Table 4.
Copy number loss lesions detected by SNP-A and affected candidate genes (N = 26)
| Patient no. | Disease | Chromosome | Start | Stop | Length, Mb | Affected candidate genes |
|---|---|---|---|---|---|---|
| 25 | AP | 1p34.3 | 35028712 | 36757321 | 1.73 | PSMB2, CLSPN, STK40, CSF3R |
| 26 | AP | 6q14.2q21 | 83951101 | 110175307 | 26.22 | PRSS35, SNAP91, NT5E, SNHG5, RARS2, CNR1, MAP3K7, EPHA7, TSG1, FHL5, FBXL4, USP45, SIM1, GRIK2, HACE1, BVES, PRDM1, ATG5, PDSS2, SCML4, SNX3, FOXO3, SESN1, FIG4, WASF1 |
| 42 | Myeloid BP | 7 | 153672 | 158821424 | 158.67 | Monosomy 7 |
| 25 | AP | 8q11.1q11.21 | 47062007 | 49246034 | 2.18 | CEBPD, PRKDC, MCM4 |
| 34 | Myeloid BP | 9p21.3p13.2 | 20934558 | 37208231 | 16.27 | PTPLAD2, IFNA5, KLHL9, MTAP, CDKN2A, ELAVL2, TUSC1, PLAA, IFT74, TEK, IFNK, ACO1, APTX, SMU1, NFX1, NOL6, PRSS3, CNTFR, GALT, VCP, FANCG, TESK1, RECK, CLTA, GNE, MELK, PAX5 |
| 40 | Myeloid BP | 9q34.11q34.12 | 130686250 | 132652879 | 1.97 | PHYHD1, SH3GLB2, DOLPP1, PPP2R4, ASB6, PIG12, FNBP1, ASS1, FUBP3, ABL1 |
| 28 | AP | 9q34.11q34.12 | 130900242 | 132604796 | 1.7 | ASB6, PIG12, FNBP1, ASS1, FUBP3, ABL1 |
| 27 | AP | 10q22.1q22.2 | 73539669 | 76313833 | 2.77 | DNAJB12, ANXA7, SEC24C, CAMK2G, VCL, AP3M1, ADK |
| 26 | AP | 11p15.5p15.2 | 1613884 | 14397978 | 12.78 | H19, IGF2, ASCL2, TSSC4, CDKN1C, NAP1L4, NUP98, RRM1, ILK, TPP1, NLRP10, STK33, ST5, WEE1, SBF2, AMPD3, MRVI1, EIF4G2, DKK3, TEAD1, ARNTL, RRAS2 |
| 27 | AP | 11q23.3 | 115868656 | 119126150 | 3.26 | BACE1, FXYD2, FXYD6, IL10RA, MLL, DDX6, BCL9L, CBL |
| 26 | AP | 15q21.2q22.2 | 49041794 | 58605542 | 9.56 | DMXL2, SCG3, TMOD2, LEO1, MAPK6, BCL2L10, GNB5, RAB27A, CCPG1, DYX1C1, NEDD4, TCF12, GCOM1, ADAM10, SLTM, BNIP2, ANXA2 |
| 34 | Myeloid BP | 16p11.2 | 32045466 | 33703188 | 1.66 | TP53TG3 |
| 34 | Myeloid BP | 17p13.3p11.2 | 18901 | 18868271 | 18.85 | GLOD4, ABR, YWHAE, SMYD4, METT10D, GARNL4, ITGAE, MINK1, CAMTA2, DHX33, NLRP1, XAF1, BCL6B, CLEC10A, TP53, JMJD3, HES7, AURKB, PIK3R5, NTN1, GAS7, MAP2K4, ELAC2, NCOR1, TNFRSF13B, NT5M, PEMT, DRG2, ALKBH5, LLGL1, SHMT1, FBXW10, PRPSAP2 |
| 27 | AP | 17q11.2 | 24504173 | 28343137 | 3.84 | GOSR1, NF1, SUZ12, CDK5R1 |
| 23 | AP | 21q22.12 | 34958486 | 36169173 | 1.21 | RUNX1 |
| 28 | AP | 22q11.23 | 21963842 | 22551295 | 0.59 | BCR, IGLL1, Ini1 |
| 40 | Myeloid BP | 22q11.23q12.3 | 21963842 | 35542482 | 13.58 | BCR, IGLL1, Ini1, Chk2, XBP1, KREMEN1, EWSR1, NF2, LIF, DUSP18, LIMK2, PATZ1, EIF4ENIF1, YWHAH, TOM1, MCM5, RASD2, RBM9, |
| 30 | Myeloid BP | Y | 3259468 | 23370508 | 20.11 | Whole Y chromosome deletion |
AP indicates phase; and BP, blast phase.