Table 3.
Most Frequent Microalterations Involving Single Genes in 15 Cortisol-Secreting ACAs According to CNAs Detected by High-resolution SNP Arrays.
| Cytoband | n (%) | CNA | CN Score | Gene | Description |
| 12q12 | 3 (20) | Gain | 5.23 | Contained within C12orf40 | Chromosome 12 open reading frame 40 |
| 6q16.1 | 3 (20) | Gain | 4.33 | Contained within EPHA7 | Ephrin receptor 7 |
| 9q34.3 | 3 (20) | Gain | 3.64 | Overlap with 51% of FAM157B | Family with sequence similarity 157, member B |
| 2q11.2 | 2 (13) | Gain | 4.71 | Intron of C2orf55 | Chromosome 2 open reading frame 55 |
| Xq22.3 | 2 (13) | Gain | 4.60 | Contained within IL1RAPL2 | Interleukin 1 receptor accessory protein-like 2 |
| 11q14.1 | 2 (13) | Gain | 4.57 | Intron of DLG2 | Discs large homolog 2 |
| 12q21.31 | 2 (13) | Gain | 4.51 | Intron of MGAT4C | Mannosyl-glycoprotein β-1,4-N-acetylglucosaminyltransferase, isozyme C |
| 2q24.3 | 2 (13) | Gain | 4.36 | Contained within SCN9A | Sodium channel, voltage-gated, type IX, α subunit |
| 12q21.32 | 2 (13) | Gain | 4.27 | Intron of KITLG | KIT ligand |
| 14q21.3 | 2 (13) | Gain | 4.26 | Contained within MDGA2 | MAM domain containing glycosylphosphatidylinositol anchor 2 |
| 12q13.3 | 2 (13) | Gain | 4.02 | TAC3 | Tachykinin 3 |
| 4p15.31 | 2 (13) | Gain | 4.00 | Intron of KCNIP4 | Kv channel interacting protein 4 |
| 3p14.2 | 2 (13) | Gain | 3.95 | Intron of FHIT | Fragile histidine triad gene |
| 10q11.21 | 2 (13) | Gain | 3.92 | Overlap with 54% of ZNF33B | Zinc finger protein 33B |
| 10p11.21 | 2 (13) | Gain | 3.91 | Contained within ANKRD30A | Ankyrin repeat domain 30A |
| 2p12 | 2 (13) | Gain | 3.85 | Intron of LRRTM4 | Leucine-rich repeat transmembrane neuronal 4 |
| 10q21.1 | 2 (13) | Gain | 3.81 | Intron of PRKG1 | Protein kinase, cGMP-dependent, type I |
| 13q14.2 | 2 (13) | Gain | 3.79 | Intron of CAB39L | Calcium binding protein 39-like |
| 1q44 | 2 (13) | Gain | 3.68 | Intron of KIF26B | Kinesin family member 26B |
| 18q12.3 | 2 (13) | Gain | 3.49 | Intron of RIT2 | Ras-like without CAAX 2 |
| 11p11.12 | 2 (13) | Gain | 3.34 | OR4A5 | Olfactory receptor family 4 subfamily A member 5 |
| 7p13 | 2 (13) | Gain | 3.10 | Contained within CAMK2B | Calcium/calmodulin-dependent protein kinase II β |
| Xq28 | 2 (13) | Gain | 2.91 | Overlap with 88% of IDH3G | Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial precursor |
| Xq28 | 2 (13) | Gain | 2.83 | Intron of F8 | Coagulation factor VIII precursor |
| 7p22.2 | 2 (13) | Gain | 2.73 | Intron of GNA12 | G protein alpha 12 |
| 8q24.3 | 2 (13) | Gain | 2.64 | CYP11B1 | Cytochrome P450 11B1, mitochondrial precursor |
| 8q24.3 | 2 (13) | Gain | 2.64 | C8orf33 | Chromosome 8 open reading frame 33 |
| 5p15.33 | 2 (13) | Gain | 2.61 | IRX4 | Iroquois homeobox 4 |
| 6q23.2 | 2 (13) | Loss | 0.84 | Contained within SGK1 | Serum/glucocorticoid-regulated kinase 1 |
| 2q11.2 | 2 (13) | Loss | 0.88 | Intron of NPAS2 | Neuronal PAS domain protein 2 |
| 3p22.1 | 2 (13) | Loss | 0.96 | Contained within CTNNB1 | Catenin (cadherin-associated protein), β 1 |
| 6q22.31 | 2 (13) | Loss | 1.00 | HEY2 | Hairy/enhancer-of-split related with YRPW motif 2 |
| 6q26 | 2 (13) | Loss | 1.01 | Contained within QKI | Quackin protein |
| 18q11.2 | 2 (13) | Loss | 1.10 | Contained within LAMA3 | Laminin subunit alpha-3 precursor |
| 6q21 | 2 (13) | Loss | 1.02 | Overlap with 70% of REV3L | DNA polymerase zeta catalytic subunit |
| 2p16.2-.1 | 2 (13) | Loss | 1.03 | Overlap with 50% of EML6 | Echinoderm microtubule-associated protein like 6 |
| 1q23.1 | 2 (13) | Loss | 1.12 | CD5L | CD5 antigen-like precursor |
| 6q23.3 | 2 (13) | Loss | 1.13 | Contained within KIAA1244 | |
| 1p36.11 | 2 (13) | Loss | 1.16 | Overlap with 60% of TMEM57 | Macoilin (transmembrane protein 57) |
| 11q23.2 | 2 (13) | Loss | 1.16 | FAM55D | Family with sequence similarity 55, member D |
| 18q12.2 | 2 (13) | Loss | 1.18 | Intron of FHOD3 | FH1/FH2 domain-containing protein 3 |
| 6q23.1 | 2 (13) | Loss | 1.29 | Contained within EPB41L2 | Erythrocyte membrane band 4.1-like protein 2 |
| 6q25.2 | 2 (13) | Loss | 1.31 | Overlap with 81% of RGS17 | Regulator of G protein signaling 17 |
| 1p33 | 2 (13) | Loss | 1.34 | STIL | SCL-interrupting locus protein |
| 6q26 | 2 (13) | Loss | 1.35 | Intron of PACRG | PARK2 coregulated |
| 6q25.1-.2 | 2 (13) | Loss | 1.36 | Overlap with 80% of SYNE1 | Synaptic nuclear envelope protein 1 |
Only CNAs involving one entire gene or contained within one gene or overlapping with more than 50% of one gene are reported.
Genes in bold: genes considered relevant for tumorigenesis or glucocorticoid production/effects. They include potential oncogenes and tumor suppressor genes, growth or transcription factors, cell differentiation markers, protein kinases (according to GSEA; see also Table W4), genes involved in steroidogenesis (underlined) or glucocorticoid regulation or in Wnt/β-catenin signaling.