Personalized Computer Simulations of Breast Cancer Tumors Treated with Neoadjuvant Chemotherapy and Bevacizumab

Poster presented at Personalized Cancer Care Symposium, Oslo 2016: http://pccradiumhospital.org/<div><br></div

DataSheet_1_Complex molecular profile of DNA repair genes in epithelial ovarian carcinoma patients with different sensitivity to platinum-based therapy.pdf

Epithelial ovarian carcinoma (EOC) is known for high mortality due to diagnosis at advanced stages and frequent therapy resistance. Previous findings suggested that the DNA repair system is involved in the therapeutic response of cancer patients and DNA repair genes are promising targets for novel therapies. This study aimed to address complex inter-relations among gene expression levels, methylation profiles, and somatic mutations in DNA repair genes and EOC prognosis and therapy resistance status. We found significant associations of DUT expression with the presence of peritoneal metastases in EOC patients. The high-grade serous EOC subtype was enriched with TP53 mutations compared to other subtypes. Furthermore, somatic mutations in XPC and PRKDC were significantly associated with worse overall survival of EOC patients, and higher FAAP20 expression in platinum-resistant than platinum-sensitive patients was observed. We found higher methylation of RAD50 in platinum-resistant than in platinum-sensitive patients. Somatic mutations in BRCA1 and RAD9A were significantly associated with higher RBBP8 methylation in platinum-sensitive compared to platinum-resistant EOC patients. In conclusion, we discovered associations of several candidate genes from the DNA repair pathway with the prognosis and platinum resistance status of EOC patients, which deserve further validation as potential predictive biomarkers.</p

Additional file 2: of Epigenetic modifications in KDM lysine demethylases associate with survival of early-stage NSCLC

Table S1. Annotation of CpG sites in KDM gene family. (PDF 677 kb

Additional file 1: of Epigenetic modifications in KDM lysine demethylases associate with survival of early-stage NSCLC

Figure S1. Quality control processes for DNA methylation chip data. Quality control measures and exclusion criteria as applied to Harvard, Spain, Norway, Sweden, and The Cancer Genome Atlas (TCGA) sample cohorts. (PDF 642 kb

Additional file 4: of Epigenetic modifications in KDM lysine demethylases associate with survival of early-stage NSCLC

Figure S2. Analysis work flow. Adenocarcinoma and squamous cell carcinoma samples from Harvard, Spain, Norway, and Sweden cohorts were used for the discovery phase of analysis. Data from The Cancer Genome Atlas (TCGA) were used for Validation. Ranger is a weighted version of random forest for controlling for the covariates including age, gender, smoking status, and histological stage. Variable importance score (VIS) was estimated for each CpG site and was ranked in descending order. CpG sites ranked in top 10% in both discovery and validation sets were selected for further evaluation by Cox regression. Multiple testing correction by false discovery rate (FDR) method was used if necessary. (PDF 357 kb

Additional file 3: of Epigenetic modifications in KDM lysine demethylases associate with survival of early-stage NSCLC

Table S2. Distributions of CpG sites in KDM genes. (PDF 153 kb