Trait: secondary malignant neoplasm

Trait Information
Identifier MONDO_0024881
Description A malignant neoplasm that arises from a pre-existing lower grade lesion, or as a result of a primary lesion that has spread to secondary sites, or due to a complication of a cancer treatment. [NCIT: C4968]
Trait category
Other trait
Synonyms 3 synonyms
  • secondary cancer
  • secondary malignancy
  • secondary malignant neoplasm

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS018595
(TPMI_198_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Secondary malignant neoplasm secondary malignant neoplasm 6
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018595/ScoringFiles/PGS018595.txt.gz
PGS018596
(TPMI_198_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Secondary malignant neoplasm secondary malignant neoplasm 939,881
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018596/ScoringFiles/PGS018596.txt.gz
PGS018597
(TPMI_198_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Secondary malignant neoplasm secondary malignant neoplasm 507,026
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018597/ScoringFiles/PGS018597.txt.gz
PGS018598
(TPMI_198_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Secondary malignant neoplasm secondary malignant neoplasm 983,823
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018598/ScoringFiles/PGS018598.txt.gz
PGS018599
(TPMI_198_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Secondary malignant neoplasm secondary malignant neoplasm 983,738
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018599/ScoringFiles/PGS018599.txt.gz
PGS018600
(TPMI_198.6_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Secondary malignancy of bone secondary malignant neoplasm 1
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018600/ScoringFiles/PGS018600.txt.gz
PGS018601
(TPMI_198.6_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Secondary malignancy of bone secondary malignant neoplasm 29,941
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018601/ScoringFiles/PGS018601.txt.gz
PGS018602
(TPMI_198.6_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Secondary malignancy of bone secondary malignant neoplasm 543,774
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018602/ScoringFiles/PGS018602.txt.gz
PGS018603
(TPMI_198.6_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Secondary malignancy of bone secondary malignant neoplasm 983,823
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018603/ScoringFiles/PGS018603.txt.gz
PGS018604
(TPMI_198.6_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Secondary malignancy of bone secondary malignant neoplasm 1,012,364
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018604/ScoringFiles/PGS018604.txt.gz

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		Evaluated Score PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM036777 PGS018595
(TPMI_198_Lassosum2)
 PSS012503|
East Asian Ancestry|
17,306 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Secondary malignant neoplasm — AUROC: 0.67617 R²: 0.03737 sex, age, array, PCs 1-10 —
PPM036778 PGS018596
(TPMI_198_LDpred2)
 PSS012502|
East Asian Ancestry|
17,306 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Secondary malignant neoplasm — AUROC: 0.67812 R²: 0.03797 sex, age, array, PCs 1-10 —
PPM036779 PGS018597
(TPMI_198_MegaPRS)
 PSS012504|
East Asian Ancestry|
17,306 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Secondary malignant neoplasm — AUROC: 0.67751 R²: 0.03789 sex, age, array, PCs 1-10 —
PPM036780 PGS018598
(TPMI_198_PRS-CS)
 PSS012505|
East Asian Ancestry|
17,306 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Secondary malignant neoplasm — AUROC: 0.67671 R²: 0.03753 sex, age, array, PCs 1-10 —
PPM036781 PGS018599
(TPMI_198_SBayesR)
 PSS012506|
East Asian Ancestry|
17,306 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Secondary malignant neoplasm — AUROC: 0.67667 R²: 0.03746 sex, age, array, PCs 1-10 —
PPM036782 PGS018600
(TPMI_198.6_Lassosum2)
 PSS012498|
East Asian Ancestry|
17,034 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Secondary malignancy of bone — AUROC: 0.69259 R²: 0.01217 sex, age, array, PCs 1-10 —
PPM036783 PGS018601
(TPMI_198.6_LDpred2)
 PSS012497|
East Asian Ancestry|
17,034 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Secondary malignancy of bone — AUROC: 0.69156 R²: 0.01214 sex, age, array, PCs 1-10 —
PPM036784 PGS018602
(TPMI_198.6_MegaPRS)
 PSS012499|
East Asian Ancestry|
17,034 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Secondary malignancy of bone — AUROC: 0.69067 R²: 0.01217 sex, age, array, PCs 1-10 —
PPM036785 PGS018603
(TPMI_198.6_PRS-CS)
 PSS012500|
East Asian Ancestry|
17,034 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Secondary malignancy of bone — AUROC: 0.69099 R²: 0.01214 sex, age, array, PCs 1-10 —
PPM036786 PGS018604
(TPMI_198.6_SBayesR)
 PSS012501|
East Asian Ancestry|
17,034 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Secondary malignancy of bone — AUROC: 0.69091 R²: 0.01214 sex, age, array, PCs 1-10 —

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS012497 198.5, 209.73,C79.5, C7B.03 —
[
  • 166 cases
  • , 16,868 controls
]
,
46.87 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012498 198.5, 209.73,C79.5, C7B.03 —
[
  • 166 cases
  • , 16,868 controls
]
,
46.87 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012499 198.5, 209.73,C79.5, C7B.03 —
[
  • 166 cases
  • , 16,868 controls
]
,
46.87 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012500 198.5, 209.73,C79.5, C7B.03 —
[
  • 166 cases
  • , 16,868 controls
]
,
46.87 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012501 198.5, 209.73,C79.5, C7B.03 —
[
  • 166 cases
  • , 16,868 controls
]
,
46.87 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012502 196, 197, 198, 209.7, 511.81, 789.51,C77, C78, C79.0, C79.1, C79.2, C79.3, C79.4, C79.5, C79.6, C79.7, C79.8, C79.9, C7B.01, C7B.02, C7B.03, C7B.04, C7B.09, C7B.8, J91.0, R18.0 —
[
  • 438 cases
  • , 16,868 controls
]
,
46.78 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012503 196, 197, 198, 209.7, 511.81, 789.51,C77, C78, C79.0, C79.1, C79.2, C79.3, C79.4, C79.5, C79.6, C79.7, C79.8, C79.9, C7B.01, C7B.02, C7B.03, C7B.04, C7B.09, C7B.8, J91.0, R18.0 —
[
  • 438 cases
  • , 16,868 controls
]
,
46.78 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012504 196, 197, 198, 209.7, 511.81, 789.51,C77, C78, C79.0, C79.1, C79.2, C79.3, C79.4, C79.5, C79.6, C79.7, C79.8, C79.9, C7B.01, C7B.02, C7B.03, C7B.04, C7B.09, C7B.8, J91.0, R18.0 —
[
  • 438 cases
  • , 16,868 controls
]
,
46.78 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012505 196, 197, 198, 209.7, 511.81, 789.51,C77, C78, C79.0, C79.1, C79.2, C79.3, C79.4, C79.5, C79.6, C79.7, C79.8, C79.9, C7B.01, C7B.02, C7B.03, C7B.04, C7B.09, C7B.8, J91.0, R18.0 —
[
  • 438 cases
  • , 16,868 controls
]
,
46.78 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012506 196, 197, 198, 209.7, 511.81, 789.51,C77, C78, C79.0, C79.1, C79.2, C79.3, C79.4, C79.5, C79.6, C79.7, C79.8, C79.9, C7B.01, C7B.02, C7B.03, C7B.04, C7B.09, C7B.8, J91.0, R18.0 —
[
  • 438 cases
  • , 16,868 controls
]
,
46.78 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —