Table 2.
Comparison of Tumor Location, Patient Age, and Recurrent Copy Number Alterations in Copy Number Studies of Chordomas.
| Study | Diaz et al. (this study) | Le et al. [33] | Hallor et al. [12] | Scheil et al. [19] |
| Total number of tumors | 22 | 20 | 26 | 16 |
| Location | ||||
| Clivus | 21 | 2 | 0 | 5 |
| Mobile spine | 1 | 7 | 2 | 1 |
| Sacrum | 0 | 11 | 24* | 10 |
| Primary samples | 19 | 17 | 18 | 7 |
| Median age (years) | 38 | 61.5 | 60 | 61 |
| Platform | Affymetrix 500K | Agilent 250K | BAC array CGH | CGH |
| Broad significance copy number changes† (frequency) | ||||
| Gains | 1q21.1-q25.2; 1q31.3-q43 | |||
| 5p15.33; 5q31.1-q31.2; 5q35.1-q35.3 | 5q (0.38) | |||
| 6q25.3-q27 | ||||
| 7 (0.68) | 7p36.3-p22.3 (0.25) | 7 | 7q (0.69) | |
| 8q24.3 (0.35) | 8q24.21-q24.22 | |||
| 11q12.2-q13.4 (0.30) | ||||
| 12p13.33-p12.1; 12q13.11-q13.13 | 12q (0.38) | |||
| 15q11.2 | ||||
| 16q21-q22.2 | ||||
| 17q11.1-q25.3 (0.25) | ||||
| 19p (0.55); 19q (0.55) | 19p13.3-q13.43 (0.30) | 19p13.3-p13.2; 19q12-q13.43 | ||
| 20q11.21-q13.12; 20q13.33 | 20 (0.50) | |||
| Losses | 1p36.33-p11.1 | 1p (0.44) | ||
| 2q34-q37.3 | ||||
| 3 (0.45) | 3p29-p26.3 (0.75) | 3 | 3p (0.5) | |
| 4p16.3-q35.2 (0.40) | 4 | |||
| 6q21-q22.33 (0.25) | 6p21.1 | |||
| 7q11.22-q11.23 | ||||
| 8p12-p11.1 | ||||
| 9p24.3-q34.3 (0.25) | 9p24.3-q31.3; 9q33.3-q34.3 | |||
| 10p (0.61); 10q (0.57) | 10p15.3-q26.3 (0.65) | 10 | ||
| 11p15.5-p11.12 (0.30) | 11p15.5-p15.3; 11p14.3-p11.2; 11q12.2-q13.2; 11q14.3-q25 | |||
| 12p11.21-p11.1; 12q24.31 | ||||
| 13q (0.61) | 13q11-q34 (0.60) | 13 | ||
| 14q (0.65) | 14q11.1-q32.33 (0.65) | 14 | ||
| 15q11.2; 15q15.1-q21.1 | ||||
| 16p13.3; 16p12.3-q24.3 | ||||
| 17p13.3-p11.1 (0.35) | 17p13.3-p11.1; 17q25.1-q21.3 | |||
| 18p11.32-q23 (0.40) | 18 | |||
| 19p13.3-p11 | ||||
| 19q13.11-q13.43 | ||||
| 20p11.21-q11.21 | ||||
| 22q (0.71) | 22q11.1-q13.33 (0.45) | |||
| 21q22.2-q22.3 | ||||
| Xp22.33 | ||||
| Yp11.2; Yq11.22-q11.23 |
*
Includes 4 coccyx chordomas and 20 sacral chordomas.
†
All four studies differ in the reporting of significant broad copy number alterations. We use z-scores of >2 or <0.5 and q-values < 0.05 regardless of frequency. Long et al. list copy changes occurring in >25% of cases. Hallor et al. report copy changes occurring in greater than or equal to five cases with individual frequencies not provided. Scheil et al. reports the most frequent gains and losses.