Table 1.

Significant regions of chromosomal copy gain in melanoma

ChromosomeCytobandQ valueGISTIC peak (Mb)Genes in regionCandidate genes
11q21.36.10e−09chr1:147.2-149.253ARNT, * CDC42SE1, ECM1, ENSA, FAM63A, LASS2, MLLT11 *, MRPL9, PIK4CB, PIP5K1A, POGZ, PRUNE, PSMB4, PSMD4, RFX5, SETDB1, TARSL1 [36 NS genes]
33p139.36e−17chr3:69.87-70.221MITF
55p15.331.37e−01chr5:1e-6-1.6803CTNND2, DNAH5, TRIO
66p25.15.70e−08chr6:4.07-5.629C6orf146, C6orf201, CDYL, FARS2, KU-MEL-3, LYRM4, PECI, PRPF4B, RPP40
77p21.32.78e−20chr7:12.1-13.12ARL4A, SCIN
77q32.31.18e−27chr7:129.6-130.46COPG2, CPA1, KLF14, MEST, TSGA1, TSGA14
77q345.07e−26chr7:139.03-140.4812BRAF *, MKRN1, NDUFB2 [9 NS genes]
88q24.211.73e−05chr8:121.7-129.033MYC *, RNF139, C8orf32, DERL1, WDR67 [28 NS genes]
1111q13.31.02e−04chr11:69.0-69.87FLJ42258, FGF4, FADD, FGF19, FGF3 TMEM16A, CCND1 *, ORAOV1
1212p11.229.90e−02chr12:24.3-32.944DDX11, DNM1L, FAM60A, KRAS *, MRPS35, YARS2 [38 NS genes]
1515q26.12.63e−06chr15:87.5-89.124AP3S2, IDH2, IQGAP1, POLG [20 NS genes]
1717q25.32.25e−08chr17:74.7-77.125KIAA1618 *, MGC15523, TBC1D16 [22 NS genes]
2020q13.21.75e−23chr20:49.1-50.54ATP9A, NFATC2, SALL4, ZFP64
2222q13.28.32e−09chr22:39.7-40.928EP300 *, NAGA, PMM1 [25 NS genes]
  • NOTE: Bold font denotes significant differentially expressed genes by whole-genome SAM analysis (median false genes = 0; see text). NS denotes genes in the region whose differential expression is not significant based on SAM analysis (see Supplementary Materials for full gene list).

  • * Known cancer gene ( 49).