Gender
## Metastatic.yes.no Gender N percent
## 1: yes f 33 49.25
## 2: yes m 34 50.75
## 3: no f 63 60.00
## 4: no m 42 40.00
Number of Patients that are BRAF mutant
## BRAF N percent
## 1: wild type 31 46.27
## 2: unknown 30 44.78
## 3: mutation (V600E) 5 7.46
## 4: mutation (D594N) 1 1.49
## 5: NA 105 156.72
Number of Patients that are NRAS mutant
## NRAS N percent
## 1: wild type 16 23.88
## 2: unknown 42 62.69
## 3: mutation (G12D) 1 1.49
## 4: mutation (G13D) 1 1.49
## 5: mutation (G12R) 1 1.49
## 6: mutation (Q61R) 2 2.99
## 7: mutation (G13V) 1 1.49
## 8: mutation (G13D, E63G) 1 1.49
## 9: mutation (Q61K) 1 1.49
## 10: mutation (G12C) 1 1.49
## 11: NA 105 156.72
Number of Patients that are cKIT mutant
## c.KIT..for.exons.9.11.13.17.18. N percent
## 1: mutation (Exon 13) 1 1.49
## 2: wild type 16 23.88
## 3: mutation (pM541L) 1 1.49
## 4: mutation (11,13) 1 1.49
## 5: unknown 46 68.66
## 6: mutation (L576P) 1 1.49
## 7: mutation (K642E) 1 1.49
## 8: NA 105 156.72
Number of Patients for Digitum vs Planta Palma
## Digitum.versus.Planta.Palma Metastatic.yes.no N percent
## 1: Dig I yes 19 28.36
## 2: Dig II yes 5 7.46
## 3: planta yes 35 52.24
## 4: Dig IV yes 1 1.49
## 5: Dig III yes 5 7.46
## 6: Dig V yes 2 2.99
## 7: Dig III no 5 4.76
## 8: Dig I no 33 31.43
## 9: planta no 52 49.52
## 10: palm no 3 2.86
## 11: Dig II no 6 5.71
## 12: Dig V no 5 4.76
## 13: Dig IV no 1 0.95
T staging
## T_stage Metastatic.yes.no N percent
## 1: T2 yes 7 10.45
## 2: T3 yes 27 40.30
## 3: T4 yes 25 37.31
## 4: T1 yes 5 7.46
## 5: unknown yes 3 4.48
## 6: T2 no 27 25.71
## 7: T1 no 33 31.43
## 8: T3 no 22 20.95
## 9: in situ no 18 17.14
## 10: T4 no 4 3.81
## 11: unknown no 1 0.95
Ulceration
## Ulceration Metastatic.yes.no N percent
## 1: yes yes 33 49.25
## 2: no yes 26 38.81
## 3: unknown yes 8 11.94
## 4: no no 45 42.86
## 5: unknown no 22 20.95
## 6: not applicable no 18 17.14
## 7: yes no 20 19.05
Sentinel Lymph node biopsy
## Sentinel.lymph.node.biopsy..SLNB. Metastatic.yes.no N percent
## 1: positive yes 27 40.30
## 2: not performed yes 25 37.31
## 3: negative yes 15 22.39
## 4: negative no 50 47.62
## 5: not performed no 55 52.38
Overall survival
Overall survival mets versus no mets
calculate overall survival since first distant met
calculate overall survival for stage iv patients
analysis for clinical benefit and systemic drug
## Clinical.benefit..cancer.shrinks.or.remains.stable.
## First.systemic.treatment no unknown yes
## Chemotherapy 9 1 7
## Immunotherapy 8 3 7
## none/others 0 0 1
## Others 0 0 5
clinical benefit, time to next treatment, PFS
## Clinical.benefit..cancer.shrinks.or.remains.stable.
## First.systemic.treatment no unknown yes
## Chemotherapy 9 1 7
## Immunotherapy 8 3 7
## none/others 0 0 1
## Others 0 0 5
## First.systemic.treatment V1
## 1: Chemotherapy 88.94118 days
## 2: Immunotherapy 102.72222 days
## 3: none NA days
## 4: Others 259.20000 days
## 5: none/others 0.00000 days
## 6: NA NA days
## first_pfs
## First.systemic.treatment none progression unknown
## Chemotherapy 0 16 1
## Immunotherapy 4 12 2
## none/others 0 0 1
## Others 0 5 0
Second line
## Clinical.benefit..cancer.shrinks.or.remains.stable..1
## Second.line.therapy no unknown yes
## Chemotherapy 5 2 3
## Immunotherapy 6 0 4
## none 0 0 1
## Others 3 0 6
## Second.line.therapy V1
## 1: Others 65.66667 days
## 2: Chemotherapy 72.10000 days
## 3: Immunotherapy 94.70000 days
## 4: none NA days
## 5: Radiotherapy Brain (none systemic) NA days
## 6: NA NA days
## second_pfs
## Second.line.therapy none progression unknown
## Chemotherapy 0 8 2
## Immunotherapy 1 9 0
## none 1 0 0
## Others 1 6 2
Third line
## Clinical.benefit..cancer.shrinks.or.remains.stable..2
## Third.line.therapy no unknown yes
## Chemotherapy 2 2 1
## Immunotherapy 3 1 0
## Others 2 0 2
## Third.line.therapy V1
## 1: Immunotherapy 62.00 days
## 2: none NA days
## 3: Chemotherapy 63.40 days
## 4: Others 314.75 days
## 5: none (Interferon) NA days
## 6: no NA days
## 7: NA NA days
## third_pfs
## Third.line.therapy progression unknown
## Chemotherapy 1 4
## Immunotherapy 3 1
## Others 4 0
Fourth line
## Clinical.benefit..cancer.shrinks.or.remains.stable..3
## Fourth.line.therapy no unknown yes
## Chemotherapy 1 1 0
## Immunotherapy 1 0 0
## Others 2 0 1
## Fourth.line.therapy V1
## 1: Others 176.3333 days
## 2: none NA days
## 3: Chemotherapy 24.5000 days
## 4: Immunotherapy 21.0000 days
## 5: NA NA days
## fourth_pfs
## Fourth.line.therapy progression unknown
## Chemotherapy 1 1
## Immunotherapy 1 0
## Others 2 1
Fifth line
## Clinical.benefit..cancer.shrinks.or.remains.stable..4
## Fifth.line.therapy no unknown yes
## Chemotherapy 1 0 1
## Others 0 1 0
## Fifth.line.therapy V1
## 1: NA NA days
## 2: Chemotherapy 86.5 days
## 3: Others 8.0 days
## fifth_pfs
## Fifth.line.therapy progression unknown
## Chemotherapy 2 0
## Others 0 1
Sixth line
## Clinical.benefit..cancer.shrinks.or.remains.stable..5
## Sixth.line.therapy unknown
## Chemotherapy 1
## Sixth.line.therapy V1
## 1: NA NA days
## 2: Chemotherapy 24 days
## sixth_pfs
## Sixth.line.therapy unknown
## Chemotherapy 1
ipi then chemo and ipi
## , , First.systemic.treatment = Chemotherapy
##
## Clinical.benefit..cancer.shrinks.or.remains.stable..1
## Second.line.therapy no unknown yes
## Chemotherapy 1 1 2
## Immunotherapy 4 0 0
## none 0 0 0
## Others 2 0 3
##
## , , First.systemic.treatment = Immunotherapy
##
## Clinical.benefit..cancer.shrinks.or.remains.stable..1
## Second.line.therapy no unknown yes
## Chemotherapy 3 1 1
## Immunotherapy 1 0 3
## none 0 0 0
## Others 1 0 2
##
## , , First.systemic.treatment = Others
##
## Clinical.benefit..cancer.shrinks.or.remains.stable..1
## Second.line.therapy no unknown yes
## Chemotherapy 1 0 0
## Immunotherapy 1 0 1
## none 0 0 1
## Others 0 0 1
## First.systemic.treatment Second.line.therapy
## 1: Chemotherapy Others
## 2: Immunotherapy Chemotherapy
## 3: Immunotherapy Immunotherapy
## 4: none none
## 5: Others Others
## 6: Chemotherapy Immunotherapy
## 7: Immunotherapy none
## 8: Chemotherapy Chemotherapy
## 9: Chemotherapy none
## 10: Immunotherapy Others
## 11: Others Chemotherapy
## 12: Others none
## 13: Others Immunotherapy
## 14: none/others none
## 15: Immunotherapy Radiotherapy Brain (none systemic)
## 16: NA NA
## V1
## 1: 82.40000 days
## 2: 71.20000 days
## 3: 147.75000 days
## 4: NA days
## 5: 42.00000 days
## 6: 68.00000 days
## 7: NA days
## 8: 84.25000 days
## 9: NA days
## 10: 45.66667 days
## 11: 28.00000 days
## 12: 0.00000 days
## 13: 42.00000 days
## 14: NA days
## 15: NA days
## 16: NA days
Percentage of secondary therapies
## Second.line.therapy N
## 1: Others 9
## 2: Chemotherapy 10
## 3: Immunotherapy 10
## 4: none 37
## 5: Radiotherapy Brain (none systemic) 1
## 6: NA 105
## Second.line.therapy
## First.systemic.treatment Chemotherapy Immunotherapy none Others
## Chemotherapy 4 4 4 5
## Immunotherapy 5 4 5 3
## none 0 0 26 0
## none/others 0 0 1 0
## Others 1 2 1 1
## Second.line.therapy
## First.systemic.treatment Radiotherapy Brain (none systemic)
## Chemotherapy 0
## Immunotherapy 1
## none 0
## none/others 0
## Others 0
shortest and longets time for first treatment
## First.systemic.treatment V1
## 1: Chemotherapy 14 days
## 2: Immunotherapy 0 days
## 3: none NA days
## 4: Others 37 days
## 5: none/others 0 days
## 6: NA NA days
## First.systemic.treatment V1
## 1: Chemotherapy 244 days
## 2: Immunotherapy 1050 days
## 3: none NA days
## 4: Others 370 days
## 5: none/others 0 days
## 6: NA NA days
not enough patients to do MEK analysis
calculate overall survival for SLNB
calculate overall survival for ulceration
calculate overall survival for T_stage
calculate overall survival for SLNB negative and mets
SLNB who get mets
## , , vital_status2 = 0
##
## Sentinel.lymph.node.biopsy..SLNB.
## Metastatic.yes.no negative not performed positive
## no 49 45 0
## yes 5 6 16
##
## , , vital_status2 = 1
##
## Sentinel.lymph.node.biopsy..SLNB.
## Metastatic.yes.no negative not performed positive
## no 1 10 0
## yes 10 19 11
organ mets first diagnosis
## Organ.metastases.at.first.diagnosis....0..1..2..3...4. N
## 1: 0 64
## 2: 1 2
## 3: ?4 1
## 4: NA 105
Organ mets at last followup or death
## Organs N percent
## 1: 2 12 17.91
## 2: ?4 14 20.90
## 3: 0 27 40.30
## 4: 3 6 8.96
## 5: 1 8 11.94
## 6: NA 105 156.72
number of lung mets
## lung.metastases.at.death.last.followup N percent
## 1: yes 30 44.78
## 2: no 37 55.22
## 3: NA 105 156.72
number of liver mets
## liver.metastases.at.death.last.followup N percent
## 1: no 42 62.69
## 2: yes 25 37.31
## 3: NA 105 156.72
number of brain mets
## brain.metastases.at.death.last.followup N percent
## 1: yes 12 17.91
## 2: no 55 82.09
## 3: NA 105 156.72
number of bone mets
## bone.metastases.at.death.last.followup N percent
## 1: no 45 67.16
## 2: yes 22 32.84
## 3: NA 105 156.72
## exact.localisation.of.bone.metastases N
## 1: NA 150
## 2: spine, rib, glenoid, acetabulum 1
## 3: rib 1
## 4: spine 4
## 5: spine, os ileum 1
## 6: spine, rib 2
## 7: spine, os ileum, sacrum, scapula, glenoid 1
## 8: rib, scapula 1
## 9: os sacrum 2
## 10: spine, scapula, tibia, femur, acetabulum, glenoid 1
## 11: spine, os ileum, rib, sternum 1
## 12: rib, sternum, os ileum, jaw 1
## 13: femur 2
## 14: spine, scapula 1
## 15: os ileum 1
## 16: spine, os sacrum, rib, femur 1
## 17: os ischiadicum 1
## patients.with.bone.metastases..number.of.affected.regions N
## 1: NA 150
## 2: 4 4
## 3: 1 11
## 4: 2 5
## 5: 5 1
## 6: 6 1
number of visceral mets
## other.visceral.metastases.at.death.last.followup N percent
## 1: no 49 73.13
## 2: yes 18 26.87
## 3: NA 105 156.72
number of other mets
## Other_mets N percent
## 1: no 66 98.51
## 2: yes 1 1.49
## 3: NA 105 156.72
number of distant mets
## Distant_mets N percent
## 1: yes 41 61.19
## 2: no 26 38.81
## 3: NA 105 156.72
Stage 3 patients with lymph node mets and/or intransit mets
## StageIII_mets N percent
## 1: NA 147 588
## 2: Lymphknoten (Nxb) 5 20
## 3: Lymphknoten (Nxa) 10 40
## 4: both, mit Lymphknoten (Nxb) 5 20
## 5: Intransit 3 12
## 6: both, mit Lymphknoten (Nxa) 2 8
Stage 4 patients with lymph node mets and/or intransit mets
## StageIV_mets N percent
## 1: both 7 16.67
## 2: both, mit Lymphknoten (Nxa) 4 9.52
## 3: NA 130 309.52
## 4: Lymphknoten (Nxb) 15 35.71
## 5: Intransit 2 4.76
## 6: SLNB not performed, then systemic met 3 7.14
## 7: none 1 2.38
## 8: both, mit Lymphknoten (Nxb) 10 23.81
looking at SLNB
nothing significant
## term estimate std.error
## 1 (Intercept) -16.50551978 2215.1226641
## 2 T_stageT1 15.56779461 2215.1227669
## 3 T_stageT2 16.51213801 2215.1225947
## 4 T_stageT3 17.35338477 2215.1226549
## 5 T_stageT4 19.27874060 2215.1228509
## 6 T_stageunknown -0.35189530 4534.1076062
## 7 Genderm -0.05458158 0.5712228
## 8 Ulcerationunknown -0.37017416 0.9826386
## 9 Ulcerationyes -0.70865341 0.8070031
## 10 Digitum.versus.Planta.PalmaDig II 1.13735719 1.5311256
## 11 Digitum.versus.Planta.PalmaDig III 0.89603488 1.3784016
## 12 Digitum.versus.Planta.PalmaDig IV 16.58144763 3956.1805797
## 13 Digitum.versus.Planta.PalmaDig V -16.29233549 2746.4482298
## 14 Digitum.versus.Planta.Palmapalm -15.78408676 3956.1804626
## 15 Digitum.versus.Planta.Palmaplanta -1.88162211 0.7958618
## 16 Primary.tumor.sitehand -1.73401838 1.0514469
## statistic p.value
## 1 -7.451289e-03 0.99405479
## 2 7.027960e-03 0.99439255
## 3 7.454277e-03 0.99405240
## 4 7.834051e-03 0.99374940
## 5 8.703238e-03 0.99305591
## 6 -7.761071e-05 0.99993808
## 7 -9.555218e-02 0.92387625
## 8 -3.767144e-01 0.70638583
## 9 -8.781297e-01 0.37987333
## 10 7.428242e-01 0.45758810
## 11 6.500536e-01 0.51565762
## 12 4.191277e-03 0.99665585
## 13 -5.932147e-03 0.99526686
## 14 -3.989729e-03 0.99681667
## 15 -2.364257e+00 0.01806626
## 16 -1.649174e+00 0.09911208
calculate overall survival for cKit patients
Interferon
## Interferon N percent
## 1: no 52 77.61
## 2: yes 15 22.39
## 3: NA 105 156.72
## got..Interferon..in.stage.III.yes.no
## Sentinel.lymph.node.biopsy..SLNB. no yes
## negative 12 3
## not performed 20 5
## positive 20 7