# Variant allele frequency (VAF)

Source: https://onco.cc/terms/vaf/  
OnCo record `vaf` (Term). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

The fraction of DNA reads carrying a mutation. Tells you how much of the sample is mutant and how clonal it is.

## Summary

Variant allele frequency (VAF) is the fraction of sequencing reads at a position that carry a given mutation, and it tells you how much of a sample is mutant and how clonal the mutation is. The value depends on tumour purity, copy number and clonality, so it must be read with those in mind. In ctDNA, VAF tracks tumour burden over time, and very low values require error-suppressed sequencing. The term is linked to Comprehensive genomic profiling and Liquid biopsy (ctDNA), to the Clonal evolution & minimal residual disease and Clonal haematopoiesis (CHIP) pathways, and to the bottleneck on tumour heterogeneity. Ideas built on it include a clone report from blood at every treatment cycle and truncal or branch labelling of mutations, and it features in the GALAXY paper.

## Fields

- Kind: Term
- Last checked: 2026-09-04

## Sources

- Wikipedia: https://en.wikipedia.org/wiki/Allele_frequency
- Li et al., Standards and guidelines for the interpretation and reporting of sequence variants in cancer: AMP, ASCO and CAP joint consensus (Journal of Molecular Diagnostics 2017): https://doi.org/10.1016/j.jmoldx.2016.10.002

## Connected records

- technologies: [Comprehensive genomic profiling](https://onco.cc/technologies/cgp/), [Liquid biopsy (ctDNA)](https://onco.cc/technologies/liquid-biopsy/)
- key papers: [Circulating tumor DNA in stage III colorectal cancer, beyond minimal residual disease detection, toward assessment of adjuvant therapy efficacy and clinical behavior of recurrences](https://onco.cc/key-papers/paper-henriksen-ctdna-stage-iii-colorectal-improve-it-ccr-2022/), [GALAXY: tumour DNA in blood four weeks after bowel cancer surgery predicts relapse tenfold](https://onco.cc/key-papers/paper-galaxy-signatera-nat-med-2023/), [Gerlinger: a single biopsy misses most of the mutations in a kidney tumour](https://onco.cc/key-papers/paper-gerlinger-intratumour-heterogeneity-nejm-2012/), [Jaiswal: clonal haematopoiesis, the pre-leukaemic clones in most people over 70](https://onco.cc/key-papers/paper-jaiswal-chip-nejm-2014/), [Martincorena: normal sun-exposed skin is a patchwork of cancer-mutation clones](https://onco.cc/key-papers/paper-martincorena-somatic-mutations-normal-skin-science-2015/), [Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists](https://onco.cc/key-papers/paper-li-j-mol-diagn/)
- bottlenecks: [Tumour heterogeneity and clonal evolution](https://onco.cc/bottlenecks/b-tumor-heterogeneity/)
- ideas: [A clone report from blood at every treatment cycle](https://onco.cc/ideas/idea-bio1-ctdna-clone-report/), [An annual blinded shoot-out for liquid biopsy tests](https://onco.cc/ideas/idea-tr2-liquid-biopsy-challenge/), [Certified reference samples to benchmark every tumour-DNA blood test](https://onco.cc/ideas/idea-tr2-ctdna-reference-plasma/), [Label every targetable mutation as truncal or branch on the report](https://onco.cc/ideas/idea-bio1-truncal-branch-labelling/), [Look for the resistant sub-population before the first dose](https://onco.cc/ideas/idea-bio1-baseline-ultradeep-resistant-clones/), [Push residual disease detection a hundredfold deeper with whole-genome methods](https://onco.cc/ideas/idea-bio2-whole-genome-mrd-depth/), [Reference materials and open proficiency testing for residual disease tests](https://onco.cc/ideas/idea-bio2-mrd-reference-standards/)
- pathways: [Clonal evolution & minimal residual disease](https://onco.cc/pathways/clonal-evolution/), [Clonal haematopoiesis (CHIP)](https://onco.cc/pathways/clonal-haematopoiesis/), [Intravasation & circulating tumour cells](https://onco.cc/pathways/intravasation-ctc-survival/)
- terms: [Ageing tissue and clonal fields: cancer as a disease of old tissue](https://onco.cc/terms/ageing-tissue-field-theory/), [Genomic profiling](https://onco.cc/terms/genomic-profiling/), [MPN driver mutations (JAK2 V617F, CALR, MPL) and allele burden](https://onco.cc/terms/mpn-driver-mutations/)

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