Since the completion of the initial sequencing of the human genome [1
] there has been more than a decade of refinement and optimization of whole genome sequencing [3
]. In 2007, when it was still too expensive to sequence whole genomes in any large quantity, it was first demonstrated that one can capture and sequence the protein coding exons from individual human genomes [5
]. This was followed by the first in-depth analysis of an 'exome', defined as 'the set of exons in a genome' [7
]. The next year saw the sequencing of 12 human exomes [8
], followed a year later by the use of exome sequencing to determine the genetic basis for cases of Bartter syndrome [9
], Miller syndrome [10
] and Kabuki syndrome [11
]. By 2010, with the cost of sequencing plummeting due to the rapid development of newer and better technologies, the question arose concerning when and whether it would be better and more cost-effective to go straight to whole genome sequencing (WGS). This was demonstrated by the simultaneous detection of the mutation underlying Miller syndrome by WGS of a family consisting of two affected siblings and their parents with the added bonus of being able to calculate a human intergenerational mutation rate of approximately 1.1 × 10-8
per position per haploid genome [12
]. Many researchers have previously reviewed the success and promises of whole exome or genome sequencing in research settings [13
]. Here, we describe the ongoing developments and challenges for the clinical application of whole exome or genome sequencing, and we discuss strategies to move the field forward.
There are ongoing and rapid developments in sequencing technology (Boxes 1 and 2). We consider whether a centralized model for whole exome or genome sequencing might take advantage of economies of scale and increased efficiency brought about by sequencing in a central location. Such a model of centralized WGS could be a much needed 'disruptive innovation' [20
], if implemented well. When the company Amazon first started, not many people would have predicted that it would supplant many physical bookstores, but that is indeed what has occurred. Similarly, a company that can implement an effective centralized sequencing facility and return of genomic data via the internet or using a secure cloud computing architecture could capture a portion of consumer- and hospital-oriented WGS, perhaps augmenting the efforts of localized and academic-based sequencing centers. The industrialization of WGS could also raise the quality standards. An example of industrialization relates to the current manufacturing of oligonucleotide primers used all over the world for polymerase chain reaction (PCR): nowadays most researchers order primers from centralized companies rather than synthesizing primers at local laboratories, mainly because these companies have achieved higher quality at a reduced price. Some WGS is indeed already being performed in central locations by at least two companies: Illumina (San Diego, California, USA) and Complete Genomics (Mountain View, California, USA). The key question will be whether clinicians and hospitals will be willing to send out DNA samples to a centralized location, rather than setting up the sequencing machines and bioinformatics resources locally. A compromise might be along the lines of what has occurred with the disruptive technology magnetic resonance imaging (MRI), which has been deployed in many hospitals but also at stand-alone MRI diagnostic centers throughout the USA.
Over the past 3 years, there has been a period of primarily exome sequencing while awaiting a further decrease in cost for WGS [22
]. There have now been, as of July 2012, 747 publications involving exome studies (according to PubMed searching with the term 'exome'). So far, the main achievements of exon capture and high-throughput sequencing in genomic medicine have been the identification of the causes of many clinically characterized Mendelian disorders (that is, single gene disorders). Furthermore, exome sequencing has been applied to the study of a multigenerational pedigree [23
] and has also been used in molecular diagnostics (for example, to diagnose neonatal diabetes [24
] and an X-linked inhibitor of apoptosis deficiency, with the latter prompting an allogeneic hematopoietic progenitor cell transplantation with promising results [25
]). In 2011, X-chromosome exon capture and sequencing was used to determine the genetic basis of a previously undescribed and idiopathic disorder, later named Ogden syndrome, which was shown to result from a defect in the amino-terminal acetylation of proteins [26
]. Since that time, many other idiopathic disorders have been identified and their genetic basis determined via exome sequencing [27
]. Many groups are also applying exome sequencing to the study of complex diseases or traits such as height, hypertension, diabetes and autism, resulting in the identification of rare variants that might play a role in human diseases [31
As the cost of capturing and sequencing exomes has decreased, it has become easier to identify the genetic causes of very rare Mendelian diseases. The major caveat here is that the causative mutation must be present in the currently annotated exome, and we do not have a clear idea of how many diseases will be caused by mutations outside the exome, including in non-coding regulatory regions [35
]. Informal polling of many human geneticists suggests that exome sequencing projects currently identify a truly causative variant in only about 10% to 50% of cases, although this estimate is very rough given that most researchers do not publish their results (or lack thereof) when exome sequencing fails to identify a causative variant. This estimate is also crucially dependent on one's definition and threshold for proof of causation.