo. Nature 511:611-615.
38. Team RC. 2013. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. Available at: URL: http://www.R-project.org/. Vienna, Austria.
39. Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Gayther SA, Apostolidou S, Jones A, Lechner M, Beck S, Jacobs IJ, et al. 2009. An epigenetic signature in peripheral blood predicts active ovarian cancer. PLoS One 4:e8274.
40. Turgeon ML. 2011. Clinical Hematology Theory and Procedures, 5th ed., Lippincott Williams & Wilkins: Philadelphia, PA, pp 40-45.
41. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, Schübeler D. 2005. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37:853-862.