Exome and whole-genome sequencing as clinical tests: a transformative practice in molecular diagnostics.

In the last few years, next-generation sequencing (NGS) has revolutionized the approaches by which we interrogate the genetic causes of rare single-gene disorders (1 ). More recently, NGS has been rapidly moving into the clinical diagnostics arena and transforming the practice of molecular diagnostics testing. Many NGSbased tests for multigene panels are available in clinical laboratories. Now, proof-of-principle studies are demonstrating the feasibility of using exome sequencing for clinical testing (2– 4 ). Dixon-Salazar et al. used exome sequencing to interrogate a cohort of 118 probands with recessive neurodevelopmental disorders and identified disease-causing mutations in 19% of the probands. Importantly, exome sequencing uncovered mutations in 10 probands (8% of the cohort) that altered the initial clinical diagnosis and led in some cases to a change in patient management (2 ). Calvo et al. tested 42 infants with mitochondrial diseases with the “MitoExome” (mitochondrial DNA plus exons of approximately 1000 nuclear genes) and confirmed that 10 patients (24% of the cohort) had pathogenic mutations. In addition, these investigators identified 2 novel disease-causing genes (3 ). Need et al. used exome sequencing in family trios to investigate patients with a broad range of phenotypic presentations and reported a 33% diagnostic yield: 4 of 12 patients with apparently causal mutations in 2 potentially novel disease-causing genes (4 ). Although the number of patients tested thus far by whole-exome sequencing (WES) or wholegenome sequencing (WGS) is still small, the data reported in these recent studies have defined the minimal diagnostic yields of such NGS-based clinical tests at their early stage of implementation, thus demonstrating the practicality of NGS-based tests. We anticipate that the clinical utility of NGS-based tests will improve further in the next few years and that more patients will benefit from improved diagnostic accuracy and moreappropriate treatment. Conventional molecular diagnostics tests evaluate a defined number of exons for one or more genes, the selection of which is based on the best clinical judgment after thorough evaluation of the patient’s clinical presentation. These tests, which are performed in CLIA-certified laboratories, are mainly for mendelian disorders with well-established causal relationships between genes and diseases. NGS-based comprehensive gene panels, WES-based tests, or WGS-based tests, however, assay for a substantially larger number of genes and genomic regions, only a small proportion of which would potentially be associated with the patient’s condition. NGS-based tests are performed mainly for patients without a clear clinical diagnosis or for patients who have negative test results for genes known to be associated with the disorder. Clinical diagnostics laboratories are actively engaged in implementing NGS-based tests. We review some important characteristics of NGS-based tests and discuss a few outstanding analytical issues, with the hope of gaining a better understanding of the nature of this transformative diagnostic approach and achieving a glimpse into the future of NGS-based tests.