Exome sequencing is a genetic test that examines the protein-coding regions of an individual’s DNA. This targeted approach allows scientists and clinicians to analyze a highly functional segment of the human genome, providing insight into the genetic blueprint that directs biological processes.
What the Exome Is
The exome represents the protein-coding regions of our genome, which are called exons. These exons contain the instructions for building proteins, the molecules that perform most of the work in our cells and are responsible for the structure, function, and regulation of the body’s tissues and organs. While the entire human genome consists of approximately 3 billion DNA “letters” or base pairs, the exome makes up only about 1% to 2% of this vast genetic material, containing roughly 180,000 exons.
Imagine the entire genome as a vast library. The exome is like the collection of all instruction manuals within that library. These manuals provide direct instructions for building and operating everything, making them relevant for understanding how the body functions and where errors might occur. Focusing on this smaller, highly informative portion makes genetic analysis more efficient and cost-effective compared to sequencing the entire genome.
How Exome Sequencing Works
Exome sequencing begins by collecting a biological sample, such as blood or saliva. DNA is extracted from this sample and fragmented into smaller pieces.
After fragmentation, exome capture isolates the exonic regions. Specialized probes bind specifically to the protein-coding DNA fragments, capturing the exome and separating it from non-coding regions. The captured exonic DNA is then sequenced using high-throughput technology, which reads the genetic code by determining the order of DNA building blocks.
The final step involves data analysis, where the sequenced exome data is compared to a reference human genome. This comparison identifies variations or mutations within the exonic regions, such as single nucleotide polymorphisms (SNPs) or small insertions and deletions (indels). Bioinformatic tools then process this information to pinpoint potential genetic changes related to health conditions.
Why Exome Sequencing Is Used
Exome sequencing is increasingly used in clinical settings and research. A primary application is diagnosing rare genetic disorders, especially when symptoms are complex or other genetic tests have not yielded a clear diagnosis. It has been instrumental in uncovering the genetic causes of conditions like cystic fibrosis, muscular dystrophies, and various metabolic disorders. For example, exome sequencing can provide a diagnosis for a significant percentage of patients with primary immunodeficiencies.
This sequencing approach also aids in identifying genetic causes of complex diseases, where multiple genes and environmental factors contribute to the condition. Researchers use exome sequencing to discover new disease-causing genes, contributing to a deeper understanding of human biology. Additionally, it plays a role in guiding treatment decisions, particularly in personalized medicine for conditions like cancer, by identifying specific mutations that can inform targeted therapies. For instance, it can detect mutations in genes such as BRCA1 and BRCA2, which are associated with increased risks of breast and ovarian cancers, allowing for tailored risk assessments and preventative strategies.
What Exome Sequencing Cannot Do
Despite its utility, exome sequencing has specific limitations. It only analyzes the protein-coding regions, meaning mutations or variations located outside the exome, even those influencing gene regulation or disease, will not be detected. This means roughly 98% of the genome remains unexamined by this method.
Exome sequencing may also not reliably detect certain types of genetic changes, such as large structural variations like extensive deletions, duplications, inversions, or translocations. While some copy number variants can be inferred, the method has low sensitivity for these larger rearrangements. It also typically does not provide information on mitochondrial DNA mutations or epigenetic factors, which are changes in gene expression not caused by DNA sequence alterations. The interpretation of results can be complex, and some identified variations may be of unknown significance, requiring further investigation or re-analysis as scientific knowledge advances.