Table 2 aCGH findings in 21 chordomas
Regions lost or gained in ⩾5 cases a | Most frequently affected region per chromosome a | |||
|---|---|---|---|---|
Cytogenetic location | Start–end (Mb) | Start–end (Mb) | Frequency | Examples of candidate genes |
Copy number losses | ||||
1p36.33–p11.1 | 0.65–124.15 | 6.70–26.05 | 0.57 | RUNX3 |
60.20–67.35 | 0.57 | |||
74.85–82.85 | 0.57 | |||
2q34–q37.3 | 212.15–242.81 | 214.95–242.81 | 0.33 | |
Chromosome 3 | 0.04–199.45 | 23.05–33.35 | 0.71 | |
47.10–48.65 | 0.71 | |||
Chromosome 4 | 0.01–191.25 | 0.01–1.25 | 0.43 | |
20.20–31.50 | 0.43 | |||
89.70–108.25 | 0.43 | |||
6p21.1 | 41.60–43.80 | |||
7q11.22–q11.23 | 71.70–74.20 | |||
8p12–p11.1 | 36.90–45.15 | 37.85–42.25 | 0.29 | |
9p24.3–q31.3 | 0.03–113.20 | 20.30–24.19 | 0.76 | CDKN2A, CDKN2B |
9q33.3–q34.3 | 125.90–138.39 | |||
Chromosome 10 | 0.06–135.39 | 11.80–12.40 | 0.81 | |
11p15.5–p15.3 | 0.07–12.20 | |||
11p14.3–p11.2 | 24.75–47.95 | |||
11q12.2–q13.2 | 61.00–67.70 | |||
11q14.3–q25 | 89.85–134.43 | 106.95–107.70 | 0.38 | ATM |
12p11.21–p11.1 | 31.25–35.35 | |||
12q24.31 | 119.80–122.75 | 120.20–122.70 | 0.33 | |
Chromosome 13 | 17.92–114.12 | 53.05–66.55 | 0.33 | |
77.40–89.70 | 0.33 | |||
111.95–114.12 | 0.33 | |||
Chromosome 14 | 18.07–106.30 | 18.07–19.30 | 0.52 | |
15q11.2 | 19.78–20.32 | |||
15q15.1–q21.1 | 38.70–42.90 | 40.60–41.15 | 0.29 | TP53BP1 b |
16p13.3 | 0.01–5.00 | |||
16p12.3–q24.3 | 18.15–88.70 | 82.40–86.10 | 0.52 | |
17p13.3–p11.1 | 0–22.15 | 0–4.85 | 0.48 | TP53 b |
17q25.1–q21.3 | 69.00–78.39 | |||
Chromosome 18 | 0.02–76.10 | 17.40–17.95 | 0.48 | |
19p13.3–p11 | 0.02–28.45 | 2.05–3.95 | 0.43 | |
19q13.11–q13.43 | 37.60–63.77 | |||
20p11.21–q11.21 | 25.40–31.35 | 28.40–29.65 | 0.29 | |
21q22.2–q22.3 | 41.15–46.92 | 43.10–46.65 | 0.29 | |
Chromosome 22 | 14.44–49.46 | 38.79–40.65 | 0.67 | CHEK2 b |
Xp22.33 | 0.06–2.65 | 0.06–2.65 | 0.29 | |
Yp11.2 | 7.65–8.95 | |||
Yq11.22-q11.23 | 20.75–25.55 | |||
Copy number gains | ||||
1q21.1–q25.2 | 142.95–176.10 | |||
1q31.3–q43 | 197.45–239.20 | 201.20–202.35 | 0.38 | |
5p15.33 | 0.07–3.70 | TERT | ||
5q31.1–q31.2 | 131.80–135.65 | TGFBI | ||
5q35.1–q35.3 | 170.60–180.73 | 171.50–180.73 | 0.33 | |
6q25.3-q27 | 157.40–170.90 | 158.30–161.10 | 0.29 | |
166.05–170.75 | 0.29 | T | ||
Chromosome 7 | 0.04–158.62 | 28.05–29.90 | 0.52 | |
8q24.21–q24.22 | 130.55–135.15 | |||
12p13.33–p12.1 | 1.55–26.10 | 1.65–5.55 | 0.33 | CCND2b, FGF6b, SOX5b |
12q13.11–q13.13 | 46.40–51.55 | COL2A1 | ||
15q11.2 | 19.10–20.05 | |||
16q21–q22.2 | 61.30–69.45 | 63.65–68.50 | 0.29 | |
19p13.3–p13.2 | 4.00–8.55 | |||
19q12–q13.43 | 34.40–63.77 | 47.70–48.30 | 0.33 | TGFB1 b |
20q11.21–q13.12 | 31.40–41.90 | 35.40–36.80 | 0.29 | E2F1b, SRC |
20q13.33 | 59.20–62.43 | 59.90–61.60 | 0.29 | |
