Table 4. CN events characterizing patients achieving CR as compared to patients achieving ≤PR; for each CN lesion, the table lists the cytoband location, the dimension, the frequency in both subgroups of patients, the p level of significance and the genes included.
| Event | Cytoband Location | Region Length (bp) | Freq. in <1> (%) | Freq. in Avg of <0>(%) | p-value | Genes included within the CNA |
|---|---|---|---|---|---|---|
| CN gain | chr1q31.3 | 911 | 66,667 | 19,444 | 0,0025 | CFH |
| chr3q26.32 | 170 | 46,667 | 8,333 | 0,0039 | PIK3CA | |
| chr1q31.3 | 1273 | 66,667 | 22,222 | 0,0040 | CFH | |
| chr2p16.1 | 82365 | 26,667 | 0,000 | 0,0055 | CCDC85A | |
| chr3q13.33 | 49065 | 46,667 | 11,111 | 0,0090 | PLA1A, POPDC2 | |
| chr3q21.2 | 413 | 46,667 | 11,111 | 0,0090 | KALRN | |
| chr3q26.32 | 93 | 46,667 | 11,111 | 0,0090 | PIK3CA | |
| chr3q26.32 | 1318 | 46,667 | 11,111 | 0,0090 | PIK3CA | |
| CN loss | chr1p22.1 | 25360 | 53,333 | 11,111 | 0,0026 | TGFBR3 |
| chr1p22.1 | 606987 | 60,000 | 16,667 | 0,0052 | BRDT, EPHX4, SETSIP, BTBD8, KIAA1107, C1orf146, GLMN*, RPAP2, GFI1*, EVI5* | |
| chr4p16.3 | 1421 | 26,667 | 0,000 | 0,0055 | ZNF595, ZNF718* | |
| chr8p23.2 | 5038 | 26,667 | 0,000 | 0,0055 | CSMD1 | |
| chr8p22 | 502452 | 33,333 | 2,778 | 0,0063 | SGCZ | |
| chr8p22 | 206245 | 33,333 | 2,778 | 0,0063 | SGCZ | |
| chr8p23.1 | 665562 | 33,333 | 2,778 | 0,0063 | SGK223, CLDN23, MFHAS1 | |
| chr8p23.1 | 1049007 | 33,333 | 2,778 | 0,0063 | ERI1, MIR4660, PPP1R3B*, LOC157273, TNKS, MIR597, LINC00599, MIR124–1, MSRA | |
| chr8p23.1 - p22 | 1028933 | 33,333 | 2,778 | 0,0063 | MIR3926–1, MIR3926–2, LONRF1, LOC340357, LINC00681, KIAA1456, DLC1, C8orf48 | |
| chr1p22.1 | 1372892 | 60,000 | 19,444 | 0,0077 | EVI5*, RPL5, SNORD21, SNORA66, FAM69A, MTF2*, TMED5*, CCDC18*, LOC100131564, DR1*, FNBP1L, LOC100129046, BCAR3*, MIR760, DNTTIP2, GCLM* | |
| LOH | chr4p12 | 225913 | 40,000 | 5,556 | 0,0053 | GABRG1 |
| chr2q24.1 | 720756 | 26,667 | 0,000 | 0,0055 | GALNT5, ERMN, CYTIP | |
| chr3q11.2 | 596327 | 26,667 | 0,000 | 0,0055 | LINC00879 | |
| chr4p16.3 | 1244341 | 26,667 | 0,000 | 0,0055 | ZNF595, ZNF718, ZNF876P, ZNF732, ZNF141, ABCA11P, ZNF721, PIGG, PDE6B, ATP5I, MYL5, MFSD7, PCGF3, LOC100129917, CPLX1, GAK, TMEM175, DGKQ, SLC26A1, IDUA, FGFRL1, RNF212, TMED11P, SPON2, LOC100130872, CTBP1-AS, CTBP1, CTBP1-AS2 | |
| chr4p12 | 24856 | 26,667 | 0,000 | 0,0055 | GABRB1 | |
| chr2q11.2 | 273834 | 33,333 | 2,778 | 0,0063 | TSGA10, C2orf15, LIPT1, MITD1, MRPL30, LYG2, LYG1, TXNDC9, EIF5B | |
| chr3q26.33 | 314951 | 33,333 | 2,778 | 0,0063 | TTC14, CCDC39, LOC101928882 | |
| chr4p12 | 646737 | 33,333 | 2,778 | 0,0063 | GABRA2, COX7B2, GABRA4 | |
| chr4q22.1 | 265109 | 33,333 | 2,778 | 0,0063 | GRID2 | |
| chr11p11.2 | 222115 | 66,667 | 25,000 | 0,0098 | DGKZ, MIR4688, MDK, CHRM4, MIR3160–1, MIR3160–2, AMBRA1 |
Data are number, unless otherwise indicated (%); <1= = patients who achieved CR after induction therapy; <0= = patients who achieved PR and/or SD after induction therapy; genes with * resulted differentially expressed, either down- or over-regulated, in a comparison among CR vs. PR and/or SD patients, carrying the correspondent CNA (p<0.05); in bold are indicated tumour suppressor genes.