Editing Mutation rate (section)

==Mutation spectrum==

A mutation spectrum is a distribution of rates or frequencies for the mutations relevant in some context, based on the recognition that rates of occurrence are not all the same. In any context, the mutation spectrum reflects the details of mutagenesis and is affected by conditions such as the presence of chemical mutagens or genetic backgrounds with mutator alleles or damaged DNA repair systems. The most fundamental and expansive concept of a mutation spectrum is the distribution of rates for all individual mutations that might happen in a genome (e.g., <ref name=Lopez-Cortegano2022>{{cite journal | vauthors = López-Cortegano E, Craig RJ, Chebib J, Balogun EJ, Keightley PD | title = Rates and spectra of de novo structural mutations in <i>Chlamydomonas reinhardtii</i> | journal = Genome Research | volume = 33 | issue = 1 | pages = 45–60 | date = January 2023 | pmid = 36617667 | pmc = 9977147 | doi = 10.1101/gr.276957.122 }}</ref>).  From this full de novo spectrum, for instance, one may calculate the relative rate of mutation in [[Coding region|coding]] vs [[Noncoding DNA|non-coding]] regions.  Typically the concept of a spectrum of mutation rates is simplified to cover broad classes such as [[Transition (genetics)|transition]]s and [[transversion]]s (figure), i.e., different mutational conversions across the genome are aggregated into classes, and there is an aggregate rate for each class. 

In many contexts, a mutation spectrum is defined as the observed frequencies of mutations identified by some selection criterion, e.g., the distribution of mutations associated clinically with a particular type of cancer,<ref name=Cao2013>{{cite journal | vauthors = Cao W, Wang X, Li JC | title = Hereditary breast cancer in the Han Chinese population | journal = Journal of Epidemiology | volume = 23 | issue = 2 | pages = 75–84 | year = 2013 | pmid = 23318652 | pmc = 3700245 | doi = 10.2188/jea.je20120043 }}</ref> or the distribution of adaptive changes in a particular context such as antibiotic resistance (e.g.,
<ref name=Levy2004>{{cite journal | vauthors = Levy DD, Sharma B, Cebula TA | title = Single-nucleotide polymorphism mutation spectra and resistance to quinolones in Salmonella enterica serovar Enteritidis with a mutator phenotype | journal = Antimicrobial Agents and Chemotherapy | volume = 48 | issue = 7 | pages = 2355–2363 | date = July 2004 | pmid = 15215081 | pmc = 434170 | doi = 10.1128/AAC.48.7.2355-2363.2004 }}</ref> 
).
Whereas the spectrum of de novo mutation rates reflects mutagenesis alone, this kind of spectrum may also reflect effects of selection and ascertainment biases (e.g., both kinds of spectrum are used in <ref name=Cano2022>{{cite journal | vauthors = Cano AV, Rozhoňová H, Stoltzfus A, McCandlish DM, Payne JL | title = Mutation bias shapes the spectrum of adaptive substitutions | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 119 | issue = 7 | date = February 2022 | pmid = 35145034 | pmc = 8851560 | doi = 10.1073/pnas.2119720119 | bibcode = 2022PNAS..11919720C | doi-access = free }}</ref>).   

[[File:TsTvMutation.jpg|thumb|[[Transition (genetics)|Transition]]s (Alpha) and [[transversion]]s (Beta).]]