Exome sequencing: Dual role as a discovery and diagnostic tool

Abstract

Recent developments in high-throughput sequence capture methods and next-generation sequencing technologies have now made exome sequencing a viable approach to elucidate the genetic basis of Mendelian disorders with hitherto unknown etiology. In addition, exome sequencing is increasingly being employed as a diagnostic tool for specific genetic diseases, particularly in the context of those disorders characterized by significant genetic and phenotypic heterogeneity, for example, Charcot-Marie-Tooth disease and congenital disorders of glycosylation. Such disorders are challenging to interrogate with conventional polymerase chain reaction-Sanger sequencing methods, because of the inherent difficulty in prioritizing candidate genes for diagnostic testing. Here, we explore the value of exome sequencing as a diagnostic tool and discuss whether exome sequencing can come to serve a dual role in diagnosis and discovery. We summarize the current status of exome sequencing, the technical challenges facing it, and its adaptation to diagnostics, and make recommendations for the use of exome sequencing as a routine diagnostic tool. Finally, we discuss pertinent ethical concerns, such as the use of exome sequencing data, originally generated in a diagnostic context, in research investigations.

Exome sequencing reveals HINT1 mutations as a cause of distal hereditary motor neuropathy

“…[27][28][29] More recently, the use of exome sequencing for diagnostic purposes in genetic disorders with a high degree of genetic heterogeneity such as CMT is being explored. 30,31 Although the prize of exome sequencing is declining, the bioinformatic tools for analysis have improved and the coverage of the sequencing appears to be sufficiently high for use in the diagnostic setting, several technical and ethical challenges remain. 32 In particular, establishing the pathogenicity of newly identified genetic variants is often difficult and the possibility of finding unrelated finding requires further attention.…”

Enhanced utility of family-centered diagnostic exome sequencing with inheritance model–based analysis: results from 500 unselected families with undiagnosed genetic conditions

“…3 Whole-exome sequencing (WES) provides a one-step simultaneous interrogation of virtually all exonic and adjacent intronic sequences and has been remarkably successful both in a diagnostic setting (diagnostic exome sequencing (DES)) and as a discovery tool (research exome sequencing), 4 especially for disorders characterized by significant genetic heterogeneity. 5 The diagnostic rate for clinical DES in unselected patients, who generally underwent exhaustive single-gene or gene-panel tests before DES, is reported to be ~25%. 6,7 In this report, we analyzed 500 unselected consecutive cases that were referred to our laboratory for DES.…”

Clinical exome sequencing in neurologic disease

“…The second deals with technical issues, predominantly completeness of gene coverage, validation of results, and variant interpretation. 21,22 CES is a new and evolving technology. Some payers consider the test to be experimental and investigational.…”

“…21,22 As described above, coverage across the exome is determined on average because, typically due to structural differences, not all portions of the exome are sequenced equally and it is therefore possible that a mutation may exist in a region of reduced coverage. However, coverage and detection of variants can be improved by increasing the number of reads (the depth of exome sequencing) 30 or using targeted next-generation strategies to improve capture of troubling regions 31 so this concern is not inherent to the method itself and can be resolved through technical performance standards.…”