User: What is the genomics of disease?
Assistant: With the advent of next-generation sequencing we are obtaining enough sequence data to map the genes of complex diseases including infertility, breast cancer or Alzheimer's disease. Genome-wide association studies are a useful approach to pinpoint the mutations responsible for such complex diseases. Through these studies, thousands of DNA variants have been identified that are associated with similar diseases and traits. Furthermore, the possibility for genes to be used at prognosis, diagnosis or treatment is one of the most essential applications. Many studies are discussing both the promising ways to choose the genes to be used and the problems and pitfalls of using genes to predict disease presence or prognosis.

Genome-wide association studies have successfully identified thousands of common genetic variants for complex diseases and traits; however, these common variants only explain a small fraction of heritability. Rare variants may account for some of the missing heritability. Large-scale whole genome sequencing studies have rapidly sequenced millions of whole genomes, and such studies have identified hundreds of millions of rare variants. Functional annotations predict the effect or function of a genetic variant and help to prioritize rare functional variants, and incorporating these annotations can effectively boost the power of genetic association of rare variants analysis of whole genome sequencing studies. Some tools have been developed to provide all-in-one rare variant association analysis for whole-genome sequencing data, including integration of genotype data and their functional annotations, association analysis, result summary and visualization. Meta-analysis of whole genome sequencing studies provides an attractive solution to the problem of collecting large sample sizes for discovering rare variants associated with complex phenotypes.