Table 2 Chromosomal segments frequently gained or lost, genes involved, and respective copy numbers
Chr. | Start | End | Cytoband | Genes | Samples with copy number variation (copy numbers) | |||
|---|---|---|---|---|---|---|---|---|
‘S’ group | ‘N’ group | Case number of | ||||||
Frequently gained | Gain | Loss | ||||||
5 | 14002973 | 14469161 | p15.2 | 69.79% region overlaps with TRIO (+) | S2 (3.20), S3 (3.38), S5 (3.46), S6 (4.02) | 4 | 0 | |
7 | 25469619 | 25899147 | p15.3-p15.2 | No protein-coding gene | S2 (3.17), S6 (1.34), S7 (4.18), S8 (3.35) | N5 (3.94) | 4 | 1 |
8 | 128861562 | 128966324 | q24.21 | No protein-coding gene | S1 (3.60), S7 (3.35), S8 (3.30) | N1 (3.28), N5 (3.19) | 5 | 0 |
8 | 128966324 | 130063055 | q24.21 | No protein-coding gene | S1 (3.60), S4 (3.58), S7 (3.35), S8 (3.30) | N1 (3.28), N5 (3.19) | 6 | 0 |
8 | 130063055 | 130107139 | q24.21 | No protein-coding gene | S1 (3.60), S4 (3.58), S7 (3.35), S8 (3.30) | N5 (3.19) | 5 | 0 |
8 | 130107139 | 130190155 | q24.21 | No protein-coding gene | S1 (3.60), S4 (3.58), S7 (3.35), S8 (3.30) | 4 | 0 | |
8 | 133952710 | 134594980 | q24.22 | NDRG1 (−), SLA (−), ST3GAL1 (−), WISP1 (+), 30.27% region overlaps with TG (+) | S1 (3.60), S8 (3.30) | N1 (3.25), N5 (3.77) | 4 | 0 |
12 | 18369537 | 18390595 | p12.3 | No protein-coding gene | S1 (4.28), S2 (3.37), S4 (3.57), S7 (3.71) | 4 | 0 | |
12 | 18390595 | 18587749 | p12.3 | 87.89% region overlaps with PIK3C2G (+) | S1 (4.28), S2 (3.37), S4 (3.57), S7 (3.71) | N5 (3.79) | 5 | 0 |
12 | 18587749 | 18590323 | p12.3 | Intron of PIK3C2G (+) | S1 (4.28), S2 (3.37), S4 (3.57) | N5 (3.79) | 4 | 0 |
12 | 57314551 | 57662938 | q13.3 | GPR182 (+), LRP1 (+), MYO1A (−), NAB2 (+), NDUFA4L2 (−), NXPH4 (+), RDH16 (−), SDR9C7 (−), SHMT2 (+), STAC3 (−), STAT6 (−), TAC3 (−), TMEM194A (−), ZBTB39 (−), 4.42% region overlaps with R3HDM2 (−) | S1 (4.29), S2 (3.39), S3 (4.92) | N1 (4.51) | 4 | 0 |
12 | 57662938 | 58095994 | q13.3 | ARHGAP9 (−), ARHGEF25 (+), B4GALNT1 (−), DCTN2 (−), DDIT3 (−), DTX3 (+), GLI1 (+), INHBC (+), INHBE (+), KIF5A (+), MARS (+), MBD6 (+), PIP4K2C (+), SLC26A10 (+), 1.91% region overlaps with OS9 (+), 9.54% region overlaps with R3HDM2 (−) | S1 (4.29), S2 (3.39), S3 (4.92) | N1 (4.51), N2 (3.57) | 5 | 0 |
12 | 58095994 | 58415437 | q13.3-q14.1 | AGAP2 (−), AVIL (−), CDK4 (−), CTDSP2 (−), CYP27B1 (−), MARCH9 (+), METTL1 (−), METTL21B (+), TSFM (+), TSPAN31 (+), XRCC6BP1 (+), 6.06% region overlaps with OS9 (+) | S1 (4.29), S2 (3.39), S3 (4.92), S6 (9.20) | N1 (4.51), N2 (3.57) | 6 | 0 |
12 | 58415437 | 58463763 | q14.1 | No protein-coding gene | S2 (3.39), S3 (4.92), S6 (9.20) | N1 (4.51), N2 (3.57) | 5 | 0 |
12 | 58463763 | 59587988 | q14.1 | LRIG3 (−) | S2 (3.39), S3 (4.92), S6 (1.33) | N1 (4.51), N2 (3.57) | 4 | 1 |
12 | 66188349 | 66380269 | q14.3 | HMGA2 (+) | S2 (4.14), S3 (4.79), S6 (1.27) | N1 (4.38), N2 (3.90) | 4 | 1 |
12 | 66380269 | 66547930 | q14.3 | LLPH (−), 10.27% region overlaps with TMBIM4 (−) | S2 (4.14), S3 (4.79), S6 (9.55) | N1 (4.38), N2 (3.90) | 5 | 0 |
12 | 66547930 | 66789905 | q14.3 | HELB (+), IRAK3 (+), 20.12% region overlaps with GRIP1 (−), 6.58% region overlaps with TMBIM4 (−) | S3 (4.79), S6 (9.55) | N1 (4.38), N2 (3.90) | 4 | 0 |
12 | 68187627 | 68217137 | q15 | No protein-coding gene | S1 (5.11), S3 (4.79) | N1 (4.38), N2 (3.90) | 4 | 0 |
12 | 68217137 | 68427073 | q15 | No protein-coding gene | S1 (5.11), S3 (4.79), S6 (1.28) | N1 (4.38), N2 (3.90) | 4 | 1 |
12 | 68427073 | 69138985 | q15 | IFNG (−), IL22 (−), IL26 (−), MDM1 (−), NUP107 (+), RAP1B (+) | S1 (5.11), S3 (4.79), S6 (4.02) | N1 (4.38), N2 (3.90) | 5 | 0 |
12 | 69138985 | 70063299 | q15 | CCT2 (+), CPM (−), CPSF6 (+), FRS2 (+), LRRC10 (−), LYZ (+), MDM2 (+), SLC35E3 (+), YEATS4 (+), 1.72% region overlaps with BEST3 (−) | S1 (5.11), S3 (4.79), S6 (9.19) | N1 (4.38), N2 (3.90) | 5 | 0 |
12 | 70063299 | 70937191 | q15 | CNOT2 (+), KCNMB4 (+), RAB3IP (+), 3.04% region overlaps with PTPRB (−), 3.42% region overlaps with BEST3 (−) | S3 (4.79), S6 (9.19) | N1 (4.38), N2 (3.90) | 4 | 0 |
12 | 73087630 | 73365902 | q21.1 | No protein-coding gene | S3 (3.84), S6 (3.93) | N1 (4.38), N2 (3.90) | 4 | 0 |
12 | 91313872 | 91359718 | q21.33 | CCER1 (−), 4.94% region overlaps with EPYC (−) | S1 (3.82), S4 (3.71), S6 (1.28) | N2 (3.19), N5 (4.38) | 4 | 1 |
12 | 91359718 | 91885474 | q21.33 | DCN (−), KERA (−), LUM (−), 7.43% region overlaps with EPYC (−) | S1 (3.82), S4 (3.71), S6 (1.28), S7 (4.26) | N2 (3.19), N5 (4.38) | 5 | 1 |
14 | 68760113 | 68935899 | q24.1 | Contained within RAD51B (+) | S5 (4.02), S7 (3.76) | N1 (3.35), N5 (3.67) | 4 | 0 |
Frequently lost | ||||||||
9 | 8920634 | 10564954 | p24.1-p23 | Contained within PTPRD (−) | S1 (3.43), S3 (1.23), S5 (1.30), S6 (1.28), S8 (1.21) | 1 | 4 | |
9 | 11542643 | 13067673 | p23 | LURAP1L (+), TYRP1 (+) | S3 (1.23), S5 (1.35), S6 (1.28), S8 (1.21) | 0 | 4 | |
9 | 13067673 | 13292483 | p23 | MPDZ (−) | S1 (3.05), S3 (1.23), S5 (1.35), S6 (1.28), S8 (1.21) | 1 | 4 | |
13 | 19084823 | 19374325 | q11 | No protein-coding gene | S3 (1.43), S5 (1.28), S6 (1.29), S7 (1.49), S8 (1.27) | 0 | 5 | |
13 | 19374325 | 20220348 | q11-q12.11 | TPTE2 (−), TUBA3C (−), 1.48% region overlaps with MPHOSPH8 (+) | S3 (1.43), S5 (1.28), S6 (1.29), S7 (1.49) | 0 | 4 | |
13 | 28542151 | 28584900 | q12.2 | URAD (−), 17.52% region overlaps with FLT3 (−), 3.17% region overlaps with CDX2 (−) | S5 (1.41), S6 (1.29), S7 (1.40) | N5 (1.31) | 0 | 4 |
13 | 28584900 | 28647213 | q12.2 | Contained within FLT3 (−) | S3 (1.38), S5 (1.41), S6 (1.29), S7 (1.40) | N5 (1.31) | 0 | 5 |
13 | 28647213 | 28664099 | q12.2 | Intron of FLT3 (−) | S3 (1.38), S5 (1.41), S6 (1.29), S7 (1.40) | 0 | 4 | |
13 | 54937714 | 56044244 | q14.3-q21.1 | No protein-coding gene | S1 (1.25), S3 (1.42), S5 (1.40), S6 (1.30) | 0 | 4 | |
15 | 32477443 | 32720163 | q13.3 | GOLGA8K (−) | S5 (0.48), S6 (1.28) | N2 (1.03), N8 (0.17) | 0 | 4 |
16 | 51501932 | 52024498 | q12.1 | No protein-coding gene | S3 (1.38), S4 (3.64), S5 (1.32), S6 (1.26), S8 (1.21) | 1 | 4 | |
16 | 52024498 | 57204694 | q12.1-q13 | AKTIP (−), AMFR (−), BBS2 (−), C16orf97 (−), CAPNS2 (+), CES1 (−), CES5A (−), CETP (+), CHD9 (+), CPNE2 (+), FTO (+), GNAO1 (+), HERPUD1 (+), IRX3 (−), IRX5 (+), IRX6 (+), LOC643802 (−), LPCAT2 (+), MMP2 (+), MT1A (+), MT1B (+), MT1E (+), MT1F (+), MT1G (−), MT1H (+), MT1L (+), MT1M (+), MT1X (+), MT2A (+), MT3 (+), MT4 (+), NLRC5 (+), NUDT21 (−), NUP93 (+), OGFOD1 (+), RBL2 (+), RPGRIP1L (−), SLC12A3 (+), SLC6A2 (+), TOX3 (−), 0.35% region overlaps with FAM192A (−) | S3 (1.38), S5 (1.32), S6 (1.26), S8 (1.21) | 0 | 4 | |
16 | 78097752 | 79804205 | q23.1-q23.2 | MAF (−), WWOX (+) | S1 (1.41), S3 (1.24), S6 (1.26), S8 (1.21) | 0 | 4 | |
17 | 25326941 | 25488608 | q11.1 | No protein-coding gene | S2 (1.15), S3 (1.33), S5 (1.30), S8 (1.23) | 0 | 4 | |
17 | 25704252 | 26675625 | q11.1-q11.2 | IFT20 (−), KSR1 (+), LGALS9 (+), LYRM9 (−), NLK (+), NOS2 (−), TMEM97 (+), TNFAIP1 (+), 0.20% region overlaps with POLDIP2 (−) | S2 (1.15), S3 (1.21), S5 (1.30), S8 (1.23) | 0 | 4 | |
17 | 28464040 | 30439293 | q11.2 | ADAP2 (+), ATAD5 (+), BLMH (−), COPRS (−), CPD (+), CRLF3 (−), EVI2A (−), EVI2B (−), GOSR1 (+), LRRC37B (+), NF1 (+), OMG (−), RAB11FIP4 (+), RNF135 (+), SLC6A4 (−), SUZ12 (+), TBC1D29 (+), TEFM (−), TMIGD1 (−), UTP6 (−), 2.50% region overlaps with NSRP1 (+) | S1 (1.28), S2 (1.15), S3 (1.28), S8 (1.23) | 0 | 4 | |
17 | 31265013 | 33086047 | q11.2-q12 | ASIC2 (−), C17orf102 (−), CCL1 (−), CCL11 (+), CCL13 (+), CCL2 (+), CCL7 (+), CCL8 (+), SPACA3 (+), TMEM132E (+), 0.20% region overlaps with TMEM98 (+) | S1 (1.28), S2 (1.15), S3 (1.29), S8 (1.23) | 0 | 4 | |
22 | 24347208 | 24386848 | q11.23 | GSTT1 (−), LOC391322 (+) | S1 (0.55), S2 (4.04), S5 (0.48), S8 (3.32) | N1 (0.95), N3 (0.50), N8 (0.69) | 2 | 5 |
22 | 24386848 | 24392203 | q11.23 | No protein-coding gene | S2 (4.04), S5 (0.48), S8 (3.32) | N1 (0.95), N3 (0.50), N8 (0.69) | 2 | 4 |
