Table 1. Higher-Level Copy Number Alterations and recurrent deletions in PMBL Cell Lines.
| Chr. band | Coordinates (KBp) | Cell lines | Genes in region of interest | Co-incident previous studies | ||||
|---|---|---|---|---|---|---|---|---|
| FARAGE | KARPAS-1106P | MEDB-1 | U-2940 | Protein coding | Noncoding RNA | |||
| A: Gains (≥4x) | ||||||||
| 1p31 | 72309–72321 | 2 | 2 | 4 | 2 | NEGR1 (part) | - | |
| 1q31 | 193155–193158 | 2 | 2 | 4 | 4 | B3GALT2 (upstream), CDC73 (part) | - | |
| 2p15 | 61679–62435 | 2 | 4 | 2 | 2 | XPO1, FAM161A, CCT4, COMMD1, B3GNT2 (part) | - | [6, 26] |
| 2p14 | 66213–66220 | 4 | 3 | 4 | 2 | SLC1A4 (part) | - | |
| 2q33 | 207864–208167 | 2 | 2 | 2 | 5x | KLF7 | hsa-mir-2355, hsa-mir-1302-4 | [6 9] |
| 3q27 | 188046–188075 | 2 | 2 | 2 | 4x | LPP (part), BCL6 (regulatory region) | - | [6, 26] |
| 6q22 | 125228–126628 | 2 | 2 | 2 | 4–4.5 | NKAIN2 (part), STL, RNF217, TPD52L1, HDDC2, LOC643623,HEY2, NCOA7, TRMT11 | LOC643623 MIR5695 | |
| 9p24 | 3087–7795 | 2 | 4 | 3 | 2 | RFX3, GLIS3, PPAPDC2, SLC1A1, CDC37L1, AK3, RCL1, JAK2, INSL4, RLN2, RLN1, CD274, (INSERT), ERMP1, MLANA, IL33, GLDC, KDM4C | hsa-mir-101-2 | [6] |
| 9p24 (peak) | 5527–5766 | 3 | 4 | 4 | 2 | PDCD1lG2 (part), KIAA1432 (part) | - | |
| 8q24 | 129061–129153 | 2 | 6.5 | 2 | 0 | PVT1 (part) | [6, 26] | |
| 21q11 | 15639–16173 | 2 | 2 | 4 | 2 | ABCC13,HSPA13, SAMSN1, SAMSN1-AS1, LOC388813 | - | |
| 22q12 | 36679–36694 | 2 | 4 | 4 | 2 | MYH9 (part) | - | |
| B: Deletions (bilateral) | ||||||||
| 1p12 | 117068–117118 | 2 | 0 | 0 | 2 | CD58 | hsa-mir-320b | |
| 2p16 | 48006–48193 | 0 | 2 | 1 | 2 | MSH6, FBXO11 | - | |
| 7p22 | 60267–6095 | 2 | 2 | 2 | 0 | PMS2 (part), AIMP2, EIF2AK1 (part) | - | [26] |
| 8q24 | 128829–128990 | 2 | 3 | 2 | 0 | PVT1 | hsa miR-1204-1208 | |
| 9p21 | 21969–22067 | 1 | 0 | 3 | 0 | CDKN2A, CDKN2B | - | |
| 12q24 | 133272–133289 | 2 | 0 | 2 | 2 | PXMP2 | - | |
| 15q26 | 100148–100208 | 2 | 0 | 2 | 2 | MEF2A | - | |
| 16p13 | 10897–1099711169–11682 | 1 | 0 | 2 | 0 | FAM18A (part),CLEC16A (part), SOCS1, TNP2, PRM2, PRM1, RMI2, LITAF | hsa-mir-548h-2 | |
| 17q21 | 42570–42584 | 1 | 2 | 2 | 0 | GPATCH8 (part) | - | |
| 17q21 | 42596–42599 | 1 | 2 | 2 | 0 | GPATCH8 (5´) | - | |
| 19q13 | 34737–34809 | 2 | 2 | 3 | 0 | KIAA0355 | - | |
| 22q11 | 183978–18488 | 2 | 0 | 2 | 2 | MICAL3, | hsa-mir-648 | |
| C: Deletions (unilateral) | ||||||||
| 1p35 | 25686–25762 | 2 | 2 | 1 | 1 | RHCE | - | [26] |
| 1p13 | 110479–110484 | 1 | 1 | 2 | 2 | CSF1 (downstream) | - | [26] |
| 1q43 | 236900–236905 | 1 | 2 | 3 | 1 | ACTN2 (Part; partially overlaps deletion polymorphism) | - | |
| 1q44 | 241161–241667 | 1 | 2 | 1 | 2 | FH (part) | - | |
| 2p16 | 50546–50559 | 2 | 1 | 2 | 1 | NRXN1 (part) | - | |
| 2q11 | 100928–100951 | 2 | 2 | 1 | 1 | LONRF2 (part) | - | |
| 2q12 | 103099–103104 | 2 | 2 | 1 | 1 | SLC9M (part) | - | |
| 2q12 | 106384–106390 | 1 | 2 | 3 | 1 | NCK2 (part)17q21 | - | |
| 2q14 | 123282–123303 | 2 | 3 | 1 | 1 | - | - | |
| 2q34 | 211953–211971 | 1 | 1 | 2 | 3 | - | - | |
| 2q36 | 223660–223675 | 2 | 2 | 1 | 1 | - | - | |
| 3p21 | 50627–50638 | 2 | 1 | 2 | 1 | CISH (downstream) | - | [26] |
| 3p14 | 69532–69554 | 2 | 1 | 1 | 2 | - | - | |
| 3q13 | 117961–117972 | 1 | 1 | 2 | 1 | - | - | |
| 4p11 | 48765–48777 | 2 | 1 | 2 | 1 | FRYL (part) | - | |
| 4q13 | 62870–62877 | 2 | 2 | 1 | 1 | LPHN3 (part) | - | [26] |
| 4q32 | - | 2 | 1 | 1 | 2 | PALLD (non-overlapping losses within same gene) | - | [26] |
| 5q34 | 167062–167071 | 2 | 1 | 1 | 2 | TENM2 (part) | - | |
| 6q25 | 149377–149382 | 2 | 1 | 1 | 2 | UST (part) | - | [26] |
| 6q26 | 164446–164467 | 1 | 1 | 2 | 2 | - | - | |
| 7p21 | 11162–11167 | 2 | 2 | 1 | 1 | PHF14 (part) | - | [26] |
| 7p15 | 21579–21584 | 2 | 2 | 1 | 1 | DNAH11 (part) | - | |
| 7p15 | 27224–27236 | 1 | 1 | 2 | 2 | HOXA11 (part), HOXA11-AS | - | |
| 7p14 | 30000–30003 | 2 | 2 | 1 | 1 | SCRN1 (part) | - | |
| 7p14 | 42267–42268 | 1 | 2 | 1 | 1 | GLI3 (part) | - | |
| 7q21 | 95043–95053 | 1 | 2 | 2 | 1 | PON2 | - | |
| 8q22 | 95398–95399 | 1 | 2 | 1 | 2 | RAD54B(part) | - | |
| 8q22 | 102670–102674 | 2 | 1 | 1 | 2 | GRHL2 (part) | - | |
| 9p13 | 37997–37999 | 2 | 2 | 1 | 1 | SHB (part) | - | |
| 10q12 | 49731–49739 | 1 | 1 | 1 | 1 | ARHGAP22 (part)—adjacent to loss DGV48558) | - | |
| 10q12 | 51818–51850 | 2 | 1 | 1 | 2 | FAM21B (part) | - | |
| 10q22 | 73532–73538 | 1 | 1 | 1 | 2 | C10orf54 (5´), CDH23 (part)–adjacent to loss DGV29865 | - | |
| 10q22 | 108236–108253 | 2 | 1 | 1 | 2 | - | - | |
| 11q22 | 102212–102214 | 2 | 2 | 1 | 1 | BIRC3 (3´), BIRC2 (5´) | - | |
| 11q23 | 118140–118154 | 1 | 2 | 1 | 2 | MPZL2 (5´) | - | |
| 11q23 | - | 2 | 2 | 1 | 1 | SORL1—non-overlapping losses within same gene | - | |
| 12q23 | 101601–101611 | 1 | 2 | 1 | 2 | SLC5A8 (part) | - | |
| 13q31 | 93488–93497 | 2 | 3 | 1 | 1 | GPC5 (part)—adjacent to loss DGV86974 | - | |
| 14q22 | 52271–52276 | 2 | 1 | 2 | 1 | GNG2 (5´)–adjacent to loss DGV87223 | - | |
| 14q23 | 68248–68251 | 1 | 1 | 2 | 2 | ZFYVE26 (part) | - | |
| 14q24 | 76430–76438 | 1 | 1 | 2 | 2 | TGFB3 (part) | - | |
| 14q31 | 80199–80210 | 2 | 2 | 1 | 1 | NRXN3 (part) | - | |
| 15q26 | 101032–101037 | 1 | 1 | 2 | 2 | CERS3 (part) | - | |
| 16p13 | 7553–7561 | 1 | 2 | 2 | 1 | RBFOX1 (part) | - | |
| 16p13 | - | 1 | 2 | 1 | 2 | LOC283856 (part)—non-overlapping losses within same gene | - | |
| 18q21 | 5840–358444 | 1 | 1 | 2 | 2 | Gene desert: nearest gene CDH20 | - | |
| 19p13 | 6483–6496 | 1 | 1 | 2 | 2 | TUBB4A (part) | - | |
| 19p11 | 23557–23564 | 2 | 1 | 2 | 1 | CST9L (5´) | - | |
| 19q13 | 56076–56085 | 2 | 1 | 1 | 2 | CTCFL (part) | - | |
Table lists coordinates (HG19) and hosted loci in PMBL cell lines bearing (A) significant CNV, both gains (≥4x) and (B) losses (null) and both protein coding and noncoding RNA genes located within. Part C lists shared unilateral deletions including non-overlapping deletions in the same genes. Where multiple cell lines are involved coordinates of common affected regions are shown. DGV polymorphisms are excluded.