Table 1.
Most common somatic copy number aberrations (SCNAs) in human prostate cancer
| Cytoband | Event | Size (Mb) | Genes of interest | Reported frequency in prostate cancer | ||
|---|---|---|---|---|---|---|
| primary cancer | advanced cancer | DTC or CTC | ||||
| Xp11.22-q13.1 | Gain | 18–67.8 | AR | 50% CRPC 15, 24, 25, 68 | 45% AdvDTC6, 7, 69 | |
| 1p12-q43 | Gain | 117 | 45–65% CRPC24 | 50%69 | ||
| 1q32.1-q32.3 | Gain | 12.50 | ELK4, PTPRC, ELF3, PTPN7, MDM4, RAB7L1, RASSF5, IL24, IL10, CAMK1G | 5 | 24, 70 | 45% AdvDTC |
| 3q26.1 | Gain | 43.80 | GMPS, PIK3CA, MLF1, SKIL, CCNL1, ECT2 | 13–39%5, 71 | 24, 70 | 20%7 |
| 6q14.3-15 | Loss | 13.67 | CYB5R4, NT5E, SNX14, SYNCRIP, HTR1E, CGA, GJB7 | 40%5, 18, 64, 72, 73 | 55%64, 70, 72, 74 | 25%6, 7 |
| 7p22.3-q36.3 | Gain | 158.40 | 5, 18 | 25–55% CRPC68, 70, 72, 74 | 40%6, 7 | |
| 8p12-q24.3 | Gain | 97.64 | MYC, MAF, EYA1, MSC, TRPA1, KCNB2 | 20–30%5, 18, 64, 71–73, 75 | 64–82% CRPC15, 62, 68, 70, 72 | 50–65%6, 7, 69 |
| 8p23-p11 | Loss | 19.58 | NKX3-1 | 53–67%5, 18, 71–73, 75 | 67–74% of CRPC15, 68, 72 | 36–90% of AdvDTCs; 20-23% LocDTCs6, 7, 69 |
| 9q31.3 | Gain | 22.79 | PTPN3, AKAP2, DAPK1, SYK | 5 | 30%70, 72 | 25–45% AdvDTC6, 7, 69 |
| 10p13 | Loss | 1.12 | ITGA8, PTER, C1QL3, RSU1 | 18%64, 70, 73 | 25 | 6 |
| 10q11.21 | Loss | 0.58 | RET, RasGEF1A, HNRNPF, ZNF239, ZNF485, ZNF32 | 64, 73 | 55% AdvDTC6 | |
| 10q22-q24 | Loss | 24.91 | CFLP1, KILLIN, PTEN, RNLS, LIPJ, LIPF, LIPK, LIPN, LIPM, ANKRD22, STAMBPL1, ACTA2 | 12–25%5, 18, 62, 64, 72–75 | 36–80%15, 62, 68, 70, 74 | 36%69 |
| 11p13-p12 | Loss | 4.72 | 4, 6, 64, 70, 73 | 25 | 45% AdvDTC6 | |
| 12p13 | Loss | 1.46 | BCL2L14, LRP6, MANSC1, LOH12CR1, DUSP16, CREBL2, GPR19, CDKN1B, ETV6 | 30%5, 18 | 30–50%4, 64, 70, 72 | |
| 13q12.3- q14.2 | Loss | 2.63 | HSPH1, B3GALTL, RXFP2, EEF1DP3, FRY, ZAR1L, BRCA2, N4BP2L1, CG030, PDS5B, KL, STARD13, EXOSC8, FAM48A, CSNK1A1L, POSTN, TRPC4, UFM1, FREM2, KBTBD6, KBTBD7, MTRF1, NAA16, OR7E37P, C13ORF15, SPERT, SIAH2, RB1, FOXO1 | 11–40%5, 18, 62, 64, 71–73, 75 | 35–95% mets15, 62, 64, 68, 70, 72, 74 | 21–44% of LocDTC;36–55% AdvDTC6, 69 |
| 15q25.1-q26.3 | Loss | 21.30 | 64 | 40% CRPC | 20–25%7 | |
| 16q11.2-q24.3 | Loss | 33.56 | WWOX | 33–38%5, 18, 64, 71, 73, 75 | 57–82%72 | 33%7 |
| 17p13.1 | Loss | 4.28 | RPAIN, AIPL1, XAF, DLG4, PER1, TP53 | 20–30%5, 18, 64 | ||
| 17p13.3-p11.2 | Loss | 19.50 | 30%64, 73 | 51–61% CRPC | ||
| 17q21.31 | Loss | 0.15 | DHX8, ETV4 | 20%18 | 24 | |
| 17q24.2-q25.3 | Loss | 8.90 | 12–41% CRPC24, 70 | |||
| 18q22.3 | Loss | 0.29 | CBLN2, NETO1 | 20–25%5, 18, 71, 73 | 40%24, 72 | 50%7 |
| 21q22.3 | Loss | 0.25 | ERG, NCRNA00114, ETS2, PSMG1, BRWD1, HMGN1, WRB, LCA5L, SH3BGR, C21orf88, B3GALT5, IGSF5, PCP4, DSCAM, C21orf130, BACE2, PLAC4, FAM3B, MX2, MX1, TMPRSS2 | 33–50%5, 8, 18, 73, 75 | 33%74 | |
Note: SCNA regions are listed in chromosomal order. Well-characterized cancer genes are in bold. References are indicated for reported frequencies of SCNAs. In general, only SCNAs with a frequency >40% in at least one cancer category are listed.Size is based on reported results, and indicates the broader region of overlap across studies. Actual size reported in individual samples may vary, especially for studies using recently developed technologies such as high-density SNP CGH arrays and next-generation sequencing that permit a greater limit of resolution. In general SCNAs are smaller in primary tumors than those observed in metastases, and may only cover a portion of the region listed.