Breast cancer is a highly heterogeneous disease that is classified into multiple clonal subtypes. Despite recent improvements in targeted treatment and clonal subtype detection methods, the complex genetics of tumor diversity remain poorly understood. This project examines genetic substructure in a population of breast cancer patients from The Cancer Genome Atlas (TCGA), and identifies networks...

Please note: The pan-cancer molecular signatures disclosed in this article are the results of applying our data mining algorithm to the rich TCGA “pancan12” data sets from twelve different cancer types. These signatures have been identified as patterns, without any indication about their role or potential usefulness. We believe that each of them represents an important biomolecular event in can...

APOBEC3 enzymes are a key source of mutagenesis in breast cancer. PI3K inhibitors currently used the treatment PIK3CA-mutated advanced However, whether specific PIK3CA mutations (muts) associated with better outcomes is unclear. We developed computational framework to screen for APOBEC3-induced within TCW context using whole-exome sequencing (WES) data from cancer cohort genome atlas (TCGA-BRCA...

The clinical prognosis of patients with glioma is determined by tumor grades, but tumors of different subtypes with equal malignancy grade usually have different prognosis that is largely determined by genetic abnormalities. Oligodendrogliomas (ODs) are the second most common type of gliomas. In this study, integrative analyses found that distribution of TCGA transcriptomic subtypes was associa...

We previously reported a novel association between CDKN2A nonpromoter methylation and transcription (ARF/INK4a) in human papillomavirus associated oropharyngeal tumors. In this study we assessed whether nonpromoter CDKN2A methylation in laryngeal squamous cell carcinomas (LXSCC) conferred a similar association with transcription that predicted patient outcome. We compared DNA methylation and AR...

BACKGROUND Long noncoding RNAs (lncRNAs) with dysregulated expression levels have been investigated in numerous types of different cancer. Whether lncRNAs can predict the progression of gastric cancer (GC) still remains largely unclear. The aim of our study was to investigate whether KRT18P55, a novel intergenic lncRNA, can be a predictive biomarker for GC. METHODS To determine the expression...

Background Thyroid cancer is the most commonly reported endocrine malignancy, and its increased incidence has been the highest in all human tumors in recent decades. To investigate the mechanism of papillary thyroid cancer (PTC) occurrence and progression, we performed RNA sequencing and found an upregulated gene, LAMB3. However, the biological function of LAMB3 is still not clear. Materials ...

INTRODUCTION Annexin A1 (ANXA1) is an anti-inflammatory protein reported to play a role in cell proliferation and apoptosis, and to be deregulated in breast cancer. The exact role of annexin A1 in the biology of breast cancer remains unclear. We hypothesized that the annexin A1 plays an oncogenic role in basal subtype of breast cancer by modulating key growth pathway(s). METHODS By mining the...

The role of microRNA (miRNA)-452-5p in lung squamous cell carcinoma (LUSC) remains unclear. Therefore, the present systematic study was performed to investigate the clinical significance and the rudimentary mechanism of the function of miR-452-5p in LUSC. The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were utilized to confirm the expression level and clinical value o...

Background Never-smokers and never-drinkers patients (NSND) suffering from oral squamous cell carcinoma (OSCC) are epidemiologically different from smokers drinkers (SD). We therefore hypothesized that they harbored distinct targetable molecular alterations. Patients and methods Data from The Cancer Genome Atlas (TCGA) (discovery set), Gene Expression Omnibus and Centre Léon Bérard (CLB) (thr...