Additional file 1: of Integrative genomic analysis reveals functional diversification of APOBEC gene family in breast cancer

Tables S1 and S2. Table S1. Data characteristics in this study. Table S2. Expression levels of APOBEC family genes across ten breast cell lines. (XLSX 14 kb

Additional file 2: Figures S1–S6. of Integrative genomic analysis reveals functional diversification of APOBEC gene family in breast cancer

Figure S1. Expression profiles of APOBEC family genes in breast tumor tissues and adjacent normal tissues in relation to ER status. Figure S2. Comparison of chromatin states in APOBEC1 (A), APOBEC2 (B), APOBEC4 (C), and AICDA (D) genes in ER+ (MCF-7), ER− (HCC1954) breast cancer cells, and normal cells (HMEC). Chromatin states characterized by the ChromHMM algorithm are represented by different colors shown in the bottom. Figure S3. Kaplan-Meier curve for overall survival of four patient groups with higher (top 50 %) or lower (bottom 50 %) expression of APOBEC3B and APOBEC3C genes in breast cancer. Figure S4. Distribution of the number of somatic mutations (A) and C>T/G>A mutations (B) per tumor exome. The red curve is a kernel density estimate. Figure S5. Relationship between mRNA levels of APOBEC3B (upper panel) and APOBEC3C (lower panel) and number of somatic SNVs per tumor exome stratified by the ER status. The black lines and red curves are drawn from the linear regression model and local regression smoothing, respectively. Figure S6. Expression profiles of APOBEC family genes in breast tumor tissues in relation with copy numbers of APOBEC3B. (ZIP 559 kb

Association of GWAS-Identified T2D-Related SNPs with T2D Risk.

<p>T2D increasing risk allele identified in prior GWAS study.</p>††<p>ORs and 95% confidence intervals for association with T2D, adjusted for age, sex and BMI.</p>*<p>SNP is used in the calculation of the GRS2 genetic risk score (see Methods).</p

Joint Effects of BMI, WHR, exercise participation and combined lifestyle risk factor with GRS1categories on T2D.

*<p>Adjusted for age and sex.</p>**<p>Adjusted for age, sex and BMI.</p>+<p>The log-likelihood ratio test was used to test the interaction effect of GRS with other risk factors on T2D risk.</p

Association between the genetic risk scores and T2D^*.

*<p>Adjusted for age, sex and BMI.</p

Selected Population Characteristics by Genome-Wide Association Study Stage and Case-Control Status Among Women of European Ancestry.

<p>Abbreviations: BMI, body mass index; GRS, genetic risk score; GWAS, genome-wide association study; N, sample size; SD standard deviation.</p><p>Selected Population Characteristics by Genome-Wide Association Study Stage and Case-Control Status Among Women of European Ancestry.</p

Genetic Risk Scores Based on Biologic Single Nucleotide Polymorphism Subsets and Endometrial Cancer Risk Among Women of European Ancestry.

<p>Abbreviations: BMI, body mass index; CI, confidence interval; OR, odds ratio.</p><p>^a Unconditional logistic regression models adjusted for age at diagnosis and study were used to estimate per risk allele odds ratios and 95% confidence intervals</p><p>^b Unconditional logistic regression models were additionally adjusted for BMI</p><p>Genetic Risk Scores Based on Biologic Single Nucleotide Polymorphism Subsets and Endometrial Cancer Risk Among Women of European Ancestry.</p

Endometrial Cancer Risk within BMI and BMI GRS Subgroups.

<p>Data represent odds ratios and 95% confidence intervals of endometrial cancer for quartile 1 (Q1; 67.5–87.1 risk alleles), the interquartile range (IQR; 87.2–95.5 risk alleles), and quartile 4 (Q4; 95.6–115.3 risk alleles) categories of the BMI GRS among normal weight (<25 kg/m²), overweight (25–29.9 kg/m²), and obese (30+ kg/m²) women.</p

Body Mass Index Genetic Risk Score and Endometrial Cancer Risk Among Women of European Ancestry.

<p>Abbreviations: BMI, body mass index; CI, confidence interval; OR, odds ratio.</p><p>^a Unconditional logistic regression models adjusted for age at diagnosis and study were used to estimate odds ratios and 95% confidence intervals</p><p>^b Unconditional logistic regression models were additionally adjusted for BMI</p><p>^c Per 10 BMI risk alleles</p><p>Body Mass Index Genetic Risk Score and Endometrial Cancer Risk Among Women of European Ancestry.</p