Getting from sequence information to useful answers in exome analysis - general principles

Abstract

Analysis of the entire human exome has rapidly become a method of choice for identifying both known and new disease-causing mutations. In Mendelian disorders this approach has dramatically improved the diagnostic success rate, demonstrated that many diseases are more heterogeneous than first thought and allowed the identification of very large numbers of new genes never previously thought likely to be involved in disease. At the same time, exome sequencing data brings with it many different challenges, including a different approach to analysis. When faced with ~50,000 sequence variants from an exome, a number of different strategies can be used to identify critical variants including positive selection (known variant databases etc), negative selection (using ‘normal’ databases such as 1000 genomes) and analysis of selected pathways. Each of these approaches has advantages and disadvantages and a flexible analytical approach is likely to yield the best outcome. Incorporation of phenotype and/or ontological data can also greatly facilitate exome analyses. Finally, other approaches such as analysis of additional family members can simplify the process allowing rapid interpretation of these data. I will outline the general approaches to analysing human exomes and illustrate these approaches using recent examples from Western Australia.