Project description:Regulatory enhancer elements in solid tumours remain poorly characterized. Here we apply micro-scale chromatin profiling to survey the distal enhancer landscape of primary gastric adenocarcinoma (GC), a leading cause of global cancer mortality. Integrating 110 epigenomic profiles from primary GCs, normal gastric tissues and cell lines, we highlight 36,973 predicted enhancers and 3,759 predicted super-enhancers respectively. Cell-line-defined super-enhancers can be subclassified by their somatic alteration status into somatic gain, loss and unaltered categories, each displaying distinct epigenetic, transcriptional and pathway enrichments. Somatic gain super-enhancers are associated with complex chromatin interaction profiles, expression patterns correlated with patient outcome and dense co-occupancy of the transcription factors CDX2 and HNF4?. Somatic super-enhancers are also enriched in genetic risk SNPs associated with cancer predisposition. Our results reveal a genome-wide reprogramming of the GC enhancer and super-enhancer landscape during tumorigenesis, contributing to dysregulated local and regional cancer gene expression.

| S-EPMC5052795 | biostudies-literature

SEER Remote Access Pilot Test Data (2018)

Project description:SEER Remote Access Pilot Test Data (2018)

| PRJNA625583 | ENA

SEER Remote Access Pilot Test Data (2018)

Project description:SEER Remote Access Pilot Test Data (2018)

| PRJNA625584 | ENA

A mechanism for controlled access to GWAS data: experience of the GAIN Data Access Committee.

Project description:The Genetic Association Information Network (GAIN) Data Access Committee was established in June 2007 to provide prompt and fair access to data from six genome-wide association studies through the database of Genotypes and Phenotypes (dbGaP). Of 945 project requests received through 2011, 749 (79%) have been approved; median receipt-to-approval time decreased from 14 days in 2007 to 8 days in 2011. Over half (54%) of the proposed research uses were for GAIN-specific phenotypes; other uses were for method development (26%) and adding controls to other studies (17%). Eight data-management incidents, defined as compromises of any of the data-use conditions, occurred among nine approved users; most were procedural violations, and none violated participant confidentiality. Over 5 years of experience with GAIN data access has demonstrated substantial use of GAIN data by investigators from academic, nonprofit, and for-profit institutions with relatively few and contained policy violations. The availability of GAIN data has allowed for advances in both the understanding of the genetic underpinnings of mental-health disorders, diabetes, and psoriasis and the development and refinement of statistical methods for identifying genetic and environmental factors related to complex common diseases.

| S-EPMC3617375 | biostudies-literature

Data access committee for lung cancer

Project description:Data Access Committee EGAC00001001942

| EGAC00001001942 | EGA

Lung Cancer Single-cell Data Access Committee

Project description:Data Access Committee EGAC00001001220

| EGAC00001001220 | EGA

Lung cancer RNA Seq Data Access Committee

Project description:Data Access Committee EGAC00001003317

| EGAC00001003317 | EGA