Table 1 Top NMD-affected genes in 24 cancers.

From: A pan-cancer genome-wide analysis reveals tumour dependencies by induction of nonsense-mediated decay

Cancer type (#samples)

Top genes that frequently harbour NMD-elicit mutations (number of sample with its NMD mutants)

Adrenocortical (91)

TP53 (6), DCP1A(5), MEN1 (5)

Bladder urothelial (396)

KDM6A (69), ARID1A (62), TP53 (55), RB1 (48), STAG2 (39), TTN† (31), EP300 (23), FAT1 (23), MUC16† (23), CDKN1A (22)

Breast-invasive (982)

TP53 (93), MAP3K1 (68), CDH1 (64)

Cervical and endocervical (194)

MUC4† (14), TTN† (12)

Colon (270)

TTN† (49), APC (45), RNF43 (31), TP53 (26), BMPR2 (20), ZC3H13 (18), SYNE1 (17), ATM (16), ARID1A (14), MBD6 (14), MUC16† (14), RYR2 (14)

Diffuse large B-cell lymphoma (48)

TNFAIP3 (5), CIITA (4), ARID1A (3), HLA-A (3), SETD1B (3), SPEN (3), TET2 (3)

Oesophageal (184)

TP53 (48), TTN† (11)

Glioblastoma

ARHGAP5 (50), NF1 (17)

Head and neck squamous cell (512)

TP53 (114), FAT1 (86), NSD1 (42), CDKN2A (41), NOTCH1 (33), TTN† (29)

Kidney clear cell (213)

PBRM1 (62), CDC27 (18), FAM151A (17), OVGP1 (17), PHACTR1 (17), VHL (17), FANCE (16), DNMT1 (15), GLI1 (15), MSI1 (14)

Brain lower-grade glioma (516)

ATRX (45)

Liver hepatocellular (373)

TP53 (32), APOB (19)

Lung (543)

TP53 (65), TTN† (45), CSMD3 (33), MUC16† (33), LRP1B (31), STK11 (30), XIRP2 (28)

Lung squamous cell (178)

TP53 (32), TTN† (26), CSMD3 (19), MUC16† (12), FAT1 (11)

Ovarian (374)

TP53 (42)

Pancreatic (150)

TP53 (26), SMAD4 (13), CDKN2A (11)

Rectum (116)

APC (20), TTN† (16), TP53 (15), FBXW7 (9), MAL2 (6), VPS13C (6)

Sarcoma (259)

ATRX (30), TP53 (24), RB1 (21)

Skin cutaneous melanoma (472)

TTN† (102), NF1 (49), DNAH5† (44), ARID2 (37), MUC16† (35), LRP1B (34), DNAH7 (26), TP53 (26), DCC (25), DNAH8 (24)

Stomach (289)

ARID1A (57), RNF43 (56), TTN† (55), TP53 (44), BZRAP1 (33), XYLT2 (27), LARP4B (23), MBD6 (23), ZC3H13 (22), PLEKHA6 (19)

Uterine corpus endometrioid (248)

PTEN (96), TTN† (66), ARID1A (53), PIK3R1 (44), CTCF (30), MUC16† (21), FAT1 (20), ZFHX3 (20), DNAH11† (18), MKI67 (18)

  1. NMD, nonsense-mediated decay.
  2. Note: only the top 10 genes most frequently affected by NMD-elicit mutations are shown for each cancer. Three cancers (KIRP, PRAD and THCA) do not have top NMD-affected genes defined in Methods.
  3. COSMIC-annotated cancer drivers.
  4. †Potential false-positive cancer-associated genes.
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