Table 2.

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

Chromosome	Genes localized in bi-allelic deleted regions
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	Genes localized in amplified regions
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

The number of GISTs with the identified gene deletion is indicated in the brackets. The number of GISTs is not indicated when the gene is deleted in only one tumor. Genes with functions implicating them in GIST oncogenesis are shown in bold.