Trait: gastric carcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000178
Description A carcinoma that arises from epithelial cells of the stomach. [MONDO: DesignPattern]
Trait category
Cancer
Digestive system disorder
Synonyms 16 synonyms
  • CA IN SITU STOMACH
  • Ca fundus - stomach
  • Carcinoma in situ of stomach
  • cancer of fundus of stomach
  • carcinoma in situ of stomach (disorder)
  • carcinoma in situ of stomach NOS (disorder)
  • carcinoma of stomach
  • carcinoma of the stomach
  • fundus of stomach cancer
  • gastric carcinoma
  • gastric carcinoma in situ
  • gastric fundus cancer
  • malignant fundus of stomach neoplasm
  • malignant neoplasm of fundus of stomach
  • malignant tumor of fundus of stomach
  • stomach carcinoma
Mapped term(s) 13 mapped terms
  • DOID:10538
  • DOID:5517
  • ICD10:C16.1
  • ICD9:151.3
  • ICD9:230.2
  • MONDO:0004950
  • NCIT:C4911
  • NCIt:C4911
  • OMIM:613659
  • SCTID:187741001
  • SNOMEDCT:92756002
  • UMLS:C0153420
  • UMLS:C0699791

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)
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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 PGS Scoring File (FTP Link)
PGS000085
(CC_Stomach)
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Esophageal and stomach cancers gastric carcinoma,
Barrett's esophagus
13
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000085/ScoringFiles/PGS000085.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
PPM000205 PGS000085
(CC_Stomach)
PSS000124|
European Ancestry|
411,448 individuals
PGP000050 |
Graff RE et al. bioRxiv (2020)
|Pre
Reported Trait: Esophageal and stomach cancers OR: 1.07 [1.0, 1.13] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB

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
PSS000124 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 21010 and 21020
[
  • 1,094 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB