Clinical application of exome sequencing in undiagnosed genetic conditions

Abstract

Background: There is considerable interest in the use of next-generation sequencing to help diagnose unidentified genetic conditions, but it is difficult to predict the success rate in a clinical setting that includes patients with a broad range of phenotypic presentations.

Methods: The authors present a pilot programme of whole-exome sequencing on 12 patients with unexplained and apparent genetic conditions, along with their unaffected parents. Unlike many previous studies, the authors did not seek patients with similar phenotypes, but rather enrolled any undiagnosed proband with an apparent genetic condition when predetermined criteria were met.

Results: This undertaking resulted in a likely genetic diagnosis in 6 of the 12 probands, including the identification of apparently causal mutations in four genes known to cause Mendelian disease (TCF4, EFTUD2, SCN2A and SMAD4) and one gene related to known Mendelian disease genes (NGLY1). Of particular interest is that at the time of this study, EFTUD2 was not yet known as a Mendelian disease gene but was nominated as a likely cause based on the observation of de novo mutations in two unrelated probands. In a seventh case with multiple disparate clinical features, the authors were able to identify homozygous mutations in EFEMP1 as a likely cause for macular degeneration (though likely not for other features).

Conclusions: This study provides evidence that next-generation sequencing can have high success rates in a clinical setting, but also highlights key challenges. It further suggests that the presentation of known Mendelian conditions may be considerably broader than currently recognised.

Figure 1

Expression of endogenous NGLY1 protein in peripheral blood mononuclear cells from patient, parents and three unrelated healthy controls. The protein expression level in the patient is less than both parents and healthy controls. GAPDH, glyceraldehyde 3-phosphate dehydrogenase.

Figure 2

Expression of TCF4 variant and wild-type (WT) protein in COS-7 cells. The variant protein (V) is only seen in the presence of proteasome inhibitors. GAPDH, glyceraldehyde 3-phosphate dehydrogenase.

Figure 3

The SCN2A mutation, D1598G, is located in transmembrane segment 3 of the sodium channel protein domain 4. This residue is conserved in vertebrate, invertebrate DM (Drosophila) and bacterial (NaChBac) sodium channels. The D to Y mutation at the corresponding position of SCN1A was identified in a patient with severe myoclonic epilepsy (SME) of childhood, an early onset epileptic encephalopathy with features similar to the affected individual in trio 11 h, human; f, fish.