Over the last decade, advances in next-generation sequencing technology have given rise to many findings increasing our understanding of human disease and natural variation within species. Sequencing of the exome, the small fraction of the genome encompassing all exons of protein coding genes, has gained popularity as an inexpensive alternative to sequencing the entire genome. In a recent issue of G3, Warr et al. review details of the method of exome sequencing, its uses in humans and other species, and its potential benefits.
Researchers first used whole exome sequencing (WES) in a clinical setting only a few years ago. A 15-month-old male child presented with an inflammatory bowel disease, in a particularly rare form that stumped conventional diagnostic tools. A team of researchers used WES but were forced to analyze the sequencing data manually, as analytical software for WES had yet to be developed. Despite this impediment, the team was able to identify a variant that led to the proper diagnosis. This first success sparked the now-extensive clinical use of WES, proving particularly useful for difficult-to-diagnose cases, prenatal diagnosis, and identifying disease in young patients who have not yet exhibited full symptoms.
While exome sequencing for humans has been used primarily to discover disease-related variants, the same technology has been applied to agricultural species to identify variants leading to unwanted phenotypes and mutations involved in traits relevant to efficient production. Plant genomes are often extremely complex, limiting the possibility of genome re-sequencing. As a result, many economically important crops like wheat and barley have seen very little genetic improvement. Recently, WES has been applied to wheat, soybean, rice, and barley, allowing researchers to identify variants involved in unwanted or desired phenotypes.
Despite the obvious utility of WES, several important considerations and limitations must be kept in mind. WES is dependent on a well-annotated genome. Without one, causative genes can be missed. This is a particularly important consideration for non-human species that may have incomplete reference genomes.
When comparing whether to use whole genome sequencing or whole exome sequencing, Warr et al. stress that researchers must consider the benefits of each. Even though the cost of whole genome sequencing is decreasing, WES remains significantly less pricey, and allows researchers to sequence more samples and gain statistical power. Also, keep in mind that the development of technology for storing and analyzing the data produced by whole genome sequencing lags behind the sequencing technology itself. On the other hand, the data gleaned using WES is (in size) 100 times less than that of whole genome sequencing.
Compared to WES, whole genome sequencing covers the whole genome with more consistent coverage, does not have reference sequence bias, and provides more accurate detection of variants. Warr et al. state that while whole genome sequencing will inevitably take a leading role in sequencing studies, until storage and analytical tools catch up to handle the data produced, whole exome sequencing offers a positive ratio of cost:benefits well worth considering.
Warr, A., Robert, C., Hume, D., Archibald, A., Deeb, N. & M. Watson (2015). Exome Sequencing: Current and Future Perspectives. G3, 5(8), 1543-1550. http://doi.org/10.1534/g3.115.018564