Table 2 Genes mapping in regions with significant bi-allelic deletions and amplifications

1

AGBL4 (2), AHDC1, AMY1A, AMY2A, AMY1B, AMY2B, AMY1C, C1orf174, CEP104, DFFB, FAM76A, FGR, IFI6, RNPC3, STX12, WASF2

2

LRP1B (3)

3

FAM86D, FRG2C, LMLN

6

AGER, AGPAT1, ATF6B, BTNL24B, CREBL1, CYP21A2, CHCG4P6, EGFL8, FKBPL, HCG2P7, HLA-DQA1 (3), HLA-DQA2, HLA-DQB1 (3), HLA-DQB2, HLA-DRA, HLA-DRB1 (3), HLADRB5 (6), HLA-H, GPSM3, NOTCH4, PBX2, PPT2, PRRT1, RAGE, RNF5, STK19, TNXB

8

ADAM5P (6), ADAM3A (6)

9

CDKN2A (4), CDKN2B (3), DMRTA1, FNBP1, MTAP, TUSC1

10

PTEN

11

ELP4 (2)

14

BAZ1A, FAM177A1, IGBP1P1, PPP2R5E (2), PPPR2R3C, SGPP1 (2), SRP54, WDR89 (2)

15

A26B1 (2), GOLGA8A, PWRN2

22

CRYBB2, IGLL3, LRP5L

Chromosome

4

ANAPC4, CCDC149, CCKAR, LGI2, LOC389203, PCDH7, PI4K2B, RBPJ, SEPSECS, SLC34A2, SOD3, STIM2, TBC1D19, ZCCHC4

5

FGF10

7

ZNF680

8

ADAM3A, ADAM2

11

JRKL, CNTN5, TRIM48

19

LOC642290