Table 3.
Incidence of abnormalities (gains or losses) in breast cancers
| All Samples | Cluster Groups | ||||
|---|---|---|---|---|---|
|
|
|
||||
| Gene | Chr | n = 98 | Highly Methylated n = 16 | Sparsely Methylated n = 82 | Difference of Abnormalities |
|
|
|
||||
| Abnormalities | Abnormalities | Abnormalities | Highly-Sparsely (%) | ||
| n (%) | n (%) | n (%) | |||
| ESR1 | 06q25 | 7 (7) | 0 (0) | 7 (9) | -9 |
| EGFR | 07p11 | 15 (15) | 3 (19) | 12 (15) | 4 |
| FGFR1 | 08p12 | 40 (41) | 4 (25) | 36 (44) | -19 |
| ADAM9 | 08p11 | 26 (27) | 5 (31) | 21 (26) | 5 |
| IKBKB | 08p11 | 34 (35) | 7 (44) | 27 (33) | 11 |
| PRDM14 | 08q13 | 36 (37) | 9 (56) | 27 (33) | 23 |
| MYC | 08q24 | 39 (40) | 8 (50) | 31 (38) | 12 |
| MTDH | 08q22 | 33 (34) | 8 (50) | 25 (30) | 20 |
| CCND1 | 11q13 | 44 (45) | 7 (44) | 37 (45) | -1 |
| EMSY | 11q13 | 36 (37) | 6 (38) | 30 (37) | 1 |
| CDH1 | 16q22 | 18 (18) | 5 (31) | 13 (16) | 15 |
| CPD | 17q11 | 19 (19) | 4 (25) | 15 (18) | 7 |
| MED1 | 17q11 | 51 (52) | 12 (75) | 39 (48) | 27 |
| HER2 | 17q12 | 47 (48) | 9 (56) | 38 (46) | 10 |
| CDC6 | 17q21 | 35 (36) | 10 (62) | 25 (30) | 32 |
| TOP2A | 17q21 | 16 (16) | 3 (19) | 13 (16) | 3 |
| MAPT | 17q21 | 35 (36) | 10 (62) | 25 (30) | 32 |
| BIRC5 | 17q25 | 44 (45) | 8 (50) | 36 (44) | 6 |
| CCNE1 | 19q12 | 13 (13) | 4 (25) | 9 (11) | 14 |
| AURKA | 20q13 | 19 (19) | 6 (38) | 13 (16) | 22 |
|
| |||||
| TOTAL CNA PER PATIENT | Mean (%) | 31.0 | 40.0 | 29.2 | |
| Median (%) (Q1-Q3) | 30 (20-40) | 42.5 (30.0-50.0) | 30.0 (16.3-40.0) | ||
Chr: chromosome location; CNA: Copy Number Aberration; Bold character indicate the genes that show major differences between highly and sparsely methylated groups.