It is extremely likely that exome sequencing, and if not genome sequencing, will also have significant impact in the clinical setting, outside of identifying genes that were previously unknown to contain disease causing mutations. In the context of genetic testing, rather than screening an inherently limited panel of genes for a particular set of diseases, why not just sequence the whole exome? This opens the door to a lot of possibilities, first, rapid genetic diagnosis and screening, when known disease-causing mutations are detected; second an inevitable expansion of the phenotypic range of disease associated with particular mutations or mutations in particular genes.
Exome sequencing has already proven its worth in the former; for many neurological diseases, where there is a long list of candidate genes and loci, it is often cheaper and certainly quicker to find mutations by exome sequencing. For many diseases with a high degree of genetic heterogeneity, screenings are often only designed to catch the most common mutations, or alterations in the most frequently mutated genes. Montenegro and colleagues demonstrated the power of exome sequencing in exactly this situation, with the analysis of a family with Charcot-Marie-Tooth (CMT) disease.33
Rather than screen the 35 genes known to contain mutations causing this disease, the authors used exome sequencing in 2 affected family members; with these data they were able to identify GJB1
mutations as a cause of CMT in this family. This case is also illustrative, because GJB1
mutation would have been ruled out for screening because of a reported male-to-male inheritance, incompatible with mutation of this gene, which lies on chromosome X. The use of exome sequencing by these authors likely saved time and money in reaching a genetic diagnosis. The increasing adoption of exome sequencing in the research setting, means that these data are becoming easier to process and analyze, in addition to becoming much cheaper to generate; many laboratories are now able to generate an exome for <$1500 a sample. When compared to the costs and time required for conventional screening, such a comprehensive approach represents value for money. Despite this still being a new technology, exome sequencing in genetically heterogeneous neurological diseases has already identified TECR
mutations in non-syndromic mental retardation,10
WDR62 mutations in severe brain development malformations,34TGM6
mutations in ataxia,23
and a WRN
mutation in atypical Werner's syndrome.35
As mentioned above, exome sequencing is likely to find mutations in genes previously linked to disease, but associated with a phenotype distinct from the one being tested. This has been elegantly demonstrated with the identification of VCP
mutations as a cause of amyotrophic lateral sclerosis (ALS).15
In this article Johnson and colleagues had used exome sequencing to identify the genetic lesion responsible for an autosomal dominant form of ALS in a large pedigree from Italy. Surprisingly VCP
mutations, including the same amino-acid change identified in this ALS kindred, had previously been linked to Paget's disease, inclusion body myopathy and frontotemporal dementia. Therefore this finding broadened the clinical and pathological phenotype of VCP
mutations to include ALS and TDP-43 inclusions. Notably, further work by this group showed that VCP
mutations are an appreciable cause of familial ALS, responsible for ~2% of cases in this group. As this work shows, broadening the phenotype associated with mutations has the potential to inform on the etiologic basis of disorders by uniting what is known about the biological underpinnings of apparently unrelated disorders into a single model.
One might also predict that as exome data accumulates we will get greater resolution on the role of mutations in disease. Exome data will not only help to identify pathogenic variants, including those of previously unknown or equivocal pathogenicity, but it will also help in determining penetrance, expressivity, and prevalence of mutations in particular populations. Related to the notion of penetrance, in the sequencing of normal individuals we might expect to find variants that were previously thought to cause fully penetrant disease, and these data will call into question pathogenicity of some published variants. As recent work describing the high phenocopy rate in families with apparently monogenic PD shows, in even the most ‘simple’ families, confounding genetic, environmental, or stochastic factors likely effect presentation and penetrance.36
In the beginning exome sequencing will raise many questions and often reveal an apparently confusing relationship between genetic variants and disease, but with time, accumulating data will help bring resolution to many outstanding clinico-genetic questions.
One clinical challenge that is particular to more comprehensive genetic approaches comes with the inevitable discovery of mutations unrelated to the condition in question. These secondary, or collateral, findings will be common in exome sequencing, and indeed one of the first exome publications, which sought to identify mutations for Miller syndrome, also described the identification of mutations causing ciliary dyskinesia within the same family.20, 37
The question then arises, what does a clinician do when they identify a mutation of proven or even potential clinical relevance; how should the disclosure of these mutations be handled. These are not necessarily simple issues, particularly when considering the confounds and problems such as disclosing carrier status, non-paternity, reduced penetrance, lack of viable treatment options and interpretation of risk factors. As has been elegantly argued previously, these issues in particular will require thoughtfully constructed research37
and continuing education of both health care providers and the general public.