Reading Your Genes: Exome Sequencing

““Knowing the underlying genetic cause of a disease has the potential to play a crucial role in the diagnosis, symptomatic therapeutic development and perhaps even treatment of many illnesses.””

Finding the underlying genetic cause of a disease can be crucial for identifying possible therapeutic targets and may benefit the patient’s overall prognosis, which refers to the likely course of a disease including factors like life expectancy and a patient’s of living. Many genetic diseases occur due to mutations in exons, which are the areas of the genome that code for proteins. The rest of the genome consists of introns that do not code for proteins, hence are spliced out and degraded. The exome refers to the collection of all of the exons, and it only makes up 1% of the genome ¹ . Thus, it is much more cost effective and efficient to only scan the exon regions of the genome to identify genetic mutations that may be responsible for a particular disease. This is a technique known as whole exome sequencing (WES). As scientific advancements are made, people are discovering ways to read and interpret your genes more easily and comprehensively. It is important to analyze the current state of exome sequencing, and explore some of the latest advancements such as RNA sequencing which could supplement the data collected from other tests including exome sequencing.

Whole exome sequencing has been crucial in a number of studies that aimed to identify genetic variants, however improvements are necessary to allow for more progress. The first successful application of exome sequencing was used in a study to identify the gene for a rare genetic disorder, Miller syndrome, which affects the development of the face and limbs of children ³ . The study captured and sequenced the exons of four affected individuals and identified a single gene -DHODH -as the one causing the disorder, even when the clinical patient group was a small sample of people. This example demonstrates the benefits of WES, which include rapid diagnosis and conclusivity of disease causing genetic variants with smaller populations of individuals - which is the very definition of rare diseases. It is extremely useful for rare genetic diseases because unlike other techniques and cohort studies, which often require a large number of people, it works just as well with the few diagnosed people that can participate in the study.

WES allows for identification of novel disease mechanisms which were previously unknown, greatly increasing the ability to diagnose rare diseases, and develop improved therapeutic plans for the management of rare genetic disorders ² . One of the problems with WES that currently exists is that many tests come back negative, which means no genetic cause is discovered. This is primarily due to the fact that many mutations that cause diseases have not yet been identified, especially for complex disease phenotypes that result from a variety of genetic mutations and interactions. Presently, around 10 000 genetic disorders are listed in the Online Mendelian Inheritance in Man (OMIM) database, but only half of these diseases have the responsible genes identified ¹ . This illustrates how much progress still needs to be made and how the development of more diagnostic testing that can account for genetic mutations and multigene interactions is needed to supplement the WES test.

Current research being done that is addressing the gap of knowledge from whole exome sequencing is transcriptome sequencing (also known as RNAseq). The transcriptome is all of the messenger RNA (mRNA) that has been transcribed from the DNA which will later be translated in order to make functional proteins. Think of DNA as the cake mix, mRNA as the cake batter, and protein as the final delicious cake that we eat. It is useful to study the transcriptome in order to get a better diagnosis of disease because we can analyze protein product variety due to alternatively spliced mRNA and post-transcriptional modifications ⁴ . In other words, our cake batter can be divided into multiple portions to make many different types of cakes. Once DNA has been transcribed, different exons can be retained in the final mRNA through splicing, therefore incorrect retention or exclusion of exons and introns can lead to various genetic diseases. Just as how adding Smarties or Oreo pieces to the batter can significantly change the looks of our cake, post-translational modifications like addition of 5 prime methyl cap and poly A tail can cause disruptions and lead to different disease phenotypes (disease manifesting differently within different people).

These types of problems would not be readily seen through exome sequencing because the WES technique only looks at the DNA, and many of the disease causing issues can only be seen once the DNA is transcribed into RNA. Lee’s study showed that particularly in the rare disease cohort, RNAseq allowed for a significantly increased rate of diagnosis compared to genome sequencing analysis ⁴ . For example, for a 3 year old boy that had significant delay in cognitive and physical development as well as atrophy of the optic nerve, physicians used extensive genetic testing, including WES and got no results. Later when the study implemented the RNAseq technique, they were able to discover a problem in RNA due to splicing variants, and incorrect intron retention ⁴ . In other words, the batter tasted fine but the cake tasted wonky because some rotten smarties were added to the batter. This exemplifies how RNAseq can be a very crucial, useful diagnostic genetic tool.

Knowing the underlying genetic cause of a disease has the potential to play a crucial role in the diagnosis, symptomatic therapeutic development and perhaps even treatment of many illnesses. In the past, it has successfully enabled the development of more accessible diagnostic tools, such as screening for mutations that predispose women to breast cancer by looking at mutations in the BRCA1 or BRCA2 genes. Furthermore, it allows for progress in research looking to find potential therapeutics for genetic diseases, such as by identifying potential targets for gene editing. Overall, there is much work to be done in regards to identifying the genetic mutations responsible for rare diseases, but a combination of exome sequencing along with new techniques of analyzing the transcriptome will allow us to advance further in the journey.

Rida Shaikh

Works Cited:

1. Ng, S. B., Buckingham, K. J., Lee, C., Bigham, A. W., Tabor, H. K., Dent, K. M., Bamshad, M. J. (2009). Exome sequencing identifies the cause of a mendelian disorder.
2. Maxmen, A. (2011). Exome sequencing deciphers rare diseases. Cell, 144(5), 635-637.
3. Stranneheim, H. and Wedell, A. (2015). Exome and genome sequencing: a revolution for the discovery and diagnosis of monogenic disorders. Journal of Internal Medicine, 279(1)
4. Lee, H., Huang, A.Y., Nelson, S.F. (2019). Diagnostic utility of transcriptome sequencing for rare Mendelian diseases. Genetics in Medicine, 0 (0)

Cite This Article:

Shaikh R. Reading Your Genes: Exome Sequencing. Illustrated by J. Tamura. Rare Disease Review. November 2019. DOI:10.13140/RG.2.2.18254.00321.