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Elife. 2017 Jan 3;6. pii: e20532. doi: 10.7554/eLife.20532.

Differential methylation between ethnic sub-groups reflects the effect of genetic ancestry and environmental exposures.

Author information

1
Department of Medicine, University of California, San Francisco, United States.
2
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States.
3
Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, United States.
4
Department of Genetics, Stanford University, Stanford, United States.
5
Hospital Universitario Nuestra Señora de Candelaria, Tenerife, Spain.
6
CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
7
Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas.
8
Division of Allergy and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.
9
Kaiser Permanente-Vallejo Medical Center, Vallejo, United States.
10
Bay Area Pediatrics, Oakland, United States.
11
Department of Pediatrics, Children's Hospital and Research Center, Oakland, United States.
12
Jacobi Medical Center, Bronx, United States.
13
Veterans Caribbean Health System, San Juan, United States.
14
Division of Allergy and Immunology, The Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, United States.
15
Centro de Neumología Pediátrica, San Juan, United States.
16
Center for Genes, Environment, and Health, Department of Pediatrics, National Jewish Health, Denver, United States.
17
Graduate School of Public Health and Health Policy, City University of New York, New York, United States.

Abstract

Populations are often divided categorically into distinct racial/ethnic groups based on social rather than biological constructs. Genetic ancestry has been suggested as an alternative to this categorization. Herein, we typed over 450,000 CpG sites in whole blood of 573 individuals of diverse Hispanic origin who also had high-density genotype data. We found that both self-identified ethnicity and genetically determined ancestry were each significantly associated with methylation levels at 916 and 194 CpGs, respectively, and that shared genomic ancestry accounted for a median of 75.7% (IQR 45.8% to 92%) of the variance in methylation associated with ethnicity. There was a significant enrichment (p=4.2×10-64) of ethnicity-associated sites amongst loci previously associated environmental exposures, particularly maternal smoking during pregnancy. We conclude that differential methylation between ethnic groups is partially explained by the shared genetic ancestry but that environmental factors not captured by ancestry significantly contribute to variation in methylation.

KEYWORDS:

Latinos; chromosomes; epigenetics; ethnicity; genes; human; human biology; medicine; methylation

PMID:
28044981
PMCID:
PMC5207770
DOI:
10.7554/eLife.20532
[Indexed for MEDLINE]
Free PMC Article

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