Trait: cancer biomarker measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0005127
Description cancer biomarkers, such as cancer antigen 19-9, carcinoembryonic antigen and α fetoprotein, are used as indicators for cancer screening and as predictors for therapeutic responses and prognoses in cancer patient
Trait category
Other measurement
Child trait(s) IGF-1 measurement

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
Note: This table shows all PGS for "cancer biomarker measurement" and any child terms of this trait in the EFO hierarchy by default.
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)
PGS000687
(snpnet.IGF_1)
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 IGF-1 [nmol/L] IGF-1 measurement 23,443
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000687/ScoringFiles/PGS000687.txt.gz - Check Terms/Licenses
PGS001960
(portability-PLR_log_IGF1)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 IGF-1 IGF-1 measurement 87,149
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001960/ScoringFiles/PGS001960.txt.gz
PGS002178
(portability-ldpred2_log_IGF1)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 IGF-1 IGF-1 measurement 817,740
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002178/ScoringFiles/PGS002178.txt.gz
PGS003539
(cont-decay-log_IGF1)
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 IGF-1 IGF-1 measurement 979,739
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003539/ScoringFiles/PGS003539.txt.gz
PGS004338
(X30770.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 IGF-1 (nmol/L) IGF-1 measurement 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004338/ScoringFiles/PGS004338.txt.gz
PGS019768
(TPMI_795.8_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Abnormal tumor markers cancer biomarker measurement 141
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019768/ScoringFiles/PGS019768.txt.gz
PGS019769
(TPMI_795.8_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Abnormal tumor markers cancer biomarker measurement 939,841
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019769/ScoringFiles/PGS019769.txt.gz
PGS019770
(TPMI_795.8_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Abnormal tumor markers cancer biomarker measurement 24,096
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019770/ScoringFiles/PGS019770.txt.gz
PGS019771
(TPMI_795.8_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Abnormal tumor markers cancer biomarker measurement 983,789
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019771/ScoringFiles/PGS019771.txt.gz
PGS019772
(TPMI_795.8_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Abnormal tumor markers cancer biomarker measurement 998,333
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS019772/ScoringFiles/PGS019772.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
PPM001415 PGS000687
(snpnet.IGF_1)
 PSS000709|
African Ancestry|
5,974 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: IGF-1 [nmol/L] — — R²: 0.11454
Spearman's ρ: 0.182		 Age, sex, PCs(1-40) —
PPM001450 PGS000687
(snpnet.IGF_1)
 PSS000710|
East Asian Ancestry|
1,074 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: IGF-1 [nmol/L] — — R²: 0.17702
Spearman's ρ: 0.258		 Age, sex, PCs(1-40) —
PPM001485 PGS000687
(snpnet.IGF_1)
 PSS000711|
European Ancestry|
23,453 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: IGF-1 [nmol/L] — — R²: 0.22328
Spearman's ρ: 0.362		 Age, sex, PCs(1-40) —
PPM001520 PGS000687
(snpnet.IGF_1)
 PSS000712|
South Asian Ancestry|
7,283 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: IGF-1 [nmol/L] — — R²: 0.20212
Spearman's ρ: 0.313		 Age, sex, PCs(1-40) —
PPM001555 PGS000687
(snpnet.IGF_1)
 PSS000713|
European Ancestry|
63,393 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: IGF-1 [nmol/L] — — R²: 0.20434
Spearman's ρ: 0.369		 Age, sex, PCs(1-40) —
PPM007360 PGS000687
(snpnet.IGF_1)
 PSS007166|
African Ancestry|
6,058 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: IGF-1 — — R²: 0.08755 [0.07443, 0.10068]
Incremental R2 (full-covars): 0.00429
PGS R2 (no covariates): 0.03282 [0.0243, 0.04133]		 age, sex, UKB array type, Genotype PCs —
PPM007361 PGS000687
(snpnet.IGF_1)
 PSS007167|
East Asian Ancestry|
1,609 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: IGF-1 — — R²: 0.14261 [0.11193, 0.1733]
Incremental R2 (full-covars): 0.00641
PGS R2 (no covariates): 0.06187 [0.03976, 0.08399]		 age, sex, UKB array type, Genotype PCs —
PPM007362 PGS000687
(snpnet.IGF_1)
 PSS007168|
European Ancestry|
23,653 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: IGF-1 — — R²: 0.10834 [0.10105, 0.11562]
Incremental R2 (full-covars): 0.01189
PGS R2 (no covariates): 0.12448 [0.11681, 0.13216]		 age, sex, UKB array type, Genotype PCs —
PPM007363 PGS000687
(snpnet.IGF_1)
 PSS007169|
South Asian Ancestry|
7,373 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: IGF-1 — — R²: 0.11511 [0.10181, 0.1284]
Incremental R2 (full-covars): 0.00941
PGS R2 (no covariates): 0.08722 [0.07528, 0.09915]		 age, sex, UKB array type, Genotype PCs —
PPM007364 PGS000687
(snpnet.IGF_1)
 PSS007170|
European Ancestry|
64,106 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: IGF-1 — — R²: 0.07984 [0.07592, 0.08377]
Incremental R2 (full-covars): 0.01227
PGS R2 (no covariates): 0.12763 [0.12293, 0.13233]		 age, sex, UKB array type, Genotype PCs —
PPM010555 PGS001960
(portability-PLR_log_IGF1)
 PSS009435|
European Ancestry|
18,901 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: IGF-1 — — Partial Correlation (partial-r): 0.3977 [0.3856, 0.4096] sex, age, birth date, deprivation index, 16 PCs —
PPM010556 PGS001960
(portability-PLR_log_IGF1)
 PSS009209|
European Ancestry|
3,935 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: IGF-1 — — Partial Correlation (partial-r): 0.3641 [0.3366, 0.391] sex, age, birth date, deprivation index, 16 PCs —
PPM010557 PGS001960
(portability-PLR_log_IGF1)
 PSS008763|
European Ancestry|
6,290 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: IGF-1 — — Partial Correlation (partial-r): 0.3719 [0.3503, 0.393] sex, age, birth date, deprivation index, 16 PCs —
PPM010558 PGS001960
(portability-PLR_log_IGF1)
 PSS008537|
Greater Middle Eastern Ancestry|
1,118 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: IGF-1 — — Partial Correlation (partial-r): 0.3755 [0.3236, 0.4253] sex, age, birth date, deprivation index, 16 PCs —
PPM010559 PGS001960
(portability-PLR_log_IGF1)
 PSS008315|
South Asian Ancestry|
5,961 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: IGF-1 — — Partial Correlation (partial-r): 0.3361 [0.3134, 0.3585] sex, age, birth date, deprivation index, 16 PCs —
PPM010560 PGS001960
(portability-PLR_log_IGF1)
 PSS008092|
East Asian Ancestry|
1,710 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: IGF-1 — — Partial Correlation (partial-r): 0.2886 [0.2443, 0.3317] sex, age, birth date, deprivation index, 16 PCs —
PPM010561 PGS001960
(portability-PLR_log_IGF1)
 PSS007879|
African Ancestry|
2,328 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: IGF-1 — — Partial Correlation (partial-r): 0.1917 [0.1521, 0.2307] sex, age, birth date, deprivation index, 16 PCs —
PPM010562 PGS001960
(portability-PLR_log_IGF1)
 PSS008983|
African Ancestry|
3,637 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: IGF-1 — — Partial Correlation (partial-r): 0.2039 [0.1725, 0.2349] sex, age, birth date, deprivation index, 16 PCs —
PPM012271 PGS002178
(portability-ldpred2_log_IGF1)
 PSS009435|
European Ancestry|
18,901 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: IGF-1 — — Partial Correlation (partial-r): 0.3913 [0.3791, 0.4033] sex, age, birth date, deprivation index, 16 PCs —
PPM012272 PGS002178
(portability-ldpred2_log_IGF1)
 PSS009209|
European Ancestry|
3,935 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: IGF-1 — — Partial Correlation (partial-r): 0.3623 [0.3347, 0.3892] sex, age, birth date, deprivation index, 16 PCs —
PPM012273 PGS002178
(portability-ldpred2_log_IGF1)
 PSS008763|
European Ancestry|
6,290 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: IGF-1 — — Partial Correlation (partial-r): 0.3614 [0.3397, 0.3827] sex, age, birth date, deprivation index, 16 PCs —
PPM012275 PGS002178
(portability-ldpred2_log_IGF1)
 PSS008315|
South Asian Ancestry|
5,961 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: IGF-1 — — Partial Correlation (partial-r): 0.3299 [0.3071, 0.3524] sex, age, birth date, deprivation index, 16 PCs —
PPM012276 PGS002178
(portability-ldpred2_log_IGF1)
 PSS008092|
East Asian Ancestry|
1,710 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: IGF-1 — — Partial Correlation (partial-r): 0.2809 [0.2364, 0.3242] sex, age, birth date, deprivation index, 16 PCs —
PPM012277 PGS002178
(portability-ldpred2_log_IGF1)
 PSS007879|
African Ancestry|
2,328 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: IGF-1 — — Partial Correlation (partial-r): 0.1863 [0.1466, 0.2254] sex, age, birth date, deprivation index, 16 PCs —
PPM012278 PGS002178
(portability-ldpred2_log_IGF1)
 PSS008983|
African Ancestry|
3,637 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: IGF-1 — — Partial Correlation (partial-r): 0.2085 [0.1771, 0.2395] sex, age, birth date, deprivation index, 16 PCs —
PPM012274 PGS002178
(portability-ldpred2_log_IGF1)
 PSS008537|
Greater Middle Eastern Ancestry|
1,118 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: IGF-1 — — Partial Correlation (partial-r): 0.3575 [0.3048, 0.408] sex, age, birth date, deprivation index, 16 PCs —
PPM017551 PGS003539
(cont-decay-log_IGF1)
 PSS010820|
European Ancestry|
3,924 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: IGF-1 — — partial-R2: 0.13 sex, age, deprivation index, PC1-16 —
PPM017467 PGS003539
(cont-decay-log_IGF1)
 PSS010904|
European Ancestry|
19,017 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: IGF-1 — — partial-R2: 0.16 sex, age, deprivation index, PC1-16 —
PPM017635 PGS003539
(cont-decay-log_IGF1)
 PSS010652|
European Ancestry|
6,139 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: IGF-1 — — partial-R2: 0.13 sex, age, deprivation index, PC1-16 —
PPM017719 PGS003539
(cont-decay-log_IGF1)
 PSS010568|
Greater Middle Eastern Ancestry|
1,089 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: IGF-1 — — partial-R2: 0.12 sex, age, deprivation index, PC1-16 —
PPM017803 PGS003539
(cont-decay-log_IGF1)
 PSS010232|
European Ancestry|
2,227 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: IGF-1 — — partial-R2: 0.17 sex, age, deprivation index, PC1-16 —
PPM017887 PGS003539
(cont-decay-log_IGF1)
 PSS010484|
South Asian Ancestry|
5,908 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: IGF-1 — — partial-R2: 0.11 sex, age, deprivation index, PC1-16 —
PPM017971 PGS003539
(cont-decay-log_IGF1)
 PSS010400|
East Asian Ancestry|
1,699 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: IGF-1 — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM018055 PGS003539
(cont-decay-log_IGF1)
 PSS010316|
African Ancestry|
2,316 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: IGF-1 — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM018139 PGS003539
(cont-decay-log_IGF1)
 PSS010736|
African Ancestry|
3,608 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: IGF-1 — — partial-R2: 0.04 sex, age, deprivation index, PC1-16 —
PPM020453 PGS004338
(X30770.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: IGF-1 (nmol/L) — — PGS R2 (no covariates): 0.28637 — —
PPM037950 PGS019768
(TPMI_795.8_Lassosum2)
 PSS013666|
East Asian Ancestry|
19,661 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Abnormal tumor markers — AUROC: 0.7395 R²: 0.01644 sex, age, array, PCs 1-10 —
PPM037951 PGS019769
(TPMI_795.8_LDpred2)
 PSS013665|
East Asian Ancestry|
19,661 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Abnormal tumor markers — AUROC: 0.74457 R²: 0.01701 sex, age, array, PCs 1-10 —
PPM037952 PGS019770
(TPMI_795.8_MegaPRS)
 PSS013667|
East Asian Ancestry|
19,661 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Abnormal tumor markers — AUROC: 0.73716 R²: 0.01579 sex, age, array, PCs 1-10 —
PPM037953 PGS019771
(TPMI_795.8_PRS-CS)
 PSS013668|
East Asian Ancestry|
19,661 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Abnormal tumor markers — AUROC: 0.74155 R²: 0.01621 sex, age, array, PCs 1-10 —
PPM037954 PGS019772
(TPMI_795.8_SBayesR)
 PSS013669|
East Asian Ancestry|
19,661 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Abnormal tumor markers — AUROC: 0.74098 R²: 0.01618 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
PSS010400 — — 1,699 individuals,
33.0 % Male samples
 Mean = 52.4 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS007879 — — 2,328 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008537 — — 1,118 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009435 — — 18,901 individuals — European UK (+ Ireland) UKB —
PSS000709 — — 5,974 individuals — African unspecified — UKB —
PSS000710 — — 1,074 individuals — East Asian — UKB —
PSS000711 — — 23,453 individuals — European Non-British White UKB —
PSS000712 — — 7,283 individuals — South Asian — UKB —
PSS000713 — — 63,393 individuals — European
(British)		 — UKB —
PSS010820 — — 3,924 individuals,
38.0 % Male samples
 Mean = 54.4 years
Sd = 7.5 years		 European Polish UKB —
PSS010568 — — 1,089 individuals,
60.0 % Male samples
 Mean = 51.9 years
Sd = 7.9 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010316 — — 2,316 individuals,
37.0 % Male samples
 Mean = 52.5 years
Sd = 8.1 years		 African American or Afro-Caribbean Caribbean UKB —
PSS009209 — — 3,935 individuals — European Poland (NE Europe) UKB —
PSS008315 — — 5,961 individuals — South Asian India (South Asia) UKB —
PSS007166 — — 6,058 individuals — African unspecified — UKB —
PSS007167 — — 1,609 individuals — East Asian — UKB —
PSS007168 — — 23,653 individuals — European non-white British ancestry UKB —
PSS007169 — — 7,373 individuals — South Asian — UKB —
PSS007170 — — 64,106 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS010736 — — 3,608 individuals,
46.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS008983 — — 3,637 individuals — African unspecified Nigeria (West Africa) UKB —
PSS010484 — — 5,908 individuals,
54.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS008092 — — 1,710 individuals — East Asian China (East Asia) UKB —
PSS010232 — — 2,227 individuals,
45.0 % Male samples
 Mean = 58.1 years
Sd = 7.0 years		 European Ashkenazi UKB —
PSS011364 — — 56,192 individuals — European — UKB —
PSS013665 795.81, 795.82, 795.89,R97 —
[
  • 195 cases
  • , 19,466 controls
]
,
46.16 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013666 795.81, 795.82, 795.89,R97 —
[
  • 195 cases
  • , 19,466 controls
]
,
46.16 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013667 795.81, 795.82, 795.89,R97 —
[
  • 195 cases
  • , 19,466 controls
]
,
46.16 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013668 795.81, 795.82, 795.89,R97 —
[
  • 195 cases
  • , 19,466 controls
]
,
46.16 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS013669 795.81, 795.82, 795.89,R97 —
[
  • 195 cases
  • , 19,466 controls
]
,
46.16 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS008763 — — 6,290 individuals — European Italy (South Europe) UKB —
PSS010904 — — 19,017 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010652 — — 6,139 individuals,
45.0 % Male samples
 Mean = 54.4 years
Sd = 8.4 years		 European Italian UKB —