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Table 3 The number of mutation-bearing CSF samples (total number of investigated CSF samples: 45) per cancer-associated gene (total number of investigated genes: 143)

From: Detection of genes mutations in cerebrospinal fluid circulating tumor DNA from neoplastic meningitis patients using next generation sequencing

Genes NM (Our cohort) Lung cancer (COSMIC database) p-value
ABL1 1/45 (2.22%) 64/5425 (1.18%) 0.417
AKT1 1/45 (2.22%) 63/10898 (0.58%) 0.232
APC 17/45 (37.78%) 200/5979 (3.35%) < 0.001
ATM 3/45 (6.67%) 288/5300 (5.43%) 0.974
BAP1 1/45 (2.22%) 51/4574 (1.11%) 0.401
BCL9 1/45 (2.22%) 0/2603 (0.00%) 0.017
BRAF 4/45 (8.89%) 596/26989 (2.21%) 0.033
BRCA1 2/45 (4.44%) 122/4786 (2.55%) 0.744
BRCA2 7/45 (15.56%) 156/4753 (3.28%) < 0.001
CBL 5/45 (11.11%) 69/4871 (1.42%) 0.001
CDH1 1/45 (2.22%) 50/5014 (1.00%) 0.367
CDK4 1/45 (2.22%) 11/4572 (0.24%) 0.111
CDKN2A 14/45 (31.11%) 558/7621 (7.32%) < 0.001
CSF1R 3/45 (6.67%) 82/4775 (1.72%) 0.044
CTNNB1 3/45 (6.67%) 157/6679 (2.35%) 0.161
DDR2 2/45 (4.44%) 139/6918 (2.01%) 0.231
DNMT3A 2/45 (4.44%) 104/4644 (2.24%) 0.627
EGFR 39/45 (86.67%) 26,099/98618 (26.46%) < 0.001
ESR1 1/45 (2.22%) 64/4425 (1.45%) 0.484
FBXW7 1/45 (2.22%) 131/5455 (2.4%) 1.000
FGFR2 1/45 (2.22%) 64/5603 (1.14%) 0.407
FGFR3 1/45 (2.22%) 65/6466 (1.01%) 0.369
FGFR4 1/45 (2.22%) 57/4569 (1.25%) 0.436
FLT3 10/45 (22.22%) 103/5948 (1.73%) < 0.001
GNA11 1/45 (2.22%) 18/4780 (0.38%) 0.163
GNAQ 14/45 (31.11%) 24/5036 (0.48%) < 0.001
HRAS 2/45 (4.44%) 33/7105 (0.46%) 0.020
IFITM1 2/45 (4.44%) 3/2468 (0.12%) 0.003
JAK2 1/45 (2.22%) 102/6912 (1.48%) 0.490
JAK3 2/45 (4.44%) 88/5176 (1.7%) 0.181
KDR 5/45 (11.11%) 218/5112 (4.26%) 0.060
KIT 3/45 (6.67%) 120/6695 (1.79%) 0.048
KRAS 2/45 (4.44%) 6809/42506 (16.02%) 0.034
MAP2K1 3/45 (6.67%) 58/9328 (0.62%) 0.003
MAP2K2 1/45 (2.22%) 23/4529 (0.51%) 0.212
MLH1 5/45 (11.11%) 36/4969 (0.72%) < 0.001
MPL 2/45 (4.44%) 39/4946 (0.79%) 0.052
MSH2 3/45 (6.67%) 54/4595 (1.18%) 0.017
MYCN 1/45 (2.22%) 34/4544 (0.75%) 0.293
NF1 1/45 (2.22%) 303/4814 (6.29%) 0.416
NF2 2/45 (4.44%) 51/4865 (1.05%) 0.084
NFE2L2 1/45 (2.22%) 212/5626 (3.77%) 0.881
NOTCH1 11/45 (24.44%) 197/6456 (3.05%) < 0.001
NRAS 4/45 (8.89%) 128/16010 (0.8%) 0.001
PIK3CA 2/45 (4.44%) 719/16029 (4.49%) 1.000
PTCH1 7/45 (15.56%) 86/5107 (1.68%) < 0.001
PTEN 27/45 (60.00%) 233/8576 (2.72%) < 0.001
PTPN11 2/45 (4.44%) 54/5910 (0.91%) 0.066
RB1 2/45 (4.44%) 369/5651 (6.53%) 0.794
RET 3/45 (6.67%) 142/5818 (2.44%) 0.181
SMARCB1 1/45 (2.22%) 31/4968 (0.62%) 0.251
SMO 2/45 (4.44%) 72/5105 (1.41%) 0.136
STK11 2/45 (4.44%) 594/8028 (7.4%) 0.646
TET2 18/45 (40.00%) 90/4349 (2.07%) < 0.001
TP53 38/45 (84.44%) 4456/11831 (37.66%) < 0.001
TSC1 3/45 (6.67%) 70/4775 (1.47%) 0.030
TSC2 4/45 (8.89%) 125/4800 (2.6%) 0.032
VHL 9/45 (20.00%) 23/5332 (0.43%) < 0.001
WT1 2/45 (4.44%) 62/4634 (1.34%) 0.125
  1. The differences between the mutation rates observed in our cohort and those noted in the COSMIC database (https://cancer.sanger.ac.uk) were statistically compared. Significant p-values are marked with bold text