Trait: benign colon neoplasm

Trait Information
Identifier MONDO_0002278
Description A non-metastasizing neoplasm arising from the wall of the colon. [NCIT: C2894]
Trait categories
Cancer
Digestive system disorder
Synonyms 10 synonyms
  • benign colon neoplasm
  • benign colon tumor
  • benign colonic neoplasm
  • benign colonic tumor
  • benign neoplasm of colon
  • benign neoplasm of the colon
  • benign tumor of colon
  • benign tumor of the colon
  • colon benign neoplasm
  • colonic Mass
Mapped terms 5 mapped terms
  • DOID:235
  • ICD9:211.3
  • NCIT:C2894
  • SCTID:92065004
  • UMLS:C0004991

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 Scoring File (FTP Link)
PGS001811
(portability-PLR_208)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Benign neoplasm of colon benign colon neoplasm 2,231
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001811/ScoringFiles/PGS001811.txt.gz
PGS002019
(portability-ldpred2_208)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Benign neoplasm of colon benign colon neoplasm 667,546
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002019/ScoringFiles/PGS002019.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
PPM011033 PGS002019
(portability-ldpred2_208)
PSS008834|
African Ancestry|
3,905 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of colon Partial Correlation (partial-r): 0.0603 [0.0289, 0.0916] sex, age, birth date, deprivation index, 16 PCs
PPM011032 PGS002019
(portability-ldpred2_208)
PSS007731|
African Ancestry|
2,469 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of colon Partial Correlation (partial-r): 0.0409 [0.0012, 0.0803] sex, age, birth date, deprivation index, 16 PCs
PPM011031 PGS002019
(portability-ldpred2_208)
PSS007950|
East Asian Ancestry|
1,800 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of colon Partial Correlation (partial-r): 0.0601 [0.0137, 0.1063] sex, age, birth date, deprivation index, 16 PCs
PPM011030 PGS002019
(portability-ldpred2_208)
PSS008163|
South Asian Ancestry|
6,307 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of colon Partial Correlation (partial-r): 0.0398 [0.0151, 0.0645] sex, age, birth date, deprivation index, 16 PCs
PPM011029 PGS002019
(portability-ldpred2_208)
PSS008385|
Greater Middle Eastern Ancestry|
1,194 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of colon Partial Correlation (partial-r): 0.0966 [0.0396, 0.153] sex, age, birth date, deprivation index, 16 PCs
PPM011028 PGS002019
(portability-ldpred2_208)
PSS008609|
European Ancestry|
6,617 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of colon Partial Correlation (partial-r): 0.0659 [0.0418, 0.0899] sex, age, birth date, deprivation index, 16 PCs
PPM011027 PGS002019
(portability-ldpred2_208)
PSS009055|
European Ancestry|
4,121 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of colon Partial Correlation (partial-r): 0.0761 [0.0456, 0.1065] sex, age, birth date, deprivation index, 16 PCs
PPM011026 PGS002019
(portability-ldpred2_208)
PSS009281|
European Ancestry|
19,812 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of colon Partial Correlation (partial-r): 0.0716 [0.0577, 0.0854] sex, age, birth date, deprivation index, 16 PCs
PPM009395 PGS001811
(portability-PLR_208)
PSS008834|
African Ancestry|
3,905 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of colon Partial Correlation (partial-r): 0.0459 [0.0145, 0.0772] sex, age, birth date, deprivation index, 16 PCs
PPM009394 PGS001811
(portability-PLR_208)
PSS007731|
African Ancestry|
2,469 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of colon Partial Correlation (partial-r): 0.0518 [0.0122, 0.0912] sex, age, birth date, deprivation index, 16 PCs
PPM009393 PGS001811
(portability-PLR_208)
PSS007950|
East Asian Ancestry|
1,800 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of colon Partial Correlation (partial-r): 0.0293 [-0.0171, 0.0757] sex, age, birth date, deprivation index, 16 PCs
PPM009392 PGS001811
(portability-PLR_208)
PSS008163|
South Asian Ancestry|
6,307 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of colon Partial Correlation (partial-r): 0.023 [-0.0017, 0.0477] sex, age, birth date, deprivation index, 16 PCs
PPM009391 PGS001811
(portability-PLR_208)
PSS008385|
Greater Middle Eastern Ancestry|
1,194 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of colon Partial Correlation (partial-r): 0.0914 [0.0344, 0.1478] sex, age, birth date, deprivation index, 16 PCs
PPM009390 PGS001811
(portability-PLR_208)
PSS008609|
European Ancestry|
6,617 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of colon Partial Correlation (partial-r): 0.0584 [0.0343, 0.0824] sex, age, birth date, deprivation index, 16 PCs
PPM009389 PGS001811
(portability-PLR_208)
PSS009055|
European Ancestry|
4,121 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of colon Partial Correlation (partial-r): 0.0651 [0.0345, 0.0955] sex, age, birth date, deprivation index, 16 PCs
PPM009388 PGS001811
(portability-PLR_208)
PSS009281|
European Ancestry|
19,812 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of colon Partial Correlation (partial-r): 0.0643 [0.0504, 0.0782] sex, age, birth date, deprivation index, 16 PCs

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
PSS008609 6,617 individuals European Italy (South Europe) UKB
PSS007950 1,800 individuals East Asian China (East Asia) UKB
PSS007731 2,469 individuals African American or Afro-Caribbean Carribean UKB
PSS009281 19,812 individuals European UK (+ Ireland) UKB
PSS009055 4,121 individuals European Poland (NE Europe) UKB
PSS008385 1,194 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008834 3,905 individuals African unspecified Nigeria (West Africa) UKB
PSS008163 6,307 individuals South Asian India (South Asia) UKB