Most common SCNAs in human prostate cancer
| Reported frequency in prostate cancera | ||||||
|---|---|---|---|---|---|---|
| Cytoband | Event | Size, Mb | Genes of interest | Primary cancer | Advanced cancer | DTCs or CTCs |
| Xp11.22-q13.1 | Gain | 18–67.8 | AR | 50% CRPC (15, 24, 25, 68) | 45% AdvDTC (6, 7, 69) | |
| 1p12-q43 | Gain | 117 | 45%–65% CRPC (24) | 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, 25) | 25% (6, 7) |
| 7p22.3-q36.3 | Gain | 158.40 | (5, 18) | 25%–55% CRPC (68, 70, 72, 25) | 40% (6, 7) | |
| 8p12-q24.3 | Gain | 97.64 | MYC, MAF, EYA1, MSC, TRPA1, KCNB2 | 20%–30% (5, 18, 64, 71–73, 74) | 64%–82% CRPC (15, 62, 68, 70, 72) | 50%–65% (6, 7, 69) |
| 8p23-p11 | Loss | 19.58 | NKX3-1 | 53%–67% (5, 18, 71–73, 74) | 67%–74% of CRPC (15, 68, 72) | 36%–90% of AdvDTCs; 20–23% LocDTCs (6, 7, 69) |
| 9q31.3 | Gain | 22.79 | PTPN3, AKAP2, DAPK1, SYK | (5) | 30% (70, 72) | 25%–45% AdvDTC (6, 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% AdvDTC (6) | |
| 10q22-q24 | Loss | 24.91 | CFLP1, KILLIN, PTEN, RNLS, LIPJ, LIPF, LIPK, LIPN, LIPM, ANKRD22, STAMBPL1, ACTA2 | 12%–25% (5, 18, 62, 64, 72–74) | 36%–80% (15, 62, 68, 70, 25) | 36% (69) |
| 11p13-p12 | Loss | 4.72 | (4, 6, 64, 70, 73) | (25) | 45% AdvDTC (6) | |
| 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, 74) | 35%–95% mets (15, 62, 64, 68, 70, 72, 25) | 21%–44% of LocDTC; 36%–55% AdvDTC (6, 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, 74) | 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% CRPC (24, 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, 74) | 33% (25) | |
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 single-nucleotide polymorphism comparative genomic hybridization (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.
↵aNumbers in parentheses correspond with studies cited as references in this article.