Table 2.
Associations among genomic and epigenomic features, and mutation rate profiles
| Germline mutations | Somatic mutations in cancer | ||||||||
|---|---|---|---|---|---|---|---|---|---|
|
|
|||||||||
| IDS++ | DS+ | I+ | IDS− | IDS−− | M+ | S | S | S | |
|
Proportion of
genome (%) |
8.0 | 18.1 | 27.8 | 36.3 | 4.4 | 5.4 | NA | NA | NA |
|
| |||||||||
|
Chromosomal
location |
Subtelom eric |
Subtelo meric |
Subtelo meric |
Internal | X chromoso me |
Interspersed | NA | NA | NA |
|
| |||||||||
| GC content | Very high (45%) |
Low (38%) |
High (42%) |
Avg (38%) | Avg (39%) (avg) |
Avg (40%) | Quadratic relationship |
Neg | NA |
|
| |||||||||
|
Replication
timing |
Early | Late | Early | Avg | Avg | Avg | Pos | Neg | Late |
|
| |||||||||
| Recombination* | High; male>>>f emale |
High; male>fe male |
High; female> male |
Low | Low; female only |
Avg | NA | Neg | NA |
|
| |||||||||
| Open chromatin | Pos | Neg | Pos | Neg | Neg | Avg | Neg and pos‡ |
Neg | Neg |
|
| |||||||||
|
Closed
chromatin |
Neg | Pos | Neg | Pos | Pos | Avg | Neg and pos‡ | Pos | Pos |
|
| |||||||||
| H3K4me1 | High | Low | High | Avg | Low | Avg | NA | Neg | Neg |
|
| |||||||||
| DHSs | High | Low | High | Avg | Low | Avg | NA | NA | Low |
|
| |||||||||
| Nuclear lamina | Low | High | Low | Avg | Avg | High | NA | NA | NA |
|
| |||||||||
| Methyl- CpG | Low | High | Low | High | Avg | Avg | NA | NA | NA |
|
| |||||||||
|
Transcription
potential (exons) |
High | Low | High | Avg | Moderatel y low |
Avg | Neg | Neg | NA |
|
| |||||||||
|
Total variability
explained (%) |
NA | NA | NA | NA | NA | NA | 40 | >55 | 74– 86 |
|
| |||||||||
| Refs | 61 | 61 | 61 | 61 | 61 | 61 | 16 | 15 | 17 |
Avg, average; D, deletion; DHS, DNase-hypersensitive site; DS+, mutational ‘warm’ state with mildly elevated deletion and substitution rates; H3K9me3, histone H3 lysine 3 trimethylation; I, insertion; I+, insertion warm state; IDS++, ‘hot’ state with highly elevated insertion, deletion and substitution rates; IDS−, mutational state with low insertion, deletion and substitution rates; NA, not applicable; M++, microsatellite state; neg, negative association; pos, positive association; S, base substitution.
*
Male and female indicate male- and female-specific recombination rates, respectively.
‡
Depends on the cancer type.