Skip to main content

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