Trait: lymphoid leukemia

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004289
Description A malignant lymphocytic neoplasm of B-cell or T-cell lineage involving primarily the bone marrow and the peripheral blood. This category includes precursor or acute lymphoblastic leukemias and chronic leukemias. [NCIT: C7539]
Trait category
Cancer
Immune system disorder
Synonyms 11 synonyms
  • Lymphoblastic Lymphoma
  • Lymphomas, Lymphoblastic
  • lymphoid leukemia
  • leukemia, LYMPHOCYTIC, malignant
  • lymphogenous leukemia
  • lymphocytic leukemia
  • lymphoid leukemia (disease)
  • Lymphoma, Lymphoblastic
  • Lymphoblastic leukaemia
  • subacute lymphoid leukemia
  • leukemia, lymphoid
Mapped term(s) 18 mapped terms
  • NCIT:C7539
  • SNOMEDCT:32280000
  • ICDO:9820/3
  • MSH:D007945
  • ICDO:981-983
  • SNOMEDCT:188725004
  • DOID:10747
  • SCTID:188726003
  • MESH:D007945
  • UMLS:C0023448
  • MONDO:0005402
  • ICD9:204.2
  • ICD9:204
  • NCIt:C7539
  • UMLS:C0152271
  • ICD9:204.20
  • ICD10:C91
  • HP:0005526

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000077 CC_LL PGP000050 Graff RE et al. bioRxiv (2020) Pre Lymphocytic leukemia lymphoid leukemia 75 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000077/ScoringFiles/PGS000077.txt.gz

PGS 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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000197 PGS000077 (CC_LL) PSS000116 PGP000050
Graff RE et al. (2020)
Pre
Reported Trait: Lymphocytic leukemia OR: 1.42[1.33, 1.51] 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 ID)
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
PSS000116 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): 35011 - 35013
[
  • 853 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB