Skip to main content

Table 1 Glossary

From: Characterizing Benzo[a]pyrene-induced lacZ mutation spectrum in transgenic mice using next-generation sequencing

Mutant – A plaque, grown on P-Gal media, that contains a loss of function mutation in the lacZ transgene.
Mutation – The change in DNA sequence (point mutation, indel) that knocks out the function of the lacZ transgene. There may also be silent mutations that can co-occur on the same lacZ copy as a loss of function mutation (“hitchhiker mutations”).
Clonal Expansion – When a cell containing a mutation produces daughter cells containing that same mutation, propagating it throughout the tissue.
False Mutation Proportion – At each nucleotide position, a proportion of the reads may contain a technical artefact and this proportion is consistent across samples. For example, if at position 25, the median frequency of G A substitutions across all samples was one in every thousand reads, the false mutation proportion would be 0.001.
Total Mutation Proportion – At each nucleotide position, this is the mutation proportion for each mutation type within a single sample. For example, if sample 3 had a G A substitutions at position 25 in 0.5 % of reads, the total mutation proportion would be 0.005.
True Mutation Proportion – The true mutation proportion of each mutation type at each position is determined by subtracting the false mutation proportion from the total mutation proportion. In the above example the true mutation proportion would be 0.004. This value is used to determine mutation counts.
Independent Mutations – Mutations that appear multiple times in a same sample due to clonal expansion are only counted as one mutation per sample. For example, if sample 1 had five G A substitutions at position 25, this would be called a single independent mutation at position 25.
Recurrent Mutations – If a mutation occurs more than once within a sample it is considered recurrent as is likely the result of clonal expansion. In the previous example there are five G A recurrent mutations at position 25.