Table 1.
Copy number alterations differentially found in FaDu resistant compared with FaDu parental cell line by whole exome sequencing and Nanostring platform.
| Chromosome | Event | Cytoband | Cancer Gene | Driver Statement by CGI |
|---|---|---|---|---|
| chr 17 | Deletion | p13.3–p11.2 | MAP2K4 | known in: PA; BRCA; COREAD |
| chr 13 | Deletion | q31.1–q32.2 | GPC5 | predicted passenger |
| chr 20 | Deletion | q11.22–q13.33 | EEF1A2 | predicted passenger |
| chr 17 | Deletion | p13.3–p11.2 | MAPK7 | predicted passenger |
| chr 17 | Deletion | p13.3–p11.2 | TP53 | known in: BCL; THYM |
| chr 11 | Deletion | p15.5–p12 | WT1 | known in: WT; DSRCT |
| chr 10 | Deletion | q22.3–q26.3 | PTEN | known in: G; PRAD; ED; CM; TH; BRCA; L; OV; PA |
| chr 7 | Deletion | p14.3–p12.1 | IKZF1 | known in: ALL; DLBCL |
| chr 10 | Deletion | q22.3–q26.3 | SUFU | known in: MB |
| chr 16 | Deletion | q24.3 | FANCA | known in: AML; LK; PRAD |
| chr 17 | Deletion | p13.3–p11.2 | FLCN | known in: TH |
| chr 17 | Deletion | q11.1–q23.1 | NF1 | known in: NF; G; MPN; CM; PLEN; HNC; SG; LK |
| chr 17 | Deletion | q11.1–q23.1 | SUZ12 | known in: CANCER |
| chr 17 | Deletion | q11.1–q23.1 | BRCA1 | known in: OV; BRCA |
| chr 12 | High Amplification | p12.1–q11 | KRAS | predicted driver |
| chr 14 | Amplification | q12–q32.33 | NKX2-1 | known in: NSCLC |
| chr 14 | High Amplification | q11.2–q12 | BCL2L2 | predicted passenger |
| chr 5 | High Amplification | p13.3–q11.2 | SKP2 | predicted passenger |
| chr 22 | Amplification | q11.1–q12.1 | CRKL | predicted passenger |
| chr 11 | High Amplification | q22.1–q22.3 | YAP1, BIRC2 | predicted passenger |
| chr 7 | High Amplification | q36.1–q36.3 | SHH | predicted passenger |
| chr 6 | Amplification | q16.2–q27 | MYB | predicted driver |
| chr 6 | Amplification | q16.2–q27 | MAP3K5 | predicted passenger |
| chr 1 | Amplification | q32.1–q32.2 | MDM4 | known in: GBM; BLCA; RB; S |
| chr 12 | Amplification | q14.3–q24.33 | MDM2, HMGA2 | known in: S; G; COREAD; LIP |
| chr 9 | Amplification | p24.2–p22.1 | JAK2 | known in: BRCA |
| chr 9 | Amplification | p24.2–p22.1 | CD274 | known in: BCC |
| chr 8 | Amplification | q12.1–q24.3 | MYC | known in: BLY; CLL; NB; COREAD; MYMA; PRAD |
| chr 5 | High Amplification | p13.3–q11.2 | RICTOR | known in: L |
| chr 6 | Amplification | q16.2–q27 | ESR1 | known in: UCEC; BRCA; OV |
| chr 12 | Amplification | p13.33–p12.1 | CCND2 | known in: L |
| chr 12 | Amplification | q14.3–q24.33 | FRS2 | known in: LIP |
| chr 14 | Amplification | q12–q32.33 | FOXA1 | Known in: COREAD |
| chr 14 | Amplification | q12–q32.33 | PAX9 | Known in: NSCLC |
| chr 14 | Amplification | q12–q32.33 | NKX2-8 | predicted passenger |
CGI: Cancer Genome interpreter; PA: Pancreas; BRCA: Breast adenocarcinoma; COREAD: Colorectal adenocarcinoma; BCL: B cell lymphoma; THYM: Thymic; WT: Wilms Tumor; G: Glioma; TH: Thyroid; DSRCT: Desmoplastic small round cell Tumor; PRAD: Prostate Adenocarcinoma; ED: Endometrium; CM: Cutaneous melanoma; L: Lung; OV: Ovary; ALL: Acute Lymphoblastic leukemia; DLBCL: Diffuse Large B cell Lymphoma; MB: Medulloblastoma; AML: Acute Myeloid Leukemia; LK: Leukemia; NF: Neurofibroma; MPN: Malignant Peripheral nerve sheath Tumor; PLEN: Plexiform Neurofibroma; HNC: Head and Neck; SG: Salivary Glands; NSCLC: Non-small lung cancer; BLCA: Bladder; GBM: Glioblastoma multiforme; RB: Retinoblastoma; S: Sarcoma; LIP: Liposarcoma; BCC: Basal cell carcinoma; BLY: Burkitt Lymphoma; CLL: Chronic Lymphocytic Leukemia; NB: Neuroblastoma; MYMA: Myeloma; UCEC: Uterine Corpus Endometroid Carcinoma.