Table 2 Summary of regions of recurrent chromosome imbalance (>5 Mb), frequencies, and Sanger Census cancer genes in the region

chr1:732,712-24,356,209

23,624

p36.33 - p36.11

Loss

20.00

375

7

TNFRSF14, PRDM16, RPL22, CAMTA1, SDHB, PAX7, MDS2

chr1:143,582,356-249,250,621

105,668

q21.1 - q44

Gain

80.00

1155

17

PDE4DIP, BCL9, ARNT, TPM3, MUC1, PRCC, NTRK1, SDHC, FCGR2B, PBX1, ABL2, TPR, MDM4, ELK4, SLC45A3, H3F3A, FH

chr4:80,505,114-115,297,840

34,793

q21.21 - q26

Loss

33.33

167

2

RAP1GDS1, TET2

chr5:0–46,279,735

46,280

p15.33 - p11

Gain

33.33

181

2

IL7R, LIFR

chr5:49,584,189-180,704,505

131,120

q11.1 - q35.3

Gain

26.67

846

11

IL6ST, PIK3R1, APC, PDGFRB, CD74, ITK, EBF1, RANBP17, TLX3, NPM1, NSD1

chr7:0–57,675,692

57,676

p22.3 - p11.2

Gain

33.33

381

10

CARD11, PMS2, ETV1, HNRNPA2B1, HOXA9, HOXA11, HOXA13, JAZF1, IKZF1, EGFR

chr7:61,750,617-159,138,663

97,388

q11.21-q36.3

Gain

40.00

757

12

SBDS, ELN, HIP1, AKAP9, CDK6, MET, SMO, CREB3L2, KIAA1549, BRAF, EZH2, MLL3

chr8:13,403,518-29,636,237

16,233

p22 - p12

Loss

33.33

116

1

PCM1

chr8:46,967,935-145,730,376

98,762

q11.1 - q24.3

Gain

60.00

501

13

CHCHD7, TCEA1, PLAG1, NCOA2, NBS1, HEY1, CBFA2T1, UBR5, COX6C, EXT1, MYC, NDRG1, RECQL4

chr9:0–45,983,160

45,983

p24.3 - p11.2

Loss

20.00

278

6

JAK2, CD274, NFIB, MLLT3, FANCG, PAX5

chr17:3,728,554-12,900,807

9,172

p13.2 - p12

Loss

40.00

205

5

USP6, TP53, PER1, GAS7, MAP2K5

chr17:13,297,102-18,590,696

5,293,594

p12 - p11.2

Loss

33.33

77

0

chrX:2,471,123-48,865,144

46,394

p22.33 - p11.23

Gain

20.00

257

7

ZRSR2, BCOR, KDM6A, SSX1, SSX4, WAS, GATA1

chrX:61,828,910-99,931,689

38,103

q11.1 - q22.1

Gain

26.67

156

4

MSN, MED12, NONO, ATRX

chrX:99,931,690-154,975,693

55,044

q22.1 - q28

Gain

33.33

613

5

SEPT6, ELF4, GPC3, PHF6, MTCP1