Considerations for whole exome sequencing

Published on 08/10/2022

6 min read

Whole exome sequencing can present a goldilocks option between targeted gene panels and whole genome sequencing. Dive into some of the considerations for adopting whole exome sequencing in your institution.

Whole exome sequencing (WES) is one of the latest advancements in next-generation sequencing (NGS) technology.This method sequences about 233,785 exons, or protein coding regions of the genome. This region is about 20,000 genes which makes up only about 1 percent of the human genome. Mutations in these regions can alter the respective proteins leading to various phenotypic implications. Analyzing the whole exome can unravel causative variants for diseases ranging from Mendelian to complex phenotypes.

When to use whole exome sequencing versus targeted or whole-genome sequencing

Targeted or panel sequencing only sequences genes that are known to be associated with a disease. It is often used, if the given disease has a clinical testing panel available and if the focus is solving the case with a short turnaround time.

However, if disease mechanisms are poorly understood, it can take several gene panels to identify the putative variant. Thus, WES allows for all protein-coding genes to be analyzed at once, which increases the probability of identifying the causative variant in a single sequencing assay. Since WES is not restricted to evaluating genes that have previously been associated with a specific disease, it gives a more comprehensive overview of the exome. Additionally, WES can help identify novel disease-gene associations in a research setting.

Another type of NGS is whole-genome sequencing (WGS), which evaluates the entire genome. This method can also be valuable for diseases with complex phenotypes or for cases where large structural variations are the primary cause of the disease. WGS can identify large structural variations and splicing variants in deep intronic regions. However, the large volumes of sequencing data pose some unique challenges for data analysis and storage. Although genomic sequencing continues to become cheaper and more accessible, it can be cost restrictive for some institutions.

Hence, WES can present a Goldilocks option between targeted gene panels and WGS. It generates a more comprehensive genomic view than targeted panels, but creates a data volume that is more manageable to analyze than that generated by WGS. In some specific cases, it also gives the researcher an opportunity to analyze copy number variations (CNV). Lastly, WES has a higher throughput and faster turnaround time compared to WGS.

Specific patient types who could benefit from whole exome sequencing

WES is an effective tool that can be used in a multitude of situations, but there are a few specific situations in which it presents significant advantages. One such situation is when an individual has overlapping phenotypes across multiple rare diseases. Using WES and taking a genotype-first approach can identify causal disease-gene associations and help diagnose overlapping conditions. This more comprehensive view can also shorten turnaround time for diagnosis compared with running a series of targeted panels.

The shorter turnaround time and higher diagnostic yield with WES also presents significant advantages for neonatal patients. Phenotypes can be difficult to assess in neonatal patients and some symptoms might not yet manifest. Comprehensive genetic testing such as WES can help to reach an early diagnosis, which not only allows for the implementation of an optimized care plan but can also provide information on any preventative measures and/or other potential complications that could arise as a result of the disorder.

Rare disease diagnosis is often an exhaustive journey for patients and family members seeking answers for their accurate diagnosis and disease management through several specialists, while undergoing multitude of tests and procedures, in pursuit of receiving the most effective treatment. WES can be a good follow-up to those initial tests, providing information that could uncover relevant variants in genes that were not previously implicated in a given disease (diagnosis).

Thus, WES cannot only be used for identifying causative variants related to the patient’s disorder, but the comprehensive approach can provide information about additional diseases or any genetic predispositions to other inherited disorders. This information is sometimes known as secondary or incidental findings and allows for patients to better manage their condition and understand the associated health risks. In some cases, this information may not be reported back to the patient, however, having the sequenced exomes allows for easier reanalysis of the data and future germline assessment of the same patient.

Considerations for implementing whole exome sequencing

A major logistical consideration for implementing WES beyond (the cost of) validating a new test is choosing which bioinformatics platform will be used to analyze the data. As touched on previously, WES produces much more data than sequencing using a targeted panel. Most whole-exome solutions sequence around 20,000 genes and a targeted panel that may sequence less than 100 genes. This larger volume of data is responsible for the advantages of WES, by creating a more comprehensive view of the genome which can increase diagnostic yield. Institutions that are interested in bringing on WES need to consider the large volume of data being generated and how this bioinformatic workflow can be challenging for finding relevant variants.

A bioinformatics platform for WES analysis should accurately and reliably identify multiple variant types in a single workflow and have a fast turnaround time and multiple filtering options to help streamline variant interpretation. The SOPHiA DDM™ Platform delivers advanced analytical performance, can complete WES analysis overnight, and has dedicated filtering features and a rich knowledgebase to help identify variants of interest associated with  rare diseases for research purposes.

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