Disease gene identification strategies for exome sequencing

Abstract

Next generation sequencing can be used to search for Mendelian disease genes in an unbiased manner by sequencing the entire protein-coding sequence, known as the exome, or even the entire human genome. Identifying the pathogenic mutation amongst thousands to millions of genomic variants is a major challenge, and novel variant prioritization strategies are required. The choice of these strategies depends on the availability of well-phenotyped patients and family members, the mode of inheritance, the severity of the disease and its population frequency. In this review, we discuss the current strategies for Mendelian disease gene identification by exome resequencing. We conclude that exome strategies are successful and identify new Mendelian disease genes in approximately 60% of the projects. Improvements in bioinformatics as well as in sequencing technology will likely increase the success rate even further. Exome sequencing is likely to become the most commonly used tool for Mendelian disease gene identification for the coming years.

Figure 1

Number of variants identified in published exome studies. (a) Number of non-synonymous variants identified in published exome studies. From left to right:^{, , , , , , , , , , , , , ,} . (b) Number of novel non-synonymous variants identified in published exome studies. From left to right:^{, , , , , , , , , , , , ,} .

Figure 2

Prioritization of NGS variants. Common prioritization of variants. The size of the enclosing ellipses is indicative of the relative number of variants that remain after each prioritization step.

Figure 3

Disease gene identification strategies for exome sequencing. The strategies (a–f) are detailed in the main text. Pedigrees indicate the inheritance model loosely underlying the strategy; filled symbols represent affected individuals, empty symbols represent presumably healthy individuals, and carriers are depicted by a symbol with a dot. Dashed rectangle encloses individuals that are exome sequenced. Circles below each pedigree symbolize sets of genetic variants identified in the exomes. Solid circles represent variants from affected individuals, whereas dashed circles represent variants from unaffected.

Figure 4

Base pair conservation of published pathogenic missense variants identified by exome sequencing. (a) Histogram plots of PhyloP evolutionary conservation score for non-synonymous variants from dbSNP and Human Genome Mutation Database, showing a clear difference. (b) Conservation of published missense mutations ranked from low to high. Each bar represents the conservation of a missense mutation. Mutations are labeled with gene name, amino-acid change and affected base within the codon (in parentheses). Horizontal dotted line indicates conservation of 2.5 where the distributions of the two distributions from panel (a) intersect. Variants from different studies are indicated by distinct colors. The color reproduction of this figure is available at the European Journal of Human Genetics online.