Table 2.

Significant regions of chromosomal copy loss in melanoma

ChromosomeCytobandQ valueGISTIC peak (Mb)Genes in regionCandidate genes
66q261.04e−10chr6:162.4-163.72PACRG, PARK2
88p23.19.27e−02chr8:6.3-9.429[29 NS genes]
99p21.31.59e−81chr9:22.0-22.10CDKN2A *, CDKN2B10
1010q23.312.14e−13chr10:89.4-90.03ATAD1, PAPSS2, PTEN *
1010p15.37.86e−12chr10:2.5-4.13KLF6 *, PFKP, PITRM1
1111q23.13.43e−09chr11:111.2-112.015[15 NS genes]
1313q12.116.17e−02chr13:19.9-90.5204ALG5, C13orf23, CLN5, CRYL1, ESD, FNDC3A, KPNA3, MED4, MTMR6, MYCBP2, NUFIP1, P2RY5, RCBTB1, RNF6, RPL21, SAP18, SPG20, SUCLA2, TPT1 [185 NS genes]
1414q32.331.83e−02chr14:102.3-103.918BAG5, C14orf2, MARK3 [15 NS genes]
1515q21.11.10e−01chr15:41.6-43.327B2M, EIF3S1, ELL3, MFAP1, PDIA3, SERF2 [21 NS genes]
1616q23.11.23e−01chr16:77.2-78.92MAF *, WWOX
1818q233.83e−03chr18:62.7-76.234MBP, TXNL4A [32 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).