Glossary
********

SNV classes
===========

Considering the pyrimidines of the Watson-Crick base pairs, there are only six different possible substitutions: C>A, C>G, C>T, T>A, T>C, T>G.

References:

- `Single Base Substitution (SBS) Signatures <https://cancer.sanger.ac.uk/signatures/sbs/>`__

Transitions (Ti) and transversions (Tv)
=======================================

DNA substitution mutations are of two types. Transitions are interchanges of two-ring purines (A↔G) or of one-ring pyrimidines (C↔T): they therefore involve bases of similar shape. Transversions are interchanges of purine for pyrimidine bases, which therefore involve exchange of one-ring and two-ring structures.

+------+--------------------+
| Type | SNV classes        |
+======+====================+
| Ti   | C>T, T>C           |
+------+--------------------+
| Tv   | C>A, C>G, T>A, T>G |
+------+--------------------+

References:

- `Transitions vs. Transversions <https://www.mun.ca/biology/scarr/Transitions_vs_Transversions.html>`__

Tumor mutational burden (TMB)
=============================

Number of genetic alternations detected within an individual.

Variant allele frequency (VAF)
==============================

VAF is used to infer whether a variant comes from somatic cells or inherited from parents when a matched normal sample is not provided. A variant is potentially a germline mutation if the VAF is approximately 50% or 100%.

References:

- `Variant Interpretation for Cancer (VIC): a computational tool for assessing clinical impacts of somatic variants <https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-019-0664-4>`__