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
  • Lymphoblastic leukaemia
  • Lymphoma, Lymphoblastic
  • Lymphomas, Lymphoblastic
  • leukemia, LYMPHOCYTIC, malignant
  • leukemia, lymphoid
  • lymphocytic leukemia
  • lymphogenous leukemia
  • lymphoid leukemia
  • lymphoid leukemia (disease)
  • subacute lymphoid leukemia
Mapped term(s) 18 mapped terms
  • DOID:10747
  • HP:0005526
  • ICD10:C91
  • ICD9:204
  • ICD9:204.2
  • ICD9:204.20
  • ICDO:981-983
  • ICDO:9820/3
  • MESH:D007945
  • MONDO:0005402
  • MeSH:D007945
  • NCIT:C7539
  • NCIt:C7539
  • SCTID:188726003
  • SNOMEDCT:188725004
  • SNOMEDCT:32280000
  • UMLS:C0023448
  • UMLS:C0152271
Child trait(s) chronic lymphocytic leukemia

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 "lymphoid leukemia" 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 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
PGS000645
(PRSWEB_PHECODE204.1_C-LYMPHOID-LEUKAEMIA_PT_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Lymphoid leukemia lymphoid leukemia 6
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000645/ScoringFiles/PGS000645.txt.gz
PGS000646
(PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_P_5e-08_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Lymphoid leukemia, chronic chronic lymphocytic leukemia 32
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000646/ScoringFiles/PGS000646.txt.gz
PGS000647
(PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_P_5e-08_UKB_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Lymphoid leukemia, chronic chronic lymphocytic leukemia 32
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000647/ScoringFiles/PGS000647.txt.gz
PGS000648
(PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_PT_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Lymphoid leukemia, chronic chronic lymphocytic leukemia 44
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000648/ScoringFiles/PGS000648.txt.gz
PGS000649
(PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_PT_UKB_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Lymphoid leukemia, chronic chronic lymphocytic leukemia 27
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000649/ScoringFiles/PGS000649.txt.gz
PGS000650
(PRSWEB_PHECODE204.12_UKBB-SAIGE-HRC-X204.12_PT_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Lymphoid leukemia, chronic chronic lymphocytic leukemia 6
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000650/ScoringFiles/PGS000650.txt.gz
PGS000651
(PRSWEB_PHECODE204.12_UKBB-SAIGE-HRC-X204.12_LASSOSUM_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Lymphoid leukemia, chronic chronic lymphocytic leukemia 76
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000651/ScoringFiles/PGS000651.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
PPM000197 PGS000077
(CC_LL)
PSS000116|
European Ancestry|
411,207 individuals
PGP000050 |
Graff RE et al. bioRxiv (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
PPM001330 PGS000645
(PRSWEB_PHECODE204.1_C-LYMPHOID-LEUKAEMIA_PT_MGI_20200608)
PSS000562|
European Ancestry|
957 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Lymphoid leukemia OR: 1.358 [1.113, 1.657]
β: 0.306 (0.102)
AUROC: 0.578 [0.517, 0.642] Nagelkerke's Pseudo-R²: 0.0193
Brier score: 0.0819
Odds Ratio (OR, top 1% vs. Rest): 3.69 [1.01, 13.4]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE204.1_C-LYMPHOID-LEUKAEMIA_PT_MGI_20200608
PPM001331 PGS000646
(PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_P_5e-08_MGI_20200608)
PSS000561|
European Ancestry|
756 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Lymphoid leukemia, chronic OR: 2.104 [1.628, 2.718]
β: 0.744 (0.131)
AUROC: 0.696 [0.628, 0.765] Nagelkerke's Pseudo-R²: 0.0973
Brier score: 0.0779
Odds Ratio (OR, top 1% vs. Rest): 11.3 [3.76, 33.9]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_P_5e-08_MGI_20200608
PPM001332 PGS000647
(PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_P_5e-08_UKB_20200608)
PSS000581|
European Ancestry|
2,758 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Lymphoid leukemia, chronic OR: 1.874 [1.639, 2.144]
β: 0.628 (0.0685)
AUROC: 0.675 [0.64, 0.707] Nagelkerke's Pseudo-R²: 0.0689
Brier score: 0.0795
Odds Ratio (OR, top 1% vs. Rest): 4.11 [1.97, 8.6]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_P_5e-08_UKB_20200608
PPM001333 PGS000648
(PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_PT_MGI_20200608)
PSS000561|
European Ancestry|
756 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Lymphoid leukemia, chronic OR: 2.124 [1.648, 2.738]
β: 0.753 (0.13)
AUROC: 0.696 [0.621, 0.764] Nagelkerke's Pseudo-R²: 0.102
Brier score: 0.0776
Odds Ratio (OR, top 1% vs. Rest): 12.9 [4.45, 37.6]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_PT_MGI_20200608
PPM001334 PGS000649
(PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_PT_UKB_20200608)
PSS000581|
European Ancestry|
2,758 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Lymphoid leukemia, chronic OR: 1.85 [1.619, 2.114]
β: 0.615 (0.0681)
AUROC: 0.672 [0.637, 0.703] Nagelkerke's Pseudo-R²: 0.0665
Brier score: 0.0796
Odds Ratio (OR, top 1% vs. Rest): 2.52 [1.04, 6.08]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_PT_UKB_20200608
PPM001335 PGS000650
(PRSWEB_PHECODE204.12_UKBB-SAIGE-HRC-X204.12_PT_MGI_20200608)
PSS000561|
European Ancestry|
756 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Lymphoid leukemia, chronic OR: 1.368 [1.097, 1.705]
β: 0.313 (0.113)
AUROC: 0.577 [0.511, 0.645] Nagelkerke's Pseudo-R²: 0.0205
Brier score: 0.0822
Odds Ratio (OR, top 1% vs. Rest): 2.0 [0.308, 13.0]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE204.12_UKBB-SAIGE-HRC-X204.12_PT_MGI_20200608
PPM001336 PGS000651
(PRSWEB_PHECODE204.12_UKBB-SAIGE-HRC-X204.12_LASSOSUM_MGI_20200608)
PSS000561|
European Ancestry|
756 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Lymphoid leukemia, chronic OR: 1.32 [1.041, 1.675]
β: 0.278 (0.121)
AUROC: 0.573 [0.503, 0.644] Nagelkerke's Pseudo-R²: 0.0145
Brier score: 0.0823
Odds Ratio (OR, top 1% vs. Rest): 4.84 [1.23, 19.0]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE204.12_UKBB-SAIGE-HRC-X204.12_LASSOSUM_MGI_20200608

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
PSS000562 PheCode:204.1; ICD9CM:204.00, 204.01, 204.02, 204.10, 204.11, 204.12, 204.20, 204.21, 204.22, 204.80, 204.81, 204.82, 204.90, 204.91, 204.92, V10.61; ICD10CM:C91, C91.0, C91.00, C91.01, C91.02, C91.1, C91.10, C91.11, C91.12, C91.3, C91.30, C91.31, C91.32, C91.4, C91.40, C91.41, C91.42, C91.5, C91.50, C91.51, C91.52, C91.6, C91.60, C91.61, C91.62, C91.9, C91.90, C91.91, C91.92, C91.A, C91.A0, C91.A1, C91.A2, C91.Z, C91.Z0, C91.Z1, C91.Z2
[
  • 87 cases
  • , 870 controls
]
European MGI
PSS000581 PheCode:204.12; ICD9:204.1; ICD10:C91.1
[
  • 249 cases
  • , 2,509 controls
]
European UKB
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
PSS000561 PheCode:204.12; ICD9CM:204.10, 204.11, 204.12; ICD10CM:C91.1, C91.10, C91.11, C91.12
[
  • 69 cases
  • , 687 controls
]
European MGI