Table 1.
Web resources and databases used in post-GWAS analysis
| Web resources | Descriptiona | URL |
|---|---|---|
| National Human Genome Research Institute (NHGRI) GWAS catalogue |
Includes studies assaying ≥100,000 SNPs in the initial stage (excludes candidate gene studies). SNP–trait associations are limited to those with P- values <1.0 × 10−5 |
http://www.genome.gov/gwastudies/ |
| Genetic Associations and Mechanisms in Oncology (GAME- ON) consortium |
The overall goal of GAME-ON is to foster an interdisciplinary and collaborative approach to the translation of promising research leads deriving from the initial wave of cancer GWAS. It is limited to breast, ovarian, prostate, lung and colorectal cancers |
http://epi.grants.cancer.gov/gameon/ |
| Collaborative Oncological Gene- environment Study (COGS) |
The central focus of the project is to define individual risk of breast, ovarian and prostate cancer; i.e. to identify individuals at an increased risk of these three cancers. It also aims to identify genetic and lifestyle factors that are associated with certain tumour subtypes and affect clinical outcome |
http://www.cogseu.org/ |
| 1000 Genomes | The goal of the 1000 Genomes project is to find most genetic variants that have frequencies of at least 1% in the populations studied |
http://www.1000genomes.org/ |
| The Cancer Genome Atlas (TCGA) |
The goal is to identify the changes in the genome in each cancer and to understanding how such changes interact to drive the disease |
http://cancergenome.nih.gov/ |
| Encyclopedia of DNA Elements (ENCODE) |
The overall aim is to identify all functional elements in the human genome sequence |
http://www.genome.gov/10005107
http://genome.ucsc.edu/ENCODE/ http://www.nature.com/encode/#/threads |
| Catalogue of Somatic Mutations in Cancer (COSMIC) |
COSMIC is designed to store and display somatic mutation information and related details, and contains information relating to human cancers |
http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/ |
| Missense Prediction Tool Catalogue – National Genetics Reference Laboratory (NGRL) |
The aim is to review and catalogue available tools for the evaluation and classification of missense variants |
http://www.ngrl.org.uk/Manchester/page/missense-prediction-tool-catalogue |
| University of California Santa Cruz (UCSC) Human Genome Browser |
Contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides portals to the ENCODE project |
http://genome.ucsc.edu/ |
| Genotype-Tissue Expression (GTex) |
The aim is to study human gene expression and regulation in multiple tissues, providing insights into the mechanisms of gene regulation |
http://commonfund.nih.gov/GTEx/ |
| Gene Expression Omnibus (GEO) |
GEO is a public functional genomics data repository supporting MIAME (Minimum Information About a Microarray Experiment)-compliant data submissions |
http://www.ncbi.nlm.nih.gov/geo/ |
a
Adapted from the original descriptions provided on the websites.