Table 2.
Recurrent focal amplifications and deletions in the chronic lymphocytic leukemia (CLL) genome, including their frequency, wide peak region, length, q-value, residual q-value, and involved genes.
| Unique Name | Cases | Cytoband | Wide Peak Boundaries | Length | Q value | Residual Q value | Genes in Wide Peak |
|---|---|---|---|---|---|---|---|
| Amplification Peak 3 | 9 | 1p31.1 | chr1:74500015–74621552 | 1.22E+05 | 4.80E−16 | 1.86E−11 | LRRIQ3, FPGT, TNNI3K |
| Amplification Peak 4 | 9 | 1p22.2 | chr1:91784576–91813183 | 2.86E+04 | 3.13E−11 | 5.32E−09 | HFM1 |
| Amplification Peak 8 | 11 | 1q25.2 | chr1:176093431–176153873 | 6.04E+04 | 2.73E−13 | 8.89E−06 | RFWD2 |
| Amplification Peak 9 | 3 | 1q42.12 | chr1:225152123–225211696 | 59,573 | 1.71E−03 | 1.71E−03 | DNAH14 |
| Amplification Peak 14 | 15 | 3q25.1 | chr3:149563840–149684409 | 120,569 | 4.78E−04 | 1.92E−03 | PFN2, RNF13 |
| Amplification Peak 15 | 14 | 3q29 | chr3:195053676–195063318 | 9.64E+03 | 1.01E−05 | 1.72E−05 | ACAP2 |
| Amplification Peak 17 | 6 | 4p16.3 | chr4:3449609–3495293 | 45,684 | 9.11E−04 | 9.11E−04 | HGFAC, DOK7 |
| Amplification Peak 18 | 5 | 4p15.2 | chr4:26622159–26641959 | 19,800 | 0.01 | 0.01 | TBC1D19 |
| Amplification Peak 19 | 5 | 4q31.21 | chr4:145658875–146010087 | 351,212 | 5.17E−03 | 5.17E−03 | ANAPC10, HHIP |
| Amplification Peak 20 | 10 | 5q35.3 | chr5:180052785–180167076 | 1.14E+05 | 1.68E−05 | 1.68E−05 | FLT4, OR2Y1 |
| Amplification Peak 22 | 4 | 6q15 | chr6:89479426–89563571 | 84,145 | 1.47E−04 | 1.47E−04 | RNGTT |
| Amplification Peak 24 | 70 | 7p14.1 | chr7:38284691–38357086 | 7.24E+04 | 1.62E−82 | 1.62E−82 | TCRG locus |
| Amplification Peak 28 | 19 | 8q24.13 | chr8:124810460–124812196 | 1,736 | 2.36E−03 | 0.02 | FAM91A1 |
| Amplification Peak 30 | 6 | 9q34.3 | chr9:138905634–139092618 | 186,984 | 0.03 | 0.03 | LHX3, C9orf69, NACC2 |
| Amplification Peak 31 | 8 | 9q34.3 | chr9:140161390–140246050 | 84,660 | 1.71E−03 | 1.71E−03 | COBRA1, C9orf167, EXD3, NRARP |
| Amplification Peak 32 | 6 | 10q24.33 | chr10:105073962–105140579 | 66,617 | 1.28E−04 | 1.28E−04 | TAF5, PCGF6 |
| Amplification Peak 33 | 26 | 11p13 | chr11:32676388–32705141 | 2.88E+04 | 7.50E−13 | 5.84E−12 | CCDC73, WT1 |
| Amplification Peak 34 | 2 | 11p11.2 | chr11:45935717–45955761 | 20,044 | 0.04 | 0.04 | PEX16, PHF21A, GYLTL1B |
| Amplification Peak 40 | 11 | 13q13.3 | chr13:35622613–35697715 | 75,102 | 5.17E−03 | 5.17E−03 | NBEA |
| Amplification Peak 41 | 4 | 13q22.1 | chr13:73530979–73643032 | 112,053 | 0.01 | 0.01 | KLF5, PIBF1 |
| Amplification Peak 42 | 188 | 14q11.2 | chr14:22749319–22925867 | 1.77E+05 | 4.44E−186 | 2.84E−185 | TCRA locus |
| Amplification Peak 45 | 12 | 14q32.33 | chr14:105059814–105172511 | 1.13E+05 | 2.70E−05 | 4.01E−04 | INF2, TMEM179, MIR4710, AKT1 |
| Amplification Peak 50 | 8 | 16q22.1 | chr16:66819728–66824959 | 5.23E+03 | 5.54E−05 | 5.54E−05 | CCDC79, NAE1 |
| Amplification Peak 51 | 12 | 17q11.2 | chr17:30228618–30321772 | 9.32E+04 | 2.72E−20 | 2.23E−17 | SUZ12, UTP6 |
| Amplification Peak 53 | 6 | 17q25.3 | chr17:79389937–79430022 | 40,085 | 0.02 | 0.02 | hsa-mir-3186, BAHCC1, MIR3186 |
| Amplification Peak 54 | 7 | 18q11.2 | chr18:21229308–21329567 | 100,259 | 0.02 | 0.02 | LAMA3, ANKRD29 |
| Amplification Peak 55 | 15 | 18q22.1 | chr18:66365105–66377388 | 12,283 | 0.03 | 0.03 | TMX3 |
| Amplification Peak 57 | 8 | 19p12 | chr19:20221949–20317969 | 96,020 | 0.02 | 0.03 | ZNF90, ZNF486 |
| Amplification Peak 59 | 3 | 20q13.12 | chr20:42694274–42813092 | 118,818 | 5.94E−03 | 5.94E−03 | JPH2, TOX2 |
| Amplification Peak 62 | 5 | 20q13.33 | chr20:62705116–62831313 | 126,197 | 0.02 | 0.02 | NPBWR2, MYT1, OPRL1, RGS19, C20orf201 |
| Amplification Peak 66 | 4 | 22q13.33 | chr22:50967459–51008050 | 40,591 | 1.39E−03 | 1.39E−03 | CPT1B, TYMP, KLHDC7B, CHKB-CPT1B, ODF3B, SYCE3 |
| Deletion Peak 7 | 193 | 2p11.2 | chr2:88894337–95722218 | 6,827,881 | 0 | 0 | IGK locus |
| Deletion Peak 8 | 4 | 2q23.3 | chr2:152234651–152663572 | 428,921 | 0.04 | 0.04 | NEB, RIF1 |
| Deletion Peak 13 | 12 | 3q25.33 | chr3:159713418–160118695 | 405,277 | 0.02 | 0.04 | IFT80, C3orf80, IL12A |
| Deletion Peak 16 | 19 | 4q13.2 | chr4:69344747–69691521 | 3.47E+05 | 7.11E−06 | 3.92E−05 | UGT2B15, UGT2B17 |
| Deletion Peak 17 | 8 | 4q13.3 | chr4:70897589–71020148 | 122,559 | 0.02 | 0.02 | HTN1, CSN1S2AP, CSN1S2BP |
| Deletion Peak 18 | 9 | 4q21.23 | chr4:84367119–84457735 | 90,616 | 1.71E−03 | 6.90E−03 | MRPS18C, FAM175A |
| Deletion Peak 21 | 15 | 6q21 | chr6:110797012–111583801 | 786,789 | 1.74E−04 | 1.74E−04 | AMD1, CDK19, RPF2, GTF3C6, SLC16A10, GSTM2P1 |
| Deletion Peak 23 | 12 | 7p22.1 | chr7:5269419–5920366 | 650,947 | 0.02 | 0.02 | hsa-mir-589, ACTB, FSCN1, RNF216, FBXL18, TNRC18, SLC29A4, ZNF815 |
| Deletion Peak 24 | 11 | 7q21.2 | chr7:92147625–92247368 | 9.97E+04 | 3.11E−05 | 9.98E−05 | RBM48, MGC16142, FAM133B, LOC728066, CDK6 |
| Deletion Peak 27 | 11 | 8q22.1 | chr8:95690341–95840099 | 149,758 | 0.02 | 0.02 | DPY19L4, ESRP1, TP53INP1 |
| Deletion Peak 29 | 3 | 9p21.2 | chr9:26116211–27109465 | 993,254 | 1.62E−03 | 1.62E−03 | PLAA, LRRC19, C9orf82, IFT74, TEK |
| Deletion Peak 32 | 33 | 11q14.3 | chr11:89185111–89443615 | 2.59E+05 | 1.36E−34 | 1.06E−22 | FOLH1B, NOX4 |
| Deletion Peak 34 | 44 | 11q22.3 | chr11:110018375–110449975 | 4.32E+05 | 1.18E−31 | 1.13E−18 | FDX1, RDX, ATM |
| Deletion Peak 37 | 12 | 12q24.33 | chr12:132335406–132436802 | 101,396 | 1.09E−03 | 1.05E−03 | ULK1, PUS1 |
| Deletion Peak 38 | 200 | 13q14.2 | chr13:50306479–51501752 | 1,195,273 | 0 | 0 | hsa-mir-15a, DLEU2, TRIM13, DLEU1, SPRYD7, ST13P4, DLEU7, CTAGE10P, KCNRG, MIR15A, MIR16-1, MIR3613 |
| Deletion Peak 40 | 41 | 14q21.1 | chr14:39721874–39871082 | 1.49E+05 | 1.56E−18 | 3.83E−10 | CTAGE5, LOC100288846, MIA2, FBXO33 |
| Deletion Peak 42 | 27 | 14q32.33 | chr14:104506663–105201322 | 6.95E+05 | 1.61E−11 | 1.05E−03 | hsa-mir-203, KIF26A, INF2, ASPG, TMEM179, C14orf180, MIR203, MIR3545, MIR4710 |
| Deletion Peak 43 | 33 | 14q32.33 | chr14:105861125–107349540 | 1.49E+06 | 1.89E−13 | 6.44E−08 | CRIP1, CRIP2, ELK2AP, ADAM6, MTA1, KIAA0125, TMEM121, C14orf80, LINC00226, LINC00221, TEX22 |
| Deletion Peak 46 | 10 | 15q15.1 | chr15:42138836–42192730 | 53,894 | 3.47E−03 | 0.01 | hsa-mir-4310, SPTBN5, MIR4310 |
| Deletion Peak 49 | 2 | 16q12.2 | chr16:53968071–55360473 | 1,392,402 | 0.01 | 0.01 | IRX5, IRX3, CRNDE |
| Deletion Peak 54 | 8 | 18q21.1 | chr18:43604458–43796648 | 192,190 | 0.04 | 0.04 | ATP5A1, HAUS1, PSTPIP2 |
| Deletion Peak 55 | 10 | 18q23 | chr18:77246915–77733812 | 486,897 | 2.64E−04 | 2.84E−04 | CTDP1, KCNG2, PQLC1, HSBP1L1, NFATC1 |
| Deletion Peak 66 | 125 | 22q11.22 | chr22:23162356–23404171 | 2.42E+05 | 2.71E−277 | 5.01E−277 | IGL locus |