Our bodies are made of trillions of cells, each containing a complete set of instructions called DNA. These instructions, organized into genes, dictate everything from our eye color to our susceptibility to certain diseases. Small changes, or “variants,” naturally occur in this DNA sequence. These genetic variations contribute to the diversity among individuals. Understanding these variations, and how common they are, is a fundamental aspect of modern genetics.
What is Variant Allele Frequency?
Variant allele frequency (VAF) quantifies how common a specific genetic variant is within a sample of DNA. To understand VAF, it helps to know about “alleles,” which are different versions of a gene found at a particular location on a chromosome. A “variant” is a specific change in the DNA sequence of an allele. VAF is calculated by comparing the number of DNA molecules that carry the variant to the total number of DNA molecules at that specific genomic location. For instance, if out of 50 DNA molecules examined, 6 carry a particular variant, the VAF would be 12%.
This metric is distinct from population allele frequency, which describes how common an allele is within an entire population. Genetic variants can be broadly categorized as germline or somatic. Germline variants are inherited from parents and are present in nearly all cells of an individual’s body. Somatic variants, in contrast, are acquired during a person’s lifetime and are not inherited. These often arise in specific cells, such as those in a tumor, and are not present in every cell of the body. VAF is applied differently depending on whether the variant is germline or somatic.
VAF’s Importance in Genetics and Disease
VAF provides insights into both inherited conditions and acquired diseases like cancer. For inherited diseases, VAF can confirm the presence of a germline variant, which is found in a high percentage of an individual’s cells. In cancer research and diagnostics, VAF helps in understanding the proportion of tumor cells that carry a specific genetic alteration. A higher VAF for a somatic mutation in a tumor sample indicates that a larger percentage of cancer cells possess that particular change, potentially making it a good target for specific therapies.
VAF can also be used to track tumor evolution and monitor treatment response. Changes in VAF over time can indicate whether a tumor is growing, shrinking, or developing resistance to treatment. For example, a decrease in the VAF of a known cancer-driving mutation after therapy suggests a positive response, while an increase might indicate disease progression or the emergence of new, resistant cell populations. This information helps guide precision oncology, allowing for more tailored and effective treatment strategies.
Interpreting VAF Values
For variants inherited from parents (germline variants), a VAF close to 50% is observed for heterozygous variants, meaning the individual has one copy of the variant allele and one copy of the normal allele. A VAF close to 100% indicates a homozygous germline variant, where both copies of the gene carry the variant.
VAFs lower than 50%, or even below 1%, can indicate the presence of somatic variants, which are acquired mutations not present in all cells. These lower VAFs can also point to mosaicism, a condition where some cells in the body have a genetic variant while others do not.
In cancer, a VAF of 15% might suggest that approximately 30% of the cells in the analyzed sample are tumor cells carrying that specific variant, assuming the tumor cells are diploid. Factors such as the presence of normal cells within the sample or changes in chromosome copy number within tumor cells can influence the observed VAF. Interpreting VAFs in cancer requires careful consideration of the tumor’s cellularity and genetic makeup.
Factors Affecting Variant Allele Frequency
Several factors can influence the observed VAF. In inherited conditions, the VAF for a germline variant in an individual’s sample is generally stable and predictable.
For somatic variants, particularly in cancer, tumor heterogeneity is a factor. This refers to the presence of different cancer cell populations within the same tumor, each potentially carrying a unique set of genetic variants. A variant present in only a subset of tumor cells will exhibit a lower VAF compared to a variant present in most tumor cells. Clonal evolution, where new subclones with different mutations emerge, directly impacts the observed VAFs.
Technical aspects of genetic testing also affect measured VAF. The quality of the sample, including the proportion of tumor cells versus normal cells, can influence the VAF. Additionally, the depth of sequencing, or how many times a particular DNA region is read, can impact the accuracy of VAF measurement, with lower sequencing depths potentially leading to less precise VAF estimations or even missed variants.