Most frequently detected CNAs associated with gene expression changes (> 8 of 77 samples, 10%; determined by the GEDI algorithm)
| MCR ID . | Chromosomal location (band; MCR core) . | Type, class of alteration . | Start core . | End core . | MCR peak . | Cyclin D1+, no. . | Cyclin D1−, no. . | Total, no. . |
|---|---|---|---|---|---|---|---|---|
| 280 | 1p31.1-p13.3 | Loss/double loss, long | 78.845412 | 108.161907 | 93.046159 | 34 | 2 | 36 |
| 519 | 17q21.31* | Loss/double loss, short | 41.560151 | 41.707907 | 41.703504 | 33 | 2 | 35 |
| 108 | 3q | Gain/amp, q-arm | 95.031169 | 199.322068 | NA | 21 | 3 | 24 |
| 238 | 17q21.31* | Gain/amp, short | 41.522422 | 41.719832 | 41.590303 | 23 | 0 | 23 |
| 479 | 13q | Loss/double loss, chromosome | 17.960319 | 114.09298 | NA | 20 | 1 | 21 |
| 421 | 9p | Loss/double loss, p-arm | 0.03091 | 44.108554 | NA | 19 | 2 | 21 |
| 451 | 11q21-q23.2 | Loss/double loss, long | 92.710683 | 114.244057 | 99.00843 | 16 | 4 | 20 |
| 452 | 11q22.3-q23.2 | Loss/double loss, short | 107.419503 | 113.384238 | 110.616957 | 18 | 1 | 19 |
| 525 | 17p | Loss/double loss, p-arm | 0.006888 | 22.069633 | NA | 18 | 0 | 18 |
| 649 | 22q11.22† | Double loss, short | 21.388199 | 21.576155 | 21.463635 | 18 | 0 | 18 |
| 122 | 5p15.33* | Gain/amp, short | 0.75219 | 0.87267 | 0.797863 | 16 | 1 | 17 |
| 379 | 6q | Loss/double loss, q-arm | 62.030184 | 170.823609 | NA | 16 | 0 | 16 |
| 408 | 8p | Loss/double loss, p-arm | 0.180568 | 43.820269 | NA | 14 | 2 | 16 |
| 637 | 17q21.31* | Double loss, short | 41.62507 | 41.707907 | 41.63558 | 13 | 2 | 15 |
| 550 | 21q11.2‡ | Loss/double loss, short | 9.887804 | 10.189118 | 9.887804 | 12 | 3 | 15 |
| 607 | 9p21.3 | Double loss, short | 21.81811 | 22.232054 | 21.976218 | 13 | 1 | 14 |
| 422 | 9q | Loss/double loss, q-arm | 64.197638 | 138.363203 | 12 | 1 | 13 | |
| 430 | 10q11.22* | Loss/double loss, short | 46.494897 | 47.030118 | 46.500913 | 12 | 1 | 13 |
| 281 | 1p21.2‡ | Loss/double loss, short | 100.510057 | 101.760343 | 101.292504 | 11 | 2 | 13 |
| 478 | 13q34 | Loss/double loss, short | 110.898938 | 114.09398 | 113.944993 | 10 | 2 | 12 |
| 416 | 9q21.11-q31.1 | Loss/double loss, long | 69.575157 | 102.187565 | 84.13048 | 10 | 0 | 10 |
| 147 | 7p | Gain/amp, p-arm | 0.141322 | 57.730637 | NA | 10 | 0 | 10 |
| 163 | 8q | Gain/amp, q-arm | 47.043376 | 146.264218 | NA | 9 | 1 | 10 |
| 283 | 1p11.2-q12 | Loss/double loss, long | 120.903122 | 142.129196 | 120.903122 | 9 | 1 | 10 |
| 424 | 10p15.2–10p15.3 | Loss/double loss, short | 0.101955 | 3.663599 | 1.913396 | 9 | 1 | 10 |
| 227 | 16p11.2* | Gain/amp, short | 34.328205 | 34.618467 | 34.454744 | 9 | 1 | 10 |
| 279 | 1p22 | Loss/double loss, short | 87.4228 | 87.424276 | 87.4228 | 8 | 2 | 10 |
| 616 | 11p15.1* | Double loss, short | 18.905796 | 18.918254 | 18.911384 | 9 | 0 | 9 |
| 420 | 9 complete | Loss/double loss, chromosome | 0.03091 | 138.363203 | NA | 8 | 1 | 9 |
| 391 | 8p23.2‡ | Loss/double loss, short | 3.469284 | 3.479449 | 3.469284 | 8 | 0 | 8 |
| 537 | 19p13.3 | Loss/double loss, short | 3.232586 | 4.439925 | 3.931367 | 8 | 0 | 8 |
| 526 | 18p11.32* | Loss/double loss, short | 1.903316 | 1.976262 | 1.960916 | 8 | 0 | 8 |
| 57 | 15q11.2* | Amp, short | 19.111608 | 19.876833 | 19.407629 | 7 | 1 | 8 |
| 646 | 21q11.2‡ | Double loss, short | 9.887804 | 10.189118 | 9.887804 | 6 | 2 | 8 |
| 220 | 15q22.2-q26.1 | Gain/amp, long | 57.914389 | 86.625684 | 65.011755 | 6 | 2 | 8 |
| MCR ID . | Chromosomal location (band; MCR core) . | Type, class of alteration . | Start core . | End core . | MCR peak . | Cyclin D1+, no. . | Cyclin D1−, no. . | Total, no. . |
|---|---|---|---|---|---|---|---|---|
| 280 | 1p31.1-p13.3 | Loss/double loss, long | 78.845412 | 108.161907 | 93.046159 | 34 | 2 | 36 |
| 519 | 17q21.31* | Loss/double loss, short | 41.560151 | 41.707907 | 41.703504 | 33 | 2 | 35 |
| 108 | 3q | Gain/amp, q-arm | 95.031169 | 199.322068 | NA | 21 | 3 | 24 |
| 238 | 17q21.31* | Gain/amp, short | 41.522422 | 41.719832 | 41.590303 | 23 | 0 | 23 |
| 479 | 13q | Loss/double loss, chromosome | 17.960319 | 114.09298 | NA | 20 | 1 | 21 |
| 421 | 9p | Loss/double loss, p-arm | 0.03091 | 44.108554 | NA | 19 | 2 | 21 |
| 451 | 11q21-q23.2 | Loss/double loss, long | 92.710683 | 114.244057 | 99.00843 | 16 | 4 | 20 |
| 452 | 11q22.3-q23.2 | Loss/double loss, short | 107.419503 | 113.384238 | 110.616957 | 18 | 1 | 19 |
| 525 | 17p | Loss/double loss, p-arm | 0.006888 | 22.069633 | NA | 18 | 0 | 18 |
| 649 | 22q11.22† | Double loss, short | 21.388199 | 21.576155 | 21.463635 | 18 | 0 | 18 |
| 122 | 5p15.33* | Gain/amp, short | 0.75219 | 0.87267 | 0.797863 | 16 | 1 | 17 |
| 379 | 6q | Loss/double loss, q-arm | 62.030184 | 170.823609 | NA | 16 | 0 | 16 |
| 408 | 8p | Loss/double loss, p-arm | 0.180568 | 43.820269 | NA | 14 | 2 | 16 |
| 637 | 17q21.31* | Double loss, short | 41.62507 | 41.707907 | 41.63558 | 13 | 2 | 15 |
| 550 | 21q11.2‡ | Loss/double loss, short | 9.887804 | 10.189118 | 9.887804 | 12 | 3 | 15 |
| 607 | 9p21.3 | Double loss, short | 21.81811 | 22.232054 | 21.976218 | 13 | 1 | 14 |
| 422 | 9q | Loss/double loss, q-arm | 64.197638 | 138.363203 | 12 | 1 | 13 | |
| 430 | 10q11.22* | Loss/double loss, short | 46.494897 | 47.030118 | 46.500913 | 12 | 1 | 13 |
| 281 | 1p21.2‡ | Loss/double loss, short | 100.510057 | 101.760343 | 101.292504 | 11 | 2 | 13 |
| 478 | 13q34 | Loss/double loss, short | 110.898938 | 114.09398 | 113.944993 | 10 | 2 | 12 |
| 416 | 9q21.11-q31.1 | Loss/double loss, long | 69.575157 | 102.187565 | 84.13048 | 10 | 0 | 10 |
| 147 | 7p | Gain/amp, p-arm | 0.141322 | 57.730637 | NA | 10 | 0 | 10 |
| 163 | 8q | Gain/amp, q-arm | 47.043376 | 146.264218 | NA | 9 | 1 | 10 |
| 283 | 1p11.2-q12 | Loss/double loss, long | 120.903122 | 142.129196 | 120.903122 | 9 | 1 | 10 |
| 424 | 10p15.2–10p15.3 | Loss/double loss, short | 0.101955 | 3.663599 | 1.913396 | 9 | 1 | 10 |
| 227 | 16p11.2* | Gain/amp, short | 34.328205 | 34.618467 | 34.454744 | 9 | 1 | 10 |
| 279 | 1p22 | Loss/double loss, short | 87.4228 | 87.424276 | 87.4228 | 8 | 2 | 10 |
| 616 | 11p15.1* | Double loss, short | 18.905796 | 18.918254 | 18.911384 | 9 | 0 | 9 |
| 420 | 9 complete | Loss/double loss, chromosome | 0.03091 | 138.363203 | NA | 8 | 1 | 9 |
| 391 | 8p23.2‡ | Loss/double loss, short | 3.469284 | 3.479449 | 3.469284 | 8 | 0 | 8 |
| 537 | 19p13.3 | Loss/double loss, short | 3.232586 | 4.439925 | 3.931367 | 8 | 0 | 8 |
| 526 | 18p11.32* | Loss/double loss, short | 1.903316 | 1.976262 | 1.960916 | 8 | 0 | 8 |
| 57 | 15q11.2* | Amp, short | 19.111608 | 19.876833 | 19.407629 | 7 | 1 | 8 |
| 646 | 21q11.2‡ | Double loss, short | 9.887804 | 10.189118 | 9.887804 | 6 | 2 | 8 |
| 220 | 15q22.2-q26.1 | Gain/amp, long | 57.914389 | 86.625684 | 65.011755 | 6 | 2 | 8 |