Table 1 Summary of relationships between each mutational signature and various genomic features.
From: The topography of mutational processes in breast cancer genomes
Mutational signature | Mutation type | Predominant features of signature | Associated mutational process | Transcriptional strand | Replicative strand | Replication time | Chromatin organization |
|---|---|---|---|---|---|---|---|
1 | Sub | C>T at CpG | Deamination of methyl-cytosine (age associated) | Some bias | Enriched late | ||
5 | Sub | T>C | Uncertain (age associated) | Some bias | Some bias | Enriched late | Slight enrichment at linker |
2 | Sub | C>T at TpCpN | APOBEC related | Some bias | Strong lagging strand bias | Enriched late | |
13 | Sub | C>G at TpCpN | APOBEC related | Some bias | Strong lagging strand bias | Flat | |
6 | Sub | C>T (and C>A and T>C) | MMR deficient | Some bias | Flat | ||
20 | Sub | C>A (and C>T and T>C) | MMR deficient | Some bias | Enriched late | ||
26 | Sub | T>C | MMR deficient | Some bias | Strong bias | Enriched late | Enriched at linker |
3 | Sub | HR deficient | Some bias | Some bias | Enriched late | ||
8 | Sub | C>A | amplified by HR deficiency? | Some bias | Enriched late | ||
18 | Sub | C>A | Uncertain | Some bias | Some bias | Enriched late | Enriched at nucleosomes and periodic |
17 | Sub | T>G | Uncertain | Some bias | Enriched late | Enriched at nucleosomes and periodic | |
30 | Sub | C>T | Uncertain | Flat | |||
RS1 | Rearr | Large tandem duplications (>100 kb) | Uncertain type of HR deficiency? | NA | NA | Enriched early | |
RS2 | Rearr | Dispersed translocations | NA | NA | Enriched early | ||
RS3 | Rearr | Small tandem duplications (<10 kb) | HR deficiency (BRCA1) | NA | NA | Enriched early | |
RS4 | Rearr | Clustered translocations | NA | NA | Enriched early | ||
RS5 | Rearr | Deletions | HR deficient | NA | NA | Enriched early | |
RS6 | Rearr | Other clustered rearrangements | NA | NA | Enriched early | ||
Repeat-med | Indel | <3 bp indel at polynucleotide repeat tract | amplified when MMR deficient | NA | NA | Enriched late | Enriched at linker and periodic |
Microhom | Indel | ≥3 bp indel with microhomology at breakpoint junction | HR deficient | NA | NA | Enriched late |
