Table 2.
Summary of genomic features of BRCA1/ER-BC and BRCA1/ER+BC
| Criteria | BRCA1/ER-BC | BRCA1/ER+BC |
|---|---|---|
| Whole genome mutation rate | 4.26 | 1.93 |
| Intronic:exonic mutation rate | 1.1 | 1.07 |
| Intergenic:genic mutation rate ratio | 1.29 | 1.17 |
| Non-expressed:expressed mutation rate ratio | 1.43 | 1.16 |
| Number of expressed genes* | 12499 | 12845 |
| Validated SNVs (% validated) | 62 (67) | 28 (55) |
| Validated in-dels (% validated) | 9 (22) | 1 (5) |
| Copy number profile | sawtooth | sawtooth |
| Number of amplified genes | 281 | 284 |
| Number of homozygously deleted genes | 30 | 0 |
| Number of total SVs | 564 | 206 |
| Number of tandem duplications | 352 | 101 |
| Number of inter-chromosomal SVs | 79 | 47 |
| Number of intra-chromosomal SVs | 485 | 159 |
| Validated gene fusions | 32 | 13 |
| In-frame validated gene fusions | 0 | 3 |
| Expressed fusion genes | 8 | 3 |
| Expressed in-frame fusion genes | 0 | 2 |
| Micro-homologies surrounding SVs | yes | yes |
| Evidence of chromothripsis[50] | no | yes |
| Mutator phenotype[26] | yes | no |
*
Determined from Affymetrix U133Plus2 arrays; in-del: insertion and deletion; SNV: single nucleotide variant; SV: structural variant