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Table 2 Regions of large-scale, chromosomal copy number variation in 29 KIT-mutant GIST (discovery set)

From: Genomic aberrations in cell cycle genes predict progression of KIT-mutant gastrointestinal stromal tumors (GISTs)

Genomic location Event Number of patients
21 total patients
Number of samples with CNV
29 total samples
Number of Genes with somatic SNV within CNV Mean fraction of chromosomal arm Fraction GIST samples with CNV SNV mutated Genes from Cell Cycle (and others) pathways found in regions of large scale CNV. Bolded gene names indicated genes mutated in more than one sample
14q LOSS 16 25 24 0.929948779 0.862068966 ACOT4, ADAM20, BCL11B, COCH, DTD2, DYNC1H1, FLVCR2, HSP90AA1, KCNH5, LTBP2, MYH7, NGB, OR4M1, OR4N2, PSMB11, RBM25, SERPINA1, SERPINA9, TMEM30B
1p LOSS 16 25 43 0.838940558 0.862068966 ABCA4, ALDH4A1, B4GALT2, C8A, CCDC24, CD2, CDCP2, CROCC, CSDE1, CYP2J2, ELTD1, FBXO2, GADD45A, GJB5, GPR153, GRIK3, HSPG2, IGSF3, JUN, KIF2C, NBPF1, PALMD, RAP1GAP, RBMXL1, RERE, SF3A3, SRRM1, SZT2, TNFRSF8, TRIM45, TTC39A, WRAP73, ZMYM4, ZNF326
22q LOSS 17 23 17 0.878011687 0.793103448 BCR, CHADL, GTPBP1, HDAC10, LZTR1, MLC1, NFAM1, NUP50, PEX26, RBFOX2, SOX10, TTC28
15q LOSS 13 21 29 0.940300484 0.724137931 ANKRD34C, CHRNA5, CSPG4, FAM169B, IGF1R, IQGAP1, MAN2A2, MAP1A, MESP2, MGA, MORF4L1, MYO5C, NEO1, RFX7, RMDN3, RNF111, RYR3, SKOR1, SPINT1, SPTBN5, STARD5, TBC1D2B, TCF12, TJP1, TP53BP1, USP3
13q LOSS 12 20 13 0.888207393 0.689655172 DACH1, LACC1, MYCBP2, PARP4, RB1, SHISA2, TPP2, ZC3H13
5p GAIN 10 14 10 0.928171594 0.482758621 ADAMTS16, CDH10, CDH6, DAB2, OXCT1, PLEKHG4B, PRDM9
5q GAIN 9 9 25 0.924167057 0.310344828 ACSL6, AGGF1, ARSI, CCNB1, CLINT1, DDX46, EBF1, FAM71B, FAT2, GNB2L1, MSH3, NDUFAF2, PCDHA1, PCDHB16, PCDHB7, PCDHGB6, PCSK1, RASGRF2, RBM27, TCOF1, TMCO6
7q GAIN 6 8 17 0.74250744 0.275862069 CCDC136, CEP41, CUL1, FKBP6, MET, NOM1, OPN1SW, PCLO, PON1, TMEM168, TMEM176A, TRPV5, ZNF425, ZNF727
8q GAIN 7 8 11 0.818582114 0.275862069 AGO2, COL14A1, EPPK1, NCOA2, PLEC, TNFRSF11B, TRPA1, ZFPM2