Functional Annotation

After using GWAS to narrow down regions in the genome to investigate, we can carry out a number of assays to functionally annotate the genome in a variety of cancer cell types:

determine the levels of gene expression with RNA-seq;
identifying active and regulatory regions with the use of ChIP-seq and ATAC-seq;
assigning enhancers to genes with 3D chromatin methods including capture HiC and Micro C;
assessing the biological consequence of genetic variants with luciferase reporter assays and Massively Parallel Reporter Assays (MPRA);
determine if variants have an effect using eQTL, TWAS, MWAS;
further integrating different datasets to determine if there is any co-localisation of the functional variants

Functional Annotation

Further Reading