Table 2. Candidates rare CNVs likely associated with malignancy.
| Chr | Start | End | CNV length (pb) | CNV type | Genes | Affected exons | Affected Pathway (KEGG/Wikipathways) | DAVID Disease Class | Network of Cancer genes annotation | KEGG/OMIM expanded disease annotation | DGV Frequency | AnnotSV ranking | Patients |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 6 | 31083803 | 31133824 | 50021 | DUP | CDSN, PSORS1C2, PSORS1C1, CCHCR1, TCF19, POU5F1 | 33 | Wnt Signaling Pathway and Pluripotency (POU5F1) | Cancer | (POU5F1) Oncogene | - | - | 4a | BC39 |
| 9 | 214510 | 340321 | 125811 | DUP | C9orf66, DOCK8 | 14 | Factors involved in megakaryocyte development and platelet production pathway (DOCK8) | Hematological | (DOCK8) Candidate cancer gene mutated in neuroblastomas [42] | (DOCK8) Autosomal dominant mental retardation / Hyper-IgE syndrome | 0.00322327 | 5b | BC40 |
| 12 | 88512261 | 88554006 | 41745 | DUP | CEP290, TMTC3 | 20 | Pathways in clear cell renal cell carcinoma (CEP290) | - | (TMTC3) A candidate cancer gene mutated in Pancreatic cancer [43] | (CEP290) Meckel syndrome /Joubert syndrome /Leber congenital amaurosis | - | 4 | BC19 |
| 17 | 43515225 | 44159908 | 644683 | DEL | PLEKHM1, CRHR1, SPPL2C, MAPT, STH, KANSL1 | 53 | MAPK Signaling Pathway (MAPT) | Cancer | (KANSL1) A candidate cancer gene mutated in Bladder cancer and in multiple other cancers [44, 45] | Koolen-De Vries syndrome /(CRHR1) breast, prostate, lung, colorectal, pancreatic, ovarian endometrial cancers/ sarcoma/ melanoma/lymphoma | - | 5 | BC37 |
| Notch Signaling Pathway (MAPT) | |||||||||||||
| Pathways Affected in Adenoid Cystic Carcinoma (KANSL) | |||||||||||||
| 17 | 43515225 | 44249509 | 734284 | DEL | PLEKHM1, CRHR1, SPPL2C, MAPT, STH, KANSL1 | 55 | MAPK Signaling Pathway (MAPT) | Cancer | (KANSL1) A candidate cancer gene mutated in Bladder cancer and in multiple other cancers [44, 45] | Koolen-De Vries syndrome /(CRHR1) breast, prostate, lung, colorectal, pancreatic, ovarian endometrial cancers/ sarcoma/ melanoma/lymphoma | - | 5 | BC39 |
| Notch Signaling Pathway (MAPT) | |||||||||||||
| Pathways Affected in Adenoid Cystic Carcinoma (KANSL1) | |||||||||||||
| 19 | 1461037 | 1483940 | 22903 | DEL | APC2, C19orf25, PCSK4 | 11 | (APC2) Wnt signaling pathway | Pharmacogenomic | - | (APC2) Colorectal cancer / Medulloblastoma | - | 4 | BC47 |
| Breast, Endometrial, Gastric and Colorectal pathways | |||||||||||||
| Chromosomal and microsatellite instability in colorectal cancer |
Abbreviations: DUP: duplication, DEL: deletion
a: Likely Pathogenic
b: Pathogenic; genes in bold: selected cancer genes.