Table 3.
Studies on variation in inter-individual methylation in human populations, describing association with genetic variants
| Ancestrya | Tissue/cell type (N) | Method (methylation/genotype chips) | # CpG | |
|---|---|---|---|---|
| Zhang et al. (2010) | European | Cerebellum (153) | Illumina 27K/Affymetrix 5.0K | 748 (out of 8.6K) |
| Gibbs et al. (2010) | European | Cerebellum (108) | Illumina 27K/Illumina 550K | >1K |
| Frontal cortex (133) | ||||
| Temporal cortex (127) | ||||
| Caudal pons regions (125) | ||||
| Bell et al. (2011) | African (Hapmap YRI) | Lymphoblastoid cell lines (referred to as “LCL”) (77) | Illumina 27K/HapMap (3.8 M) | 217 |
| Gutierrez-Arcelus et al. (2013) | European | Fibroblasts (107) | Illumina 450K/Illumina 2.5M | >14K |
| LCL (111) | ||||
| T-cells (66) | ||||
| Fraser et al. (2012) | African, European (Hapmap YRI,CEU) | LCL (90 per population) | Illumina 27K/HapMap (3.8 M) | >49 |
| Moen et al. (2013) | African, European (Hapmap YRI,CEU) | LCL (>60 per population) | Illumina 450K/HapMap (3.8 M) | 1.8K (out of 37K)b |
| Heyn et al. (2013) | African, East Asian, European | LCL (>72 per population) | Illumina 450K/Illumina 550K and 650K | 298 (out of 439)b |
Notes: Associations are given as approximate number of CpGs (“#CpG” column) that show statistical significance for association with one or more SNPs. Please note that the methods for detecting significant associations differ among studies and thus, numbers are not directly comparable. If more than one tissue or population is tested, numbers indicate the smallest value per tissue or population.
aAncestry following the designation of the International HapMap Project (Thorisson et al. 2005). YRI: Yoruba in Ibadan, Nigeria. CEU: Utah residents with ancestry from northern and western Europe.
bThese studies only search associations on a subset of CpGs that show significant differences of DNA methylation between populations.