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. Author manuscript; available in PMC: 2024 Aug 6.
Published in final edited form as: Mutat Res. 2021 Dec 14;824:111773. doi: 10.1016/j.mrfmmm.2021.111773

Table 1.

Mutation spectra highlights of tumors discussed in this report.

Tissue Mutation spectra1 References
2Pediatric adrenocortical carcinoma: mutations TP53, ATRX, CTNNB1. [42,44,45]
Adrenal gland 3Other studies: Chr19 amplification (CYP gene family), Chrlp and Chr7p loss: benign to malignant transition.
Osteosarcoma: mutations PI3K/mTOR, ADAM6, TP53, NBPF10, RB1,
Chondrosarcoma: mutations COL2A1, TP53, RB1, Hedgehog pathway, IDH1, PRMT5, IDH2.		 [48–54]
Bone 4COSU486 osteosarcoma,
chondrosarcoma, other rare subtypes: mutations TP53, SUFU, IDH2
Other studies: Osteosarcoma, mutation Chr6p12.3 amplification (COPS3, CCNE1, CDK4, MYC), TP53, RB1; Chondrosarcoma, IDH1, IDH2 mutations
Basal like breast cancer: mutations JAK2, IRAK2, CSMD1, NRK, MAP3K8, PTPRJ, WWTR1, TP53, MYCBP2, SNED1; deletions Chr5 (CTNNA1), Chr8 (NRG1), MECR; various translocations.
Breast tumor cell line: translocations t(4;11) (q32;q21) (MRE11 truncation); mutations apoptosis, MAPK signaling, cell adhesion, cytoskeleton organization and cell cycle.
Primary breast cancer: mutations TP53, GATA3, PIK3CA, MAP2K4, SMAD4, MLL2, MLL3, NCOR1; amplification ERRBB2, CCND1, MYC, MDM2, ZNF217, ZNF703; BRCA1/BRCA2 germline mutation (loss of 17q21 and 13q12).
Primary breast cancer: mutations AKT2, ARID1B, CASP8, CDKN1B, MAP3K1, MAP3K13, NCOR1, SMARCD1 and TBX3
Multifocal breast cancer: mutations TP53, PIK3CA, MAP3K1, PTEN, others.
Breast Breast cancers (various): mutations TP53, PIK3CA, MYC, CCND1, ERRBB2, RB1, GATA3, MAP3K1, MAP2K4, others.
COSU385 breast triple negative lobular cancer: mutations PIK3CA, TP53, RB1, PTEN, RP11–245C23.3, others; CNVs 1q trisomy, 4q monosomy, sub-clonal del 7, 13, 22q11, other re-arrangements that include MYC, HER2, BRCA1, BRCA2
COSU652: mutations PIK3CA, TP53, PTEN, RB1, ERRB2, RP11–245C23.3 others.
COSU668: mutations PIK3CA, RP11–245C23.3, TP53, others
Triple negative breast cancer: amplified 4q28.3, 2p, 3q24, 1q21.2, 10p, 12p11.1, 8q 20p11.22–20p11.21, 21q22.13, 6p22.1; deleted 1p36.23, 4q21.1 and 5q.
Primary breast tumors: amplified 17q11.2–12 (ERBB2).
Breast cancers (various): Chr17 centromere amplification (ERBB2), HER2 amplification.
Medulloblastoma: mutations KDM6A and other KDM members, inactivation of members that regulate the H3K27me3 histone mark, WNT signaling mutations, ZMYM3, CTNNB1; Deletion 9q34.14 (DDX31, AK8, TSC1); amplification OTX2.		 [55–63]
Central Nervous System Pediatric high-grade gliomas: mutations in genes that regulate H3K27me3, histone H3 genes H3F3A (H3.3) and HIST1H3B (H3.1), ATRX, TP53, NTRK1/2, RAS-PI3K, ACVR1.
COSU379 medulloblastoma SMO, BRAF, PIK3CA, TP53, RP11–286H14.8, FGFR1, PTEN, RP11–350N15.4, H3K27me3 dysregulation; germline TP53, PTCH1, APC, CREBBP		 [64–71]
Endometrium [72–76]
COSU677 (Uterine cancer, carcinosarcoma): mutations TP53, PTEN, KRAS, PIK3CA, RP11–245C23.3, various other cell adhesion and cell-cell interaction genes, signal transduction genes.
Type II EC and serous ovarian cancer: amplified 19q12 in.(CCNE1, URI) TCGA and ICGC study: CSMD3, TP53, APOB, others.
Uterine carcinosarcomas: amplified 19q13 in.(TGFBl).
Epithelial ovarian cancer: amplified 19p13.11 in. (MERIT40, ANKLE1)
Hematopoietic and Lymphoid Adult T-cell leukemia/lymphoma (ATL):
HTLV-1 integration; mutations CDKN2A, ATXN1, NF-kB signaling.		 [77–83]
Early T-cell precursor acute lymphoblastic leukemia (ETP ALL): RAS signaling
mutations (BRAF, JAK1/3, KRAS, NRAS FLT3, IGFR1), chromatin modification and remodeling (EZH2, EED, SUZ12, SETD2, EP300), other mutations specific to hematopoetic and lymphoid cell development, some novel mutations.
Pediatric B-acute lymphoblastic leukemia:
RAS signaling mutations (KRAS, NRAS, PTPN11, FLT3), epigenetic regulators (MLL2), cell cycle regulation (CDKN2A/B deletion, TP53 mutations), other pathways.
Chronic lymphocytic leukemia (CLL): mutations NOTCH1, MYD88, XPO1, KLHL6; deletions of 6q14q22, 13q14.
COSU340 (Chronic lymphocytic leukemia): mutations TP53, BRAF, KRAS, others
COSU440 (Burkitt lymphomas): translocations t(8;14)(q24;q32), t(2;8), t (8;22); mutations ID3, SMARCA4, DDX3X, TP53, BRAF, MYC, RHOA, FBXO11, others.
Other ATL studies: TP53, FAS, CCR4, NOTCH1, ZEB1, and CDKN2A.
Large Intestine Colorectal adenocarcinoma: translocations VTI1A-TCFL2 (TCF4) fusion, chr8–20, chr5–11; deletions EGFR, PTEN; rearrangements MACROD2, A2BP1, FHIT, IMMP2L; mutations TP53, KRAS, APC. [84]
Liver Hepatocellular carcinoma: multiple tumors with hepatitis B (HBV) and C (HCV) viral infections, two multicentric tumors sets: mutations TP53, CTNNB1, ATM, ERRFI1, WWP1, ZIC3, chromatin regulators ARID1A, ARID1B, ARID2, MLL, MLL3, others; HBV integration in TERT region
COSU322 (Viral associated hepatocellular carcinoma (Japanese cohort)): common mutations likely pathogenic TP53, RB1, PIK3CA, KRAS, NRAS, EGFR2, others including CSMD1/3, CTNNA2/3, LSAMP, CTNAP2, PCDH15, ALK, RBFOX1, chromatin remodeler HDAC9.		 [85]
Lung Small cell lung cancer (cell line, smoking):
mutations TP53, RB1, MLL2; rearrangements 1p32–36, 4q25–28, 3q, 5q; fusions, PVT1-CHD7 CREBBP2-BTBD12.
Small cell lung cancer (surgical resection): mutations PTEN, PIK3CA, TP53, RB1, SLIT2,
CREBBP, EP300, others; deletions 3p,13q (RB1 region), 17p (TP53 region); amplifications 3q (SOX2 region), 8p12 (FGFR1 region), 19q12 (CCNE1 region)
Primary and metastatic lung adenocarcinomas (NSCLC): various alterations of IQGAP3; overexpression APOBEC1, APOBEC3B, APOBEC3C, APOBEC3F; mutation BRAF, TP53, EGFR, LRP1B, KRAS, PTPRD, STK11, SMAD2, PIK3CA, BRAF, FLT1, RHPN2, GLI3, MRC2; rearrangements 1q, 3q, 5p, 7p/q, 8q, 14q, 16p, 17q, 20q; deletions 3p, 4q, 6q, 8p, 9p, 12q, 13q, 15q, 17p, 18q.		 [86–88]
Pancreas COSU328, 382 (Ductal adenocarcinoma): mutations KRAS, TP53, SMAD4, CDKN2A, PIK3CA, SMAD4.
COSU586 (endocrine neoplasms): MEN1, BRAF, CDKN2A.		 [89]
Prostate COSU661 (rare pancreatic tumors): TP53, PTEN.
Primary prostate cancer: mutations SPTA1, SPOP, TMPRSS2, chromatin modifiers CHD1, CHD5, HDAC9; re-arrangements involving CHD1, PTEN, MAGI2, CSMD3, ZNF407, TP53, MAP2K4, ABL1; fusion TMPRSS2-ERG.
Aggressive prostate tumors: BRCA2, ERG, TMPRSS2, KMT2C, TFDP1, VPS13B, FOXA1, PARK2, PTEN, SPOP, TP53.
COSU534 (early onset prostate cancer):
TP53, PTEN, BRAF, SLC2A2.
COSU537, 538, 675 (prostate adenocarcinoma): PIK3CA, RP11245C23.3,
TP53, BCL10, AR, PTEN, CTD-2350C19.1, BRAF, XPC, SARM1, SLC46A1, CTD-2350C19.2, KRAS.
COLO-829 cell line (metastatic malignant melanoma): mutations, SPDEF, MMP28, UVRAG, BRAF; deletion, PTEN; rearrangements MAGI2, FHIT, WWOX, FRA3B, FRA16D; amplification chr3 (RARB, TOP2B, NGLY1, OXSM), chr15 (MKRN3, NDN)		 [90,91]
Skin Metastatic melanoma: mutation, BRAF, NRAS, KIT; rearrangements, FHIT,
MACROD2, CSMD1, PTEN, MAGI2, A2BP1, ETV1, PREX2.
COSU656 (skin adenocarcinoma):
mutations BRAF, NRAS, KRAS, MARCh9, TSPAN31 CDK4, CSDE1.		 [92,93]
Soft Tissue Rhabdomyosarcoma: mutations, HRAS, KRAS, NRAS, FGFR4, PIK3CA, NF1, FBXW7, BCOR, TP53, CTNNB1, BUB1B, FOXM1, CCND1, CCND2, BCOR, PTPN11, ATM, ZNF350, TRPC4AP, FOXO1, ARID1A; translocations, t(2;13) (PAX3-FOXO1), t(1:13) (PAX7-FOXO1), chr2q (PAX3-INO80D); other structural variations affecting MIR17HG, CNR1, CDKN2A, ERBB4, RPTOR, FRS2, CACNA1A, NRG1, FOXP2; CNVs: LOH 11p15.5 (IGF2); amplification 12q13-q14 (CDK4), 12q5 (FRS2, MDM2), 2p24 (MYCN), PAX7-FOXO1, 13q21–32 (MIR17 G); homozygous deletion, CDKN2A. [94]
Upper Aerodigestive Tract Head and neck squamous cell carcinoma: mutations, PTEN, PIK3A, TP53, CDKN2A, HRAS, NOTCH1, NOTCH2, NOTCH3, IRF6, TP63, SYNE1, SYNE2, RIMS2, PCLO, CASP8, DDX3X, PRDM9, EZH2; deletion, CDKN2A, NOTCH3; amplification, CCND1, MYC, EGFR, ERBB2, CCNE1; [95]
Urinary tract Bladder cancers of various stages:
mutations, CDKN1A, TP53, FGFR3, ARID1A, KDM6A, STAG2, B3GNTN9, FAT1, MLL2/3, PIK3CA, others; amplification 1q, 3q, 8q, chr11q12–3 (CCND1), chr4p16.3 (FGFR3), chr12 (MDM2, NUP107, CPM, CPSF6, LYZ, YEATS4, FRS2); deletion chr9, chr9p21.3 (CDKN2A), chr4p16.3 (FGFR3), PPARGC1A, RFX3, FAT1; chromothripsis 3p, 5q, 6p, X;		 [96]
1

Highlited are some of the most likely mutated genes in the indicated cancers. Although other mutations exist, these are mutations specific to these cancers reported in the referenced articles. Please see referenced studies for more in-depth analysis.

2

These references (bold) include the main studies used for the graphs and analysis in this paper. Please see Supplementary Table S2 for the list of all studies used for the analysis in this paper.

3

These references (italicized) represent other studies characterizing similar cancers.