Association of patient characteristics with tumor p53 mutational status.

*<p><i>P</i> value comparing patient characteristics by tumor p53 mutational status</p>**<p>Cases with missing information are not included</p>***<p>Mann-Whitney rank sum test</p><p>Annual household income, race/ethnicity, and education are self-reported. Tumor-associated macrophages were counted as CD68-positive cells. Pack years: (packs smoked per day) x (years as a smoker). BMI  =  kg/m²; SD  =  standard deviation, IHC  =  immunohistochemistry.</p

Relationship between tumor p53 status and annual household income in the adjusted analysis.

<p>OR  =  odds ratio; CI  =  confidence interval; IHC  =  immunohistochemistry</p>*<p>Trend test. Shown is the OR for the stepwise increase in household income (reference: low income). Income coded as 0 (< $15,000), 1 ($15,000 to $60,000), and 2 (>$60,000); adjustments: smoking (pack years), age, and body mass index (BMI) were used as continuous data; other covariates were dichotomized for the analysis, as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057361#pone-0057361-t001" target="_blank">Table 1</a></p>**<p>adjusted for race/ethnicity, node status, tumor estrogen receptor status, and tumor grade</p

Kaplan-Meier survival curves for 5-year breast cancer-specific survival by annual household income (HI) of the patients.

<p>Log-rank test: <i>P</i> < 0.05. Within this follow-up period, 38 of the 173 patients (22%) died from breast cancer.</p

Association of household income with a mutant p53 tumor status by estrogen receptor status.

<p>Association of household income with a mutant p53 tumor status by estrogen receptor status.</p

Quantitative DNA methylation analysis in human breast tissues.

<p>The percentage of DNA methylation levels at promoter CpG islands were analyzed in bisulfite-modified genomic DNA extracted from matched pairs of non-cancerous (normal) and breast tumors (tumor) tissue samples obtained from AA and AE cancer patients. <i>Y</i> axis, percentage of methylated cytosines in the samples as obtained from pyrosequencing. <i>X</i> axis, normal and tumor tissues obtained from AA and EA. <i>P</i> value is indicated for each gene (Mann-Whitney). Adj. P: adjusted P value (Bonferroni).</p

Gene methylation status and tumor subtypes.

<p>Percentage methylation frequency stratified by subtype: <b>A.</b> Triple-negative (TN) tumors (n = 14) versus others (n = 43), <b>B.</b> Basal-like (BL) tumors (n = 13) versus others (n = 45). <b>C.</b> Luminal A (LumA) tumors (n = 21) versus others (n = 37; Mann-Whitney).</p

Gene methylation status and patient characteristics.

<p><b>A.</b> Relative methylation frequency (% methylation in tumor minus % methylation in adjacent normal) stratified by race; AA (n = 32) and EA (n = 33; Mann-Whitney). Adj. P: adjusted P value (Bonferroni) <b>B.</b> Relative methylation frequency stratified by ER- negative (−) patients with age<50 (17 cases in total; 8 AA cases and 9 EA cases) P value is shown (Mann-Whitney). <b>C.</b> Percentage methylation frequency in breast tumor cases stratified by age (age<50: n = 31; age≥50: n = 34). P value is shown (Mann-Whitney).</p

Percentage methylation frequency and neoadjuvant therapy.

<p>The % methylation in tumors with neoadjuvant therapy (n = 9−2 luminal; 4 basal-like and 3 triple-negative cases) and without (n = 53; Mann-Whitney). There were 3 cases for which neoadjuvant therapy data was not available.</p

Promoter methylation and gene expression.

<p>The ratio of gene expression data of tumor to non-cancerous (normal) from a genome-wide gene expression microarray <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037928#pone.0037928-Martin1" target="_blank">[23]</a> was correlated with the methylation difference between the tissue pairs. The log 2 ratio of gene expression in matched pair tumor and normal is shown on Y axis. The relative methylation frequency is shown on the X-axis. <i>P</i> value and the correlation index; <i>r</i> (Rho) values are from Spearman rank correlation analysis.</p

Demographic, clinicopathologic characteristics and percent ancestry of breast cancer patient cases.

<p>SD = standard deviation.</p>1<p>AA = African-American,</p>2<p>EA = European-American. Race/ethnicity is determined by self-identification;</p>3<p>AA versus EA;</p>4<p>basal-like = ER-negative, HER2-negative, and either cytokeratin 5/6-positive or EGFR-positive;</p>5<p>ER-negative versus ER-positive;</p>6<p>Unknown not included.</p