Great expectations: using massively parallel sequencing to solve inherited disorders

Abstract

The mutation discovery process for monogenic disorders is undergoing an exciting revolution. Previously dependent on linkage mapping and carefully selected gene-candidate approaches, identifying disease-causing mutations was both time consuming and frustrating. The advent of the new and emerging massively parallel sequencing technologies is driving unbiased discovery of novel disease-causing mutations at an unprecedented rate. How long will it be before the process is fully automated and the job of molecular geneticist is changed forever? We comment on the mutation-discovery strategies compatible with this technology and demonstrate that while the modern gene jockey might need to trade in the horse for something a bit faster, the finish line for interpreting human genetic variation is still a long way ahead. A recent comprehensive and highly recommended review covers the technical capabilities of massively parallel (also called next-generation) sequencing for the field of genetics [1]. Mutation-discovery applications using massively parallel sequencing survey whole-genome, wholeexome, regionor candidate-gene groupspecific DNA templates. Each strategy has strengths and weaknesses that must be considered and matched with the genetics and biology of the clinical phenotype to be studied. Whole-exome sequencing is already the method of choice for most mutation discovery efforts. Commercially available chip-based and in-solution array enrichment platforms make this protocol amenable to high-throughput automation and standardization. There are companies that offer this protocol as a fee for service, including downstream sequence analysis [101]. Currently, 86% of the 100,000 mutations cataloged in the human genome mutation database affect coding regions [2], which are captured by the whole-exome arrays. Even considering the biases, which have driven the discovery of these mutations so far, it is predicted that exome sequencing will be successful most of the time. Exome sequencing is already having an impact on patient care; in one study, mutations in SLC26A3 that are normally associated with congenital chloride-losing diarrhea (Online Mendelian Inheritance in Man [OMIM] 214700) were identified in a patient with a diagnosis of an atypical Bartter syndrome (OMIM 607364) [3]. These findings led to the re-examination of the patient to confirm the diagnosis of chloride-losing diarrhea and the subsequent identification of five additional mutations in SLC26A3 in a cohort of 39 individuals diagnosed with Bartter syndrome. In a similar study, 11 novel mutations in DHODH associated with the recessive disorder Miller syndrome (OMIM 263750) Mark Corbett