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Whole Exome Sequencing vs Whole Genome Sequencing: What are the Differences?

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?

Explain Like I’m Five…What’s WES and WGS?

Explain Like I’m Five...What’s WES and WGS

Before we go any further, let’s look at the definitions of a few important terms you’re going to encounter in this blog:

  • Genetics: Genetics is the scientific study of genes, heredity, and the variation of organisms.
  • DNA: DNA is a biological molecule that carries the genetic blueprint vital for the growth, development, functioning, and reproduction of all living organisms.
  • Gene: A gene is a DNA segment that serves as a blueprint for producing a specific protein.
  • Exon: Exons are the coding regions of a gene that direct protein synthesis. Mutations in these regions can impact health.
  • Nucleotide: Nucleotides are the basic units of DNA and RNA, consisting of adenine (A), thymine (T), guanine (G), and cytosine (C).
  • SNP: A single nucleotide polymorphism (SNP) is a variation at a specific position in the DNA sequence among individuals. It is the most prevalent type of genetic variation and can affect disease risk, physical traits, and drug responses.
  • Mutation: A mutation is an alteration in the DNA sequence, which can arise from environmental factors or replication errors. Mutations contribute to genetic diversity and new traits but can also lead to genetic disorders. SNPs are a form of mutation.

There are four types of sequencing: SNP array, gene panel, whole exome sequencing, and whole genome sequencing. 

Source: Cortney Gensemer

What is Whole Exome Sequencing (WES)?

What is Whole Exome Sequencing (WES)

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

Process of WES:

  1. The process begins with sample preparation, using sources like blood, tissue, or amniotic fluid. 
  2. DNA is extracted and fragmented, typically by physical methods such as shearing or sonication, or by enzymatic processes. 
  3. The exons are enriched and isolated from the rest of the genome using specialized technologies. 
  4. This is followed by library construction where the DNA fragments are prepared for sequencing. NGS technologies are commonly employed. 
  5. The final stage involves bioinformatic analysis where data is processed, aligned with a reference genome, and analyzed to identify mutations, such as SNPs, insertions, deletions, and copy number variations.

Source: CD Genomics

WES is crucial in clinical settings for identifying genetic disorders. Here are a few examples of genetic disorders diagnosed by WES:

  • Duchenne muscular dystrophy, a degenerative muscle condition, results from mutations in the DMD gene.
  • Cystic fibrosis, a genetic disorder affecting the lungs and digestive system, is caused by mutations in the CFTR gene.
  • Huntington's disease, an inherited neurological condition, occurs due to mutations in the HTT gene.
  • Mutations in the BRCA1 and BRCA2 genes are linked to a higher risk of breast and ovarian cancer.

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. 

Sources: Applidx, Illumina

What is Whole Genome Sequencing (WGS)?

What is Whole Genome Sequencing (WGS)

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: 

  1. Genomic DNA is isolated and randomly fragmented, fragments are size-selected via electrophoresis. 
  2. A library is constructed. This library undergoes paired-end sequencing, where both ends of the DNA fragments are sequenced, providing a comprehensive view of the genome. 
  3. Finally, genome assembly involves piecing together these sequences to reconstruct the complete genome structure.

Sources: Medline Plus, CD Genomics

Applications of WGS:

  1. Precision Medicine: WGS enables precise medical interventions based on a patient’s unique genetic makeup, crucial for diagnosing rare diseases, cancer genomics, and pharmacogenomics. 
  2. Population Genetics: WGS provides insights into genetic diversity and population structures, helping researchers understand migration patterns, evolutionary history, and the impact of genetic drift and selection. This helps in studying population health, adaptation to environments, and disease susceptibility. 
  3. Evolutionary Biology: WGS examines genomic changes over time, comparing genetic sequences across species to explore evolutionary relationships and adaptations. This helps identify the origins of genetic traits and diseases, showing how species have evolved to adapt to their environments. 

Sources: BioMed Central 

1. Genetic Coverage

1. Genetic Coverage

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.

Sources: Applidx, PacBio

2. Cost


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:

  1. Complexity of sequencing technology
  2. Labor and expertise
  3. Computational resources
  4. Depth of sequencing
  5. Sample preparation & kit prices
  6. Geographic location
  7. Insurance coverage 
  8. Result turnaround time
  9. Genetic counseling 

Source: Applidx

3. Data Volume

Data Volume

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

4. Relevance to Diseases

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

5. Detection of Variants

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.

WES and WGS are Different. Pick What’s Right for You

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.

About Fore Genomics

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.

Learn more about the 300+ conditions and medication interactions we screen for.


What is the main difference between whole exome sequencing and whole genome sequencing?

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.

Which sequencing approach is more cost-effective: WES or WGS?

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.

When is whole exome sequencing preferred over whole genome sequencing, and vice versa?

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.

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