Next-generation sequencing (NGS) revolutionizes DNA and RNA analysis by enabling rapid sequencing of vast gene arrays or entire genomes, advancing disease diagnosis, prognosis, and personalized medicine. Two methods of undertaking this are whole exome sequencing (WES) and whole genome sequencing (WGS).
Both methods are essential for advancing medical research and clinical applications.
But… What are the differences between the two?
Before we go any further, let’s look at the definitions of a few important terms you’re going to encounter in this blog:
There are four types of sequencing: SNP array, gene panel, whole exome sequencing, and whole genome sequencing.
Source: Cortney Gensemer
WES is a genetic sequencing method that analyzes the coding regions of genes (exons), which make up about 1% to 2% of the human genome and are responsible for coding proteins.
It is useful for diagnosing complex and elusive health conditions or when there is a family history of medical issues.
The dumbed down version: Imagine DNA as a vast recipe book guiding our body's operations, and Whole Exome Sequencing as a magnifying glass focused on the most summarized excerpts—exons. These excerpts instruct our body's functioning. WES helps doctors quickly detect if a genetic error within these instructions causes illness, ensuring faster and more accurate diagnoses.
Source: Yale Medicine
Source: CD Genomics
WES is crucial in clinical settings for identifying genetic disorders. Here are a few examples of genetic disorders diagnosed by WES:
In cancer research, WES is used for biomarker discovery, capturing genetic variants from blood samples, and investigating genetic factors that influence cancer susceptibility. It helps in understanding tumor genetics and identifying potential targets for therapy, making it valuable in the study of cancer biology and treatment.
WGS sequences an individual's complete (100%) DNA, capturing mutations both within and outside exons—including introns and non-coding regions. It is crucial for understanding all potential genetic disorders.
The dumbed down version: Let’s go back to that recipe book that outlines our body’s operations (our DNA). WGS reads every single word in that book instead of focusing on just the most summarized parts.
WGS includes several key steps:
Sources: Medline Plus, CD Genomics
Applications of WGS:
Sources: BioMed Central
Coverage refers to the extent to which the genomic regions are represented in the sequencing data. It's expressed as a percentage of the genome that has been sequenced.
For example, if a technique covers 90% of the genome, it means 10% might not be sequenced at all due to limitations in the sequencing technology or methodology.
WES covers only the exons, approximately 1% of the genome. WGS Covers the entire genome (100%), including exons, introns, and non-coding regions.
The cost for whole exome sequencing is generally lower because it targets a smaller portion of the genome.
WGS, being more comprehensive, generally costs more than WES. However, like WES, the cost of WGS has been decreasing over time due to advancements in sequencing technologies and increased efficiency.
The primary cost drivers include:
Source: Applidx
WES generates less data, simplifying analysis and storage. WGS produces a large amount of data, requiring more resources for analysis and storage.
Today, the accessibility of bioinformatics tools for both WES and WGS has improved, with many tools now being more user-friendly and integrated into workflows that guide the user from raw data processing to final variant interpretation.
Overall, the choice between them depends on the specific needs of the project, the available budget, and the coverage required.
Sources: Applidx
WES targets regions known to contain most disease-causing mutations.
For instance, in a pediatric cohort with kidney disease, WES established a genetic diagnosis in 37.1% of cases, showing its use in clinical diagnostics where genetic causation is strongly suspected.
Since WGS sequences the entire genome, it has been shown to detect 25.7% more diagnostic variants than WES. Studies suggest that WGS should be considered a first-line test for genetic diseases due to its comprehensive nature and ability to provide more extensive genetic insights.
In a study involving children at a dysmorphology clinic in Mexico, WGS provided a diagnosis for 68% of the cases. This shows the potential of WGS to change clinical outcomes by enabling precise genetic diagnosis, directly affecting patient management and therapy planning.
Source: Applidx, Oxford Academic, Medical Genome Initiative, medRxiv
WES identifies variants within the protein-coding regions of the genome. This includes single nucleotide variants (SNVs) and small insertions and deletions (indels). WES does not effectively capture variants in non-coding regions.
WGS detects SNVs, indels, as well as copy number variations (CNVs) and structural variants across the entire genome, including both coding and non-coding regions.
Ultimately, WGS offers a broader and more uniform coverage than WES. In clinical settings, this leads to more accurate diagnoses and the identification of potential therapeutic targets.
Whole Exome Sequencing and Whole Genome Sequencing have been game-changers in DNA analysis, shaping how we diagnose diseases and tailor treatments.
WES focuses on specific gene areas, pinpointing known genetic issues, while WGS gives us a broader view of the entire genome.
Despite their differences, both are crucial for pushing medical boundaries.
Fore Genomics is designed as the most comprehensive genetic screen possible for newborns, infants, and children. We want every family to have access to the best technologies available for their child's health. Genetic screening can be used prior to the onset of symptoms to lead to proactive management of genetic diseases.
Our goal is simple: to give parents peace of mind and help children live healthier lives.
WES focuses on sequencing only the exons, the protein-coding regions of the genome, which make up about 1-2% of the human genome. WGS sequences 100% of the genome, including both coding and non-coding regions, giving a more comprehensive view of an individual's DNA.
WES costs less than WGS because it targets a smaller portion of the genome. That being said, the cost of WGS has been decreasing over time due to developments in sequencing technologies and increased efficiency.
WES is preferred when a disease is known to be linked to mutations in protein-coding genes. WGS is preferred in more complex cases where the disease might involve non-coding DNA or when a comprehensive genetic analysis is required.