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pmid:31780779

Clinical relevance of TP53 hotspot mutations in high-grade serous ovarian cancers.

Musaffe Tuna · Zhenlin Ju · Kosuke Yoshihara · Christopher I Amos · Janos L Tanyi · Gordon B Mills

British journal of cancer · 2020 doi:10.1038/s41416-019-0654-8

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Experiment

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Data

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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1.2
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pmid:31780779
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science-record
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sha256:ce80722d627e03a0a1c204e9e51f655db198f3271da317ccaeee86d3fcc34f43
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2026-11-01T15:40:52Z
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2026-11-01T22:01:02Z
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paper object · 10 fields
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title
Clinical relevance of TP53 hotspot mutations in high-grade serous ovarian cancers.
doi
10.1038/s41416-019-0654-8
pmid
31780779
authors array · 6 items
[0]
Musaffe Tuna
[1]
Zhenlin Ju
[2]
Kosuke Yoshihara
[3]
Christopher I Amos
[4]
Janos L Tanyi
[5]
Gordon B Mills
journal
British journal of cancer
year
2020
abstract
BACKGROUND: Mutation of TP53 is the most frequent genetic alteration in high-grade serous ovarian cancer (HGSOC). The impact of hotspot mutations of TP53 and protein levels on patient outcomes in HGSOC has not been fully elucidated. METHODS: The study population (n = 791) comprised of HGSOC samples with TP53 mutation from TCGA and other publicly available data. Univariate and multivariate cox proportional hazards regression analyses were used to select variables that were correlated with patient survival. RESULTS: We assessed the effects of TP53 mutations based on type and individual hotspot mutations on patient outcomes in HGSOC. Only hotspot mutations were associated with outcomes. Three hotspot mutations: G266, Y163C, and R282, in aggregate were associated with a worsened overall and recurrence-free survival compared with other hotspot mutations (p < 0.0001 and p = 0.001), other non-hotspot missense mutations (p < 0.0001 and p = 0.008), truncated mutations (p < 0.0001 and p = 0.001), and all other mutations (p < 0.0001 and p = 0.001). Specific hotspot mutations were associated with different protein expression patterns consistent with different functions. CONCLUSIONS: This study provides evidence that individual TP53 hotspot mutations have different impact on HGSOC patient outcomes and potentially TP53 function. Thus the status of particular TP53 aberrations could influence response to therapy and selection of therapeutic agents.
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Univariate Cox proportional hazards regression analysis was used to select variables that were correlated with RFS time and/or OS time.
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methodological
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sections[4] "Statistical analysis" paragraph 2
quote
Univariate Cox proportional hazards regression analysis was used to select variables that were correlated with RFS time and/or OS time.
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complete
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claim-data-access
statement
TCGA generated data set that was analysed during the current study is available from the following URLS: http://portal.gdc.cancer.gov, http://Xena.ucsc.edu, https://www.tcpaportal.org/tcpa, and validation data set is available from the previous publications (Supplementary Table S1) and corresponding author on reasonable request.
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methodological
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sections[18] "notes" paragraph 1
quote
TCGA generated data set that was analysed during the current study is available from the following URLS: http://portal.gdc.cancer.gov, http://Xena.ucsc.edu, https://www.tcpaportal.org/tcpa, and validation data set is available from the previous publications (Supplementary Table S1) and corresponding author on reasonable request.
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https://doi.org/10.1038/s41416-019-0654-8
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10.1038/s41416-019-0654-8
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Univariate 5 years of overall survival analysis of TP53 hotspot mutations in HGSOC.
structure object · 5 fields
pmcid
PMC7000721
section_index
7
section_title
Association of TP53 mutations with survival in HGSOC
row_count
24
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13
table object · 8 fields
label
Table 1
caption
Univariate 5 years of overall survival analysis of TP53 hotspot mutations in HGSOC.
rows array · 24 items
[0] array · 4 items
[0]
Covariates
[1]
Training set (TCGA)
[2]
Validation set
[3]
Combined data
[1] array · 12 items
[0]
HR
[1]
p
[2]
q
[3]
95% CI
[4]
HR
[5]
p
[6]
q
[7]
95% CI
[8]
HR
[9]
p
[10]
q
[11]
95% CI
[2] array · 13 items
[0]
R273 vs Y220
[1]
1.16
[2]
0.314
[3]
0.461
[4]
0.87–1.56
[5]
1.11
[6]
0.482
[7]
0.675
[8]
0.83–1.48
[9]
1.14
[10]
0.220
[11]
0.372
[12]
0.93–1.39
[3] array · 13 items
[0]
R273 vs S241
[1]
1.03
[2]
0.715
[3]
0.867
[4]
0.89–1.19
[5]
[6]
[7]
[8]
[9]
0.98
[10]
0.701
[11]
0.907
[12]
0.87–1.10
[4] array · 13 items
[0]
R273 vs G245
[1]
1.03
[2]
0.749
[3]
0.867
[4]
0.85–1.24
[5]
0.96
[6]
0.613
[7]
0.693
[8]
0.80–1.14
[9]
0.99
[10]
0.837
[11]
0.969
[12]
0.87–1.12
[5] array · 13 items
[0]
R273 vs I195
[1]
1.10
[2]
0.397
[3]
0.546
[4]
0.88–1.39
[5]
[6]
[7]
[8]
[9]
1.11
[10]
0.267
[11]
0.420
[12]
0.92–1.35
[6] array · 13 items
[0]
R273 vs C176
[1]
0.99
[2]
0.938
[3]
0.977
[4]
0.81–1.22
[5]
[6]
[7]
[8]
[9]
0.99
[10]
0.960
[11]
0.998
[12]
0.85–1.17
[7] array · 13 items
[0]
R273 vs R175
[1]
0.90
[2]
0.651
[3]
0.842
[4]
0.59–1.40
[5]
1.16
[6]
0.474
[7]
0.675
[8]
0.77–1.75
[9]
0.99
[10]
0.998
[11]
0.998
[12]
0.74–1.35
[8] array · 13 items
[0]
R273 vs H193
[1]
0.95
[2]
0.272
[3]
0.427
[4]
0.86–1.04
[5]
[6]
[7]
[8]
[9]
0.99
[10]
0.570
[11]
0.799
[12]
0.91–1.05
[9] array · 13 items
[0]
R273 vs R248
[1]
2.86
[2]
0.013
[3]
0.026
[4]
1.25–6.55
[5]
1.21
[6]
0.652
[7]
0.693
[8]
0.52–2.81
[9]
1.81
[10]
0.039
[11]
0.072
[12]
1.03–3.16
[10] array · 13 items
[0]
R273 vs C238
[1]
1.09
[2]
0.125
[3]
0.212
[4]
0.98–1.23
[5]
0.96
[6]
0.383
[7]
0.670
[8]
0.88–1.05
[9]
0.99
[10]
0.801
[11]
0.970
[12]
0.93–1.06
[11] array · 13 items
[0]
R273 vs C275
[1]
1.00
[2]
0.977
[3]
0.977
[4]
0.92–1.10
[5]
1.02
[6]
0.652
[7]
0.693
[8]
0.94–1.11
[9]
1.00
[10]
0.951
[11]
0.998
[12]
0.94––1.07
[12] array · 13 items
[0]
R273 vs P278
[1]
0.99
[2]
0.824
[3]
0.906
[4]
0.87–1.12
[5]
1.10
[6]
0.189
[7]
0.378
[8]
0.96–1.25
[9]
1.03
[10]
0.581
[11]
0.799
[12]
0.94–1.12
[13] array · 13 items
[0]
R273 vs Y163C
[1]
1.29
[2]
0.003
[3]
0.009
[4]
1.09–1.52
[5]
[6]
[7]
[8]
[9]
1.25
[10]
<0.0001
[11]
<0.0001
[12]
1.11–1.39
[14] array · 13 items
[0]
R273 vs G266
[1]
1.13
[2]
0.006
[3]
0.015
[4]
1.04–1.24
[5]
[6]
[7]
[8]
[9]
1.14
[10]
<0.0001
[11]
<0.0001
[12]
1.06–1.22
[15] array · 13 items
[0]
R273 vs R282
[1]
1.10
[2]
0.013
[3]
0.026
[4]
1.02–1.19
[5]
[6]
[7]
[8]
[9]
1.08
[10]
0.007
[11]
0.014
[12]
1.02–1.15
[16] array · 13 items
[0]
R273 vs Y163C/G266/R282
[1]
5.25
[2]
<0.0001
[3]
<0.0001
[4]
2.18–12.63
[5]
4.56
[6]
0.005
[7]
0.014
[8]
1.57–13.21
[9]
4.71
[10]
<0.0001
[11]
<0.0001
[12]
2.44–9.10
[17] array · 13 items
[0]
Group 2 vs Group 1
[1]
0.18
[2]
<0.0001
[3]
<0.0001
[4]
0.10–0.34
[5]
0.25
[6]
0.001
[7]
0.004
[8]
0.11–0.56
[9]
0.21
[10]
<0.0001
[11]
<0.0001
[12]
0.13–0.34
[18] array · 13 items
[0]
Group 2 vs non-hotspot miss mut
[1]
0.29
[2]
<0.0001
[3]
<0.0001
[4]
0.16–0.52
[5]
0.36
[6]
0.013
[7]
0.030
[8]
0.16–0.81
[9]
0.57
[10]
<0.0001
[11]
<0.0001
[12]
0.45–0.72
[19] array · 13 items
[0]
Group 2 vs all other mut
[1]
0.25
[2]
<0.0001
[3]
<0.0001
[4]
0.14–0.45
[5]
0.26
[6]
0.001
[7]
0.004
[8]
0.12–0.57
[9]
0.53
[10]
<0.0001
[11]
<0.0001
[12]
0.42–0.66
[20] array · 13 items
[0]
Group 2 vs truncated
[1]
0.24
[2]
<0.0001
[3]
<0.0001
[4]
0.13–0.43
[5]
0.26
[6]
0.001
[7]
0.004
[8]
0.12–0.58
[9]
0.26
[10]
<0.0001
[11]
<0.0001
[12]
0.16–0.41
[21] array · 13 items
[0]
Group 2 vs in frame
[1]
0.39
[2]
0.031
[3]
0.057
[4]
0.17–0.92
[5]
[6]
[7]
[8]
[9]
0.26
[10]
0.001
[11]
0.002
[12]
0.11–0.59
[22] array · 13 items
[0]
Age ≤55 vs >55 years
[1]
1.61
[2]
<0.0001
[3]
<0.0001
[4]
1.25–2.08
[5]
0.94
[6]
0.693
[7]
0.693
[8]
0.71–1.26
[9]
1.31
[10]
0.005
[11]
0.011
[12]
1.09–1.59
[23] array · 13 items
[0]
Stage I and II vs Stage III and IV
[1]
2.70
[2]
0.006
[3]
0.015
[4]
1.34–5.46
[5]
2.49
[6]
<0.0001
[7]
<0.0001
[8]
1.51–4.11
[9]
2.48
[10]
<0.0001
[11]
<0.0001
[12]
1.64–3.74
row_count
24
column_count
13
numeric_cells
256
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2
locator
section[7]/table-wrap[1]#Tab1
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note
Univariate 5 years of recurrence-free survival analysis of TP53 hotspot mutations in HGSOC.
structure object · 5 fields
pmcid
PMC7000721
section_index
7
section_title
Association of TP53 mutations with survival in HGSOC
row_count
24
column_count
13
table object · 8 fields
label
Table 2
caption
Univariate 5 years of recurrence-free survival analysis of TP53 hotspot mutations in HGSOC.
rows array · 24 items
[0] array · 4 items
[0]
Covariates
[1]
TCGA
[2]
Validation
[3]
Combined
[1] array · 12 items
[0]
HR
[1]
p
[2]
q
[3]
95% CI
[4]
HR
[5]
p
[6]
q
[7]
95% CI
[8]
HR
[9]
p
[10]
q
[11]
95% CI
[2] array · 13 items
[0]
R273 vs Y220
[1]
1.20
[2]
0.204
[3]
0.408
[4]
0.90–1.61
[5]
0.76
[6]
0.108
[7]
0.212
[8]
0.54–1.06
[9]
0.98
[10]
0.830
[11]
0.913
[12]
0.80–1.20
[3] array · 13 items
[0]
R273 vs S241
[1]
1.03
[2]
0.670
[3]
0.765
[4]
0.90–1.17
[5]
[6]
[7]
[8]
[9]
0.97
[10]
0.536
[11]
0.694
[12]
0.87–1.07
[4] array · 13 items
[0]
R273 vs G245
[1]
1.02
[2]
0.834
[3]
0.834
[4]
0.86–1.21
[5]
0.87
[6]
0.120
[7]
0.212
[8]
0.74–1.04
[9]
0.95
[10]
0.412
[11]
0.567
[12]
0.85–1.07
[5] array · 13 items
[0]
R273 vs I195
[1]
1.17
[2]
0.148
[3]
0.362
[4]
0.95–1.45
[5]
[6]
[7]
[8]
[9]
1.08
[10]
0.403
[11]
0.567
[12]
0.91–1.28
[6] array · 13 items
[0]
R273 vs C176
[1]
0.95
[2]
0.571
[3]
0.737
[4]
0.79–1.14
[5]
[6]
[7]
[8]
[9]
0.92
[10]
0.248
[11]
0.495
[12]
0.79–1.06
[7] array · 13 items
[0]
R273 vs R175
[1]
0.92
[2]
0.695
[3]
0.765
[4]
0.62–1.38
[5]
0.82
[6]
0.382
[7]
0.535
[8]
0.52–1.28
[9]
0.86
[10]
0.307
[11]
0.519
[12]
0.64–1.15
[8] array · 13 items
[0]
R273 vs H193
[1]
1.02
[2]
0.573
[3]
0.737
[4]
0.95–1.10
[5]
[6]
[7]
[8]
[9]
1.04
[10]
0.270
[11]
0.495
[12]
0.97–1.10
[9] array · 13 items
[0]
R273 vs R248
[1]
1.53
[2]
0.311
[3]
0.526
[4]
0.67–3.46
[5]
0.8
[6]
0.570
[7]
0.606
[8]
0.36–1.75
[9]
1.14
[10]
0.635
[11]
0.776
[12]
0.66–1.98
[10] array · 13 items
[0]
R273 vs C238
[1]
1.02
[2]
0.759
[3]
0.795
[4]
0.92–1.12
[5]
1.02
[6]
0.535
[7]
0.606
[8]
0.96–1.09
[9]
1.03
[10]
0.330
[11]
0.519
[12]
0.97–1.08
[11] array · 13 items
[0]
R273 vs C275
[1]
1.02
[2]
0.603
[3]
0.737
[4]
0.95–1.10
[5]
0.95
[6]
0.305
[7]
0.474
[8]
0.87–1.04
[9]
0.99
[10]
0.714
[11]
0.827
[12]
0.94–1.05
[12] array · 13 items
[0]
R273 vs P278
[1]
1.03
[2]
0.578
[3]
0.737
[4]
0.92–1.16
[5]
0.96
[6]
0.606
[7]
0.606
[8]
0.83–1.12
[9]
1.00
[10]
0.921
[11]
0.921
[12]
0.92–1.10
[13] array · 13 items
[0]
R273 vs Y163C
[1]
1.11
[2]
0.185
[3]
0.407
[4]
0.95–1.31
[5]
[6]
[7]
[8]
[9]
1.11
[10]
0.102
[11]
0.249
[12]
0.98–1.25
[14] array · 13 items
[0]
R273 vs G266
[1]
1.05
[2]
0.280
[3]
0.513
[4]
0.96–1.16
[5]
[6]
[7]
[8]
[9]
1.07
[10]
0.119
[11]
0.262
[12]
0.98–1.15
[15] array · 13 items
[0]
R273 vs R282
[1]
1.11
[2]
0.007
[3]
0.040
[4]
1.03–1.20
[5]
[6]
[7]
[8]
[9]
1.06
[10]
0.016
[11]
0.044
[12]
1.01–1.12
[16] array · 13 items
[0]
R273 vs Y163C/G266/R282
[1]
2.62
[2]
0.023
[3]
0.063
[4]
1.14–6.00
[5]
2.38
[6]
0.094
[7]
0.212
[8]
0.86–6.57
[9]
2.43
[10]
0.005
[11]
0.018
[12]
1.31–4.53
[17] array · 13 items
[0]
Group 2 vs Group 1
[1]
0.43
[2]
0.009
[3]
0.040
[4]
0.23–0.81
[5]
0.43
[6]
0.050
[7]
0.212
[8]
0.18–0.99
[9]
0.41
[10]
0.001
[11]
0.006
[12]
0.25–0.68
[18] array · 13 items
[0]
Group 2 vs non-hotspot missense mut
[1]
0.45
[2]
0.017
[3]
0.053
[4]
0.23–0.87
[5]
0.51
[6]
0.121
[7]
0.212
[8]
0.21–1.20
[9]
0.70
[10]
0.008
[11]
0.025
[12]
0.54–0.91
[19] array · 13 items
[0]
Group 2 vs all other mut
[1]
0.41
[2]
0.006
[3]
0.040
[4]
0.22–0.77
[5]
0.46
[6]
0.067
[7]
0.212
[8]
0.20–1.06
[9]
0.67
[10]
0.001
[11]
0.006
[12]
0.52–0.86
[20] array · 13 items
[0]
Group 2 vs truncated
[1]
0.43
[2]
0.008
[3]
0.040
[4]
0.23–0.80
[5]
0.46
[6]
0.071
[7]
0.212
[8]
0.20–1.07
[9]
0.44
[10]
0.001
[11]
0.006
[12]
0.260.72
[21] array · 13 items
[0]
Group 2 vs in frame
[1]
0.28
[2]
0.014
[3]
0.051
[4]
0.10–0.78
[5]
[6]
[7]
[8]
[9]
0.29
[10]
0.004
[11]
0.018
[12]
0.12–0.67
[22] array · 13 items
[0]
Age ≤55 vs >55 years
[1]
1.09
[2]
0.468
[3]
0.735
[4]
0.86–1.38
[5]
0.91
[6]
0.541
[7]
0.606
[8]
0.69–1.22
[9]
1.01
[10]
0.874
[11]
0.916
[12]
0.85–1.22
[23] array · 13 items
[0]
Stage I and II vs Stage III and IV
[1]
2.81
[2]
0.001
[3]
0.022
[4]
1.54–5.13
[5]
5.79
[6]
<0.0001
[7]
<0.0001
[8]
3.06–10.95
[9]
4.00
[10]
<0.0001
[11]
<0.0001
[12]
2.59–6.21
row_count
24
column_count
13
numeric_cells
256
header_rows
2
locator
section[7]/table-wrap[2]#Tab2
[3] object · 16 fields
id
asset:table:pmid:31780779:3
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:7b1b234252629289a23c8e144f319d2f43d672a8910f1d57db856bddefbcbe38
bytes
1287
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[7]/table-wrap[3]#Tab3
version
null
note
Multivariate analysis of OS and RFS in the training, validation, and combined sets.
structure object · 5 fields
pmcid
PMC7000721
section_index
7
section_title
Association of TP53 mutations with survival in HGSOC
row_count
14
column_count
9
table object · 8 fields
label
Table 3
caption
Multivariate analysis of OS and RFS in the training, validation, and combined sets.
rows array · 14 items
[0] array · 3 items
[0]
Covariates
[1]
OS
[2]
RFS
[1] array · 8 items
[0]
HR
[1]
p
[2]
q
[3]
95% CI
[4]
HR
[5]
p
[6]
q
[7]
95% CI
[2] array · 1 item
[0]
Training set
[3] array · 9 items
[0]
Group 1 vs Group 2
[1]
5.36
[2]
<0.0001
[3]
<0.0001
[4]
2.93–9.80
[5]
2.33
[6]
0.010
[7]
0.022
[8]
1.23–4.41
[4] array · 9 items
[0]
Stage I and II vs III and IV
[1]
2.78
[2]
0.153
[3]
0.172
[4]
0.68–11.33
[5]
1.67
[6]
0.264
[7]
0.396
[8]
0.68–4.11
[5] array · 9 items
[0]
Age ≤55 vs >55 years
[1]
1.78
[2]
0.009
[3]
0.016
[4]
1.16–2.74
[5]
0.90
[6]
0.592
[7]
0.592
[8]
0.62–1.32
[6] array · 1 item
[0]
Validation set
[7] array · 9 items
[0]
Group 1 vs Group 2
[1]
3.88
[2]
0.001
[3]
0.003
[4]
1.71–8.82
[5]
1.85
[6]
0.164
[7]
0.295
[8]
0.78–4.38
[8] array · 9 items
[0]
Stage I and II vs III and IV
[1]
2.08
[2]
0.069
[3]
0.089
[4]
0.95–4.57
[5]
9.98
[6]
0.001
[7]
0.005
[8]
2.42–41.22
[9] array · 9 items
[0]
Age ≤55 vs >55 years
[1]
1.26
[2]
0.369
[3]
0.369
[4]
0.76–2.10
[5]
0.85
[6]
0.557
[7]
0.592
[8]
0.50–1.46
[10] array · 1 item
[0]
Combined set
[11] array · 9 items
[0]
Group 1 vs Group 2
[1]
4.76
[2]
<0.0001
[3]
<0.0001
[4]
2.95–7.67
[5]
2.25
[6]
0.002
[7]
0.006
[8]
1.35–3.73
[12] array · 9 items
[0]
Stage I and II vs III and IV
[1]
2.26
[2]
0.025
[3]
0.038
[4]
1.11–4.60
[5]
3.96
[6]
<0.0001
[7]
<0.0001
[8]
1.86–8.46
[13] array · 9 items
[0]
Age ≤55 vs >55 years
[1]
1.59
[2]
0.005
[3]
0.011
[4]
1.15–2.20
[5]
0.90
[6]
0.497
[7]
0.592
[8]
0.67–1.22
row_count
14
column_count
9
numeric_cells
80
header_rows
2
locator
section[7]/table-wrap[3]#Tab3
gaps array · 0 items
analysis object · 4 fields
state
partial
methods array · 4 items
[0] object · 10 fields
id
method-1
family
survival_analysis
specific
cox_proportional_hazards
label
Survival analysis
dsl_operations array · 1 item
[0]
cox_ph
missing_operations array · 0 items
expressible
true
parameters object · 0 fields
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
1
band
verbatim
quote
Univariate Cox proportional hazards regression analysis was used to select variables that were correlated with RFS time and/or OS time.
[1] object · 10 fields
id
method-2
family
group_comparison
specific
wilcoxon
label
Group comparison
dsl_operations array · 0 items
missing_operations array · 1 item
[0]
group_comparison_wilcoxon
expressible
false
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
0.8
band
high
quote
Wilcoxon
[2] object · 10 fields
id
method-3
family
survival_analysis
specific
log_rank_test
label
Survival analysis
dsl_operations array · 1 item
[0]
logrank_test
missing_operations array · 0 items
expressible
true
parameters object · 0 fields
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
0.8
band
high
quote
Log-rank
[3] object · 10 fields
id
method-4
family
contingency_analysis
specific
chi_square
label
Categorical (contingency table) analysis
dsl_operations array · 1 item
[0]
chi_square_test
missing_operations array · 0 items
expressible
true
parameters object · 0 fields
data_shapes array · 1 item
[0]
categorical_cross_tabulation
evidence object · 3 fields
score
0.8
band
high
quote
Chi-square
targets array · 0 items
gaps array · 1 item
[0]
method.reader_differs_from_extractor
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
availability_state
owned
tier_unlocked
R1
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
blocked
tier
R4
blocking_axis
data
blocked_on
data:accession_absent
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 1 item
[0]
cox_ph
missing_operations array · 0 items
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R4
reachable
false
accessions array · 0 items
resolved_accessions array · 0 items
statements array · 1 item
[0]
TCGA generated data set that was analysed during the current study is available from the following URLS: http://portal.gdc.cancer.gov, http://Xena.ucsc.edu, https://www.tcpaportal.org/tcpa, and validation data set is available from the previous publications (Supplementary Table S1) and corresponding author on reasonable request.
basis
The paper names no accession to its source data, so the data has to come from the authors.
can_run object · 3 fields
dsl_operations array · 1 item
[0]
cox_ph
assets array · 4 items
[0]
source:pmid:31780779
[1]
asset:table:pmid:31780779:1
[2]
asset:table:pmid:31780779:2
[3]
asset:table:pmid:31780779:3
steps array · 1 item
[0]
run_analysis
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:None
gaps array · 1 item
[0]
data:accession_absent
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-10-31T18:17:19Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
3
usage object · 3 fields
prompt_tokens
31466
completion_tokens
2477
cached_tokens
776
human_critique
null
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
reader
MiniMax-M3.1-Flash
provider
minimax
gaps array · 3 items
[0]
review.independent_reader
[1]
review.machine_critique
[2]
review.human_critique
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 3 items
[0] object · 3 fields
id
pmid:31780779
type
paper
label
pmid:31780779
[1] object · 3 fields
id
source:pmid:31780779
type
manuscript
label
PMID 31780779 full text
[2] object · 3 fields
id
data:geo:None
type
dataset
label
GEO None
activities array · 3 items
[0] object · 4 fields
id
activity-reading-sci-2026-11-01
type
classification
used array · 3 items
[0] object · 3 fields
id
pmid:31780779
type
paper
label
pmid:31780779
[1] object · 3 fields
id
source:pmid:31780779
type
manuscript
label
PMID 31780779 full text
[2] object · 3 fields
id
data:geo:None
type
dataset
label
GEO None
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-31780779
type
extraction
used array · 1 item
[0]
source:pmid:31780779
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-None
type
accession_resolution
used array · 1 item
[0]
data:geo:None
agent
agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
[1] object · 3 fields
id
agent:minimax-reader
type
software
label
MiniMax literature reader
source_run_id
reading-sci-2026-11-01
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:31780779
parent_hash
sha256:cef5d080809085e9a01f23e2da056a603ea3194c692cbc91b64b2a0c20d79550
fork_of
null
generation
6
gaps array · 6 items
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execution.not_run
[1]
method.reader_differs_from_extractor
[2]
review.human_critique
[3]
review.independent_reader
[4]
review.machine_critique
[5]
step:obtain_source_data blocked on data:accession_absent
assays array · 1 item
[0] object · 11 fields
role
analysis
definition_id
survival_analysis
definition_version
f2132e96ae6c7a4e
definition_digest
null
required_operations array · 1 item
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cox_ph
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
confidence
1
evidence array · 1 item
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Univariate Cox proportional hazards regression analysis was used to select variables that were correlated with RFS time and/or OS time.
order_basis
analysis_only
id
assay:1
Complete file 
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31780779", "kind": "science-record", "revision": 7, "content_hash": "sha256:ce80722d627e03a0a1c204e9e51f655db198f3271da317ccaeee86d3fcc34f43", "created_at": "2026-11-01T15:40:52Z", "updated_at": "2026-11-01T22:01:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Clinical relevance of TP53 hotspot mutations in high-grade serous ovarian cancers.", "doi": "10.1038/s41416-019-0654-8", "pmid": "31780779", "authors": ["Musaffe Tuna", "Zhenlin Ju", "Kosuke Yoshihara", "Christopher I Amos", "Janos L Tanyi", "Gordon B Mills"], "journal": "British journal of cancer", "year": 2020, "abstract": "BACKGROUND: Mutation of TP53 is the most frequent genetic alteration in high-grade serous ovarian cancer (HGSOC). The impact of hotspot mutations of TP53 and protein levels on patient outcomes in HGSOC has not been fully elucidated.\nMETHODS: The study population (n = 791) comprised of HGSOC samples with TP53 mutation from TCGA and other publicly available data. Univariate and multivariate cox proportional hazards regression analyses were used to select variables that were correlated with patient survival.\nRESULTS: We assessed the effects of TP53 mutations based on type and individual hotspot mutations on patient outcomes in HGSOC. Only hotspot mutations were associated with outcomes. Three hotspot mutations: G266, Y163C, and R282, in aggregate were associated with a worsened overall and recurrence-free survival compared with other hotspot mutations (p < 0.0001 and p = 0.001), other non-hotspot missense mutations (p < 0.0001 and p = 0.008), truncated mutations (p < 0.0001 and p = 0.001), and all other mutations (p < 0.0001 and p = 0.001). Specific hotspot mutations were associated with different protein expression patterns consistent with different functions.\nCONCLUSIONS: This study provides evidence that individual TP53 hotspot mutations have different impact on HGSOC patient outcomes and potentially TP53 function. Thus the status of particular TP53 aberrations could influence response to therapy and selection of therapeutic agents.", "claims": [{"id": "claim-method", "statement": "Univariate Cox proportional hazards regression analysis was used to select variables that were correlated with RFS time and/or OS time.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31780779", "locator": "sections[4] \"Statistical analysis\" paragraph 2", "quote": "Univariate Cox proportional hazards regression analysis was used to select variables that were correlated with RFS time and/or OS time."}], "state": "complete"}, {"id": "claim-data-access", "statement": "TCGA generated data set that was analysed during the current study is available from the following URLS: http://portal.gdc.cancer.gov, http://Xena.ucsc.edu, https://www.tcpaportal.org/tcpa, and validation data set is available from the previous publications (Supplementary Table S1) and corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31780779", "locator": "sections[18] \"notes\" paragraph 1", "quote": "TCGA generated data set that was analysed during the current study is available from the following URLS: http://portal.gdc.cancer.gov, http://Xena.ucsc.edu, https://www.tcpaportal.org/tcpa, and validation data set is available from the previous publications (Supplementary Table S1) and corresponding author on reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:31780779"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31780779", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41416-019-0654-8", "sha256": "sha256:e21f792a748280c68c4c00358a2dda39ce20c90cf3b7fd790e5dc011d41a6e42", "bytes": 35591, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41416-019-0654-8", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7000721", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:31780779:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:399de669407cbfc01e7bdf8464affed9df252bec274f7f99e22942f682c3e30f", "bytes": 3150, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#Tab1", "version": null, "note": "Univariate 5 years of overall survival analysis of TP53 hotspot mutations in HGSOC.", "structure": {"pmcid": "PMC7000721", "section_index": 7, "section_title": "Association of TP53 mutations with survival in HGSOC", "row_count": 24, "column_count": 13}, "table": {"label": "Table 1", "caption": "Univariate 5 years of overall survival analysis of TP53 hotspot mutations in HGSOC.", "rows": [["Covariates", "Training set (TCGA)", "Validation set", "Combined data"], ["HR", "p", "q", "95% CI", "HR", "p", "q", "95% CI", "HR", "p", "q", "95% CI"], ["R273 vs Y220", "1.16", "0.314", "0.461", "0.87–1.56", "1.11", "0.482", "0.675", "0.83–1.48", "1.14", "0.220", "0.372", "0.93–1.39"], ["R273 vs S241", "1.03", "0.715", "0.867", "0.89–1.19", "", "", "", "", "0.98", "0.701", "0.907", "0.87–1.10"], ["R273 vs G245", "1.03", "0.749", "0.867", "0.85–1.24", "0.96", "0.613", "0.693", "0.80–1.14", "0.99", "0.837", "0.969", "0.87–1.12"], ["R273 vs I195", "1.10", "0.397", "0.546", "0.88–1.39", "", "", "", "", "1.11", "0.267", "0.420", "0.92–1.35"], ["R273 vs C176", "0.99", "0.938", "0.977", "0.81–1.22", "", "", "", "", "0.99", "0.960", "0.998", "0.85–1.17"], ["R273 vs R175", "0.90", "0.651", "0.842", "0.59–1.40", "1.16", "0.474", "0.675", "0.77–1.75", "0.99", "0.998", "0.998", "0.74–1.35"], ["R273 vs H193", "0.95", "0.272", "0.427", "0.86–1.04", "", "", "", "", "0.99", "0.570", "0.799", "0.91–1.05"], ["R273 vs R248", "2.86", "0.013", "0.026", "1.25–6.55", "1.21", "0.652", "0.693", "0.52–2.81", "1.81", "0.039", "0.072", "1.03–3.16"], ["R273 vs C238", "1.09", "0.125", "0.212", "0.98–1.23", "0.96", "0.383", "0.670", "0.88–1.05", "0.99", "0.801", "0.970", "0.93–1.06"], ["R273 vs C275", "1.00", "0.977", "0.977", "0.92–1.10", "1.02", "0.652", "0.693", "0.94–1.11", "1.00", "0.951", "0.998", "0.94––1.07"], ["R273 vs P278", "0.99", "0.824", "0.906", "0.87–1.12", "1.10", "0.189", "0.378", "0.96–1.25", "1.03", "0.581", "0.799", "0.94–1.12"], ["R273 vs Y163C", "1.29", "0.003", "0.009", "1.09–1.52", "", "", "", "", "1.25", "<0.0001", "<0.0001", "1.11–1.39"], ["R273 vs G266", "1.13", "0.006", "0.015", "1.04–1.24", "", "", "", "", "1.14", "<0.0001", "<0.0001", "1.06–1.22"], ["R273 vs R282", "1.10", "0.013", "0.026", "1.02–1.19", "", "", "", "", "1.08", "0.007", "0.014", "1.02–1.15"], ["R273 vs Y163C/G266/R282", "5.25", "<0.0001", "<0.0001", "2.18–12.63", "4.56", "0.005", "0.014", "1.57–13.21", "4.71", "<0.0001", "<0.0001", "2.44–9.10"], ["Group 2 vs Group 1", "0.18", "<0.0001", "<0.0001", "0.10–0.34", "0.25", "0.001", "0.004", "0.11–0.56", "0.21", "<0.0001", "<0.0001", "0.13–0.34"], ["Group 2 vs non-hotspot miss mut", "0.29", "<0.0001", "<0.0001", "0.16–0.52", "0.36", "0.013", "0.030", "0.16–0.81", "0.57", "<0.0001", "<0.0001", "0.45–0.72"], ["Group 2 vs all other mut", "0.25", "<0.0001", "<0.0001", "0.14–0.45", "0.26", "0.001", "0.004", "0.12–0.57", "0.53", "<0.0001", "<0.0001", "0.42–0.66"], ["Group 2 vs truncated", "0.24", "<0.0001", "<0.0001", "0.13–0.43", "0.26", "0.001", "0.004", "0.12–0.58", "0.26", "<0.0001", "<0.0001", "0.16–0.41"], ["Group 2 vs in 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analysis of TP53 hotspot mutations in HGSOC.", "structure": {"pmcid": "PMC7000721", "section_index": 7, "section_title": "Association of TP53 mutations with survival in HGSOC", "row_count": 24, "column_count": 13}, "table": {"label": "Table 2", "caption": "Univariate 5 years of recurrence-free survival analysis of TP53 hotspot mutations in HGSOC.", "rows": [["Covariates", "TCGA", "Validation", "Combined"], ["HR", "p", "q", "95% CI", "HR", "p", "q", "95% CI", "HR", "p", "q", "95% CI"], ["R273 vs Y220", "1.20", "0.204", "0.408", "0.90–1.61", "0.76", "0.108", "0.212", "0.54–1.06", "0.98", "0.830", "0.913", "0.80–1.20"], ["R273 vs S241", "1.03", "0.670", "0.765", "0.90–1.17", "", "", "", "", "0.97", "0.536", "0.694", "0.87–1.07"], ["R273 vs G245", "1.02", "0.834", "0.834", "0.86–1.21", "0.87", "0.120", "0.212", "0.74–1.04", "0.95", "0.412", "0.567", "0.85–1.07"], ["R273 vs I195", "1.17", "0.148", "0.362", "0.95–1.45", "", "", "", "", "1.08", "0.403", "0.567", "0.91–1.28"], ["R273 vs C176", "0.95", "0.571", "0.737", "0.79–1.14", "", "", "", "", "0.92", "0.248", "0.495", "0.79–1.06"], ["R273 vs R175", "0.92", "0.695", "0.765", "0.62–1.38", "0.82", "0.382", "0.535", "0.52–1.28", "0.86", "0.307", "0.519", "0.64–1.15"], ["R273 vs H193", "1.02", "0.573", "0.737", "0.95–1.10", "", "", "", "", "1.04", "0.270", "0.495", "0.97–1.10"], ["R273 vs R248", "1.53", "0.311", "0.526", "0.67–3.46", "0.8", "0.570", "0.606", "0.36–1.75", "1.14", "0.635", "0.776", "0.66–1.98"], ["R273 vs C238", "1.02", "0.759", "0.795", "0.92–1.12", "1.02", "0.535", "0.606", "0.96–1.09", "1.03", "0.330", "0.519", "0.97–1.08"], ["R273 vs C275", "1.02", "0.603", "0.737", "0.95–1.10", "0.95", "0.305", "0.474", "0.87–1.04", "0.99", "0.714", "0.827", "0.94–1.05"], ["R273 vs P278", "1.03", "0.578", "0.737", "0.92–1.16", "0.96", "0.606", "0.606", "0.83–1.12", "1.00", "0.921", "0.921", "0.92–1.10"], ["R273 vs Y163C", "1.11", "0.185", "0.407", "0.95–1.31", "", "", "", "", "1.11", "0.102", "0.249", "0.98–1.25"], ["R273 vs G266", "1.05", "0.280", "0.513", "0.96–1.16", "", "", "", "", "1.07", "0.119", "0.262", "0.98–1.15"], ["R273 vs R282", "1.11", "0.007", "0.040", "1.03–1.20", "", "", "", "", "1.06", "0.016", "0.044", "1.01–1.12"], ["R273 vs Y163C/G266/R282", "2.62", "0.023", "0.063", "1.14–6.00", "2.38", "0.094", "0.212", "0.86–6.57", "2.43", "0.005", "0.018", "1.31–4.53"], ["Group 2 vs Group 1", "0.43", "0.009", "0.040", "0.23–0.81", "0.43", "0.050", "0.212", "0.18–0.99", "0.41", "0.001", "0.006", "0.25–0.68"], ["Group 2 vs non-hotspot missense mut", "0.45", "0.017", "0.053", "0.23–0.87", "0.51", "0.121", "0.212", "0.21–1.20", "0.70", "0.008", "0.025", "0.54–0.91"], ["Group 2 vs all other mut", "0.41", "0.006", "0.040", "0.22–0.77", "0.46", "0.067", "0.212", "0.20–1.06", "0.67", "0.001", "0.006", "0.52–0.86"], ["Group 2 vs truncated", "0.43", "0.008", "0.040", "0.23–0.80", "0.46", "0.071", "0.212", "0.20–1.07", "0.44", "0.001", "0.006", "0.260.72"], ["Group 2 vs in frame", "0.28", "0.014", "0.051", 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