Table 2.
Methylation sites associated with BMI (FDR <.05) in the Carolina Breast Cancer Study among patients with estrogen receptor-positive tumors
| Probe ID | Gene | Gene Description | CHRa | Islandb | Coefficient | p-value | q-value | Normalc | Overweightc,d | Obesec |
|---|---|---|---|---|---|---|---|---|---|---|
| DNMT3B_P352_R | DNMT3B | DNA cytosine-5 methyltransferase 3 beta isoform 2 | 20q11 | N | 0.0230 | 0.00017 | 0.03818 | 15.5% | 17.3% | 17.6% |
| IGFBP6_E47_F | IGFBP6 | Insulin-like growth factor binding protein 6 | 12q13 | N | 0.0447 | 0.00032 | 0.03818 | 37.5% | 40.5% | 43.3% |
| ERCC6_P698_R | ERCC6 | Excision repair cross-complementing rodent repair deficiency, complementation group 6 | 10q11 | Y | 0.0480 | 0.00037 | 0.03818 | 43.1% | 46.8% | 47.3% |
| SH3BP2_P771_Re | SH3BP2 | SH3-domain binding protein 2 | 4p16 | Y | 0.0324 | 0.00048 | 0.03818 | 17.4% | 20.8% | 22.7% |
| PLAGL1_E68_R | PLAGL1 | Pleiomorphic adenoma gene-like 1 isoform 1 | 6q24-25 | Y | 0.0422 | 0.00049 | 0.03818 | 69.8% | 72.5% | 75.4% |
| FZD9_E458_F | FZD9 | Frizzled 9 | 7q11 | Y | 0.0535 | 0.00096 | 0.04640 | 49.2% | 50.0% | 55.4% |
| BMPR1A_E88_F | BMPR1A | Bone morphogenetic protein receptor, type IA precursor | 10q22 | Y | 0.0320 | 0.00101 | 0.04640 | 65.0% | 66.7% | 69.2% |
| TSG101_P257_R | TSG101 | Tumor susceptibility gene 101 | 11p15 | Y | 0.0400 | 0.00132 | 0.04640 | 25.4% | 29.0% | 29.8% |
| RIPK4_E166_F | RIPK4 | receptor-interacting serine-threonine kinase 4 | 21q22 | Y | 0.0171 | 0.00133 | 0.04640 | 7.2% | 9.6% | 10.1% |
| Xist_seq_80_S95_Re | XIST | X inactive specific transcript (non-protein coding) | Xq13 | N | 0.0299 | 0.00143 | 0.04640 | 74.3% | 76.3% | 78.9% |
| TDGF1_P428_R | TDGF1 | Teratocarcinoma-derived growth factor 1 | 3p21 | N | 0.0412 | 0.00147 | 0.04640 | 40.7% | 41.8% | 44.6% |
| MCF2_P1024_R | MCF2 | MCF.2 cell line derived transforming sequence | Xq27 | N | 0.0393 | 0.00151 | 0.04640 | 77.6% | 80.6% | 82.3% |
| SPI1_E205_F | SPI1 | Spleen focus forming virus (SFFV) proviral integration oncogene spi1 | 11p11 | Y | 0.0372 | 0.00154 | 0.04640 | 54.1% | 57.8% | 58.8% |
| SH3BP2_E18_F | SH3BP2 | SH3-domain binding protein 2 | 4p16 | N | 0.0284 | 0.00208 | 0.04934 | 25.3% | 28.6% | 29.9% |
| ABO_E110_F | ABO | ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase; transferase B, alpha 1-3-galactosyltransferase) | 9q34 | Y | 0.0373 | 0.00225 | 0.04934 | 15.8% | 18.0% | 20.6% |
| CHI3L2_P226_F | CHI3L2 | Chitinase 3-like 2 isoform c | 1p13 | N | 0.0352 | 0.00227 | 0.04934 | 74.8% | 75.2% | 74.6% |
| BTK_P105_F | BTK | Bruton agammaglobulinemia tyrosine kinase | Xq21-22 | N | 0.0363 | 0.00240 | 0.04934 | 39.6% | 42.4% | 44.8% |
| SNURF_P78_F | SNURF | SNRPN upstream reading frame protein | 15q11-12 | Y | 0.0381 | 0.00254 | 0.04934 | 69.5% | 71.0% | 74.3% |
| ARHGDIB_P148_R | ARHGDIB Rho GDP dissociation inhibitor (GDI) beta | 12p12 | N | 0.0340 | 0.00255 | 0.04934 | 44.5% | 45.5% | 47.0% | |
| SEZ6L_P299_F | SEZ6L | Seizure related 6 homolog (mouse)-like precursor | 22q12 | Y | 0.0482 | 0.00255 | 0.04934 | 17.5% | 18.0% | 21.3% |
| PKD2_P336_R | PKD2 | Polycystin 2 | 4q22 | Y | 0.0260 | 0.00265 | 0.04934 | 13.1% | 14.6% | 16.5% |
a
CHR = Chromsome.
b
Island indicates whether the probe is located in a CpG Island; N = no; Y = yes.
c
Unadjusted % Methylation; Normal weight: 18.5 ≤ BMI < 25; overweight: 25 ≤ BMI < 30; obese BMI ≥ 30).
d
Overweight individuals were not included in the regression analysis, but are included here for descriptive purposes.
e
Associated with BMI in overall breast tumor tissue regression analysis