PGS Publication: PGP000171

Publication Information (EuropePMC)
Title Polygenic background modifies penetrance of monogenic variants for tier 1 genomic conditions.
PubMed ID 32820175(Europe PMC)
doi 10.1038/s41467-020-17374-3
Publication Date Aug. 20, 2020
Journal Nat Commun
Author(s) Fahed AC, Wang M, Homburger JR, Patel AP, Bick AG, Neben CL, Lai C, Brockman D, Philippakis A, Ellinor PT, Cassa CA, Lebo M, Ng K, Lander ES, Zhou AY, Kathiresan S, Khera AV.
Released in PGS Catalog: April 28, 2021

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

External PGS Evaluated By This Publication

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)
PGS000004
(PRS313_BC)
 PGP000002 |
Mavaddat N et al. Am J Hum Genet (2018)
 Breast cancer breast carcinoma 313
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000004/ScoringFiles/PGS000004.txt.gz
PGS000765
(PRS_CRC95)
 PGP000170 |
Huyghe JR et al. Nat Genet (2018)
 Colorectal cancer colorectal cancer 95
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000765/ScoringFiles/PGS000765.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
PPM001958 PGS000004
(PRS313_BC)
 PSS000979|
Multi-ancestry (including European)|
19,264 individuals
 PGP000171 |
Fahed AC et al. Nat Commun (2020)
|Ext.		 Reported Trait: Breast cancer in carriers of a hereditary breast and ovarian cancer variant OR: 1.44 [1.19, 1.74] — Odds Ratio (OR, top 20% vs bottom 20%): 3.04 [1.61, 5.73] Age, PCs (1-4) —
PPM001959 PGS000004
(PRS313_BC)
 PSS000979|
Multi-ancestry (including European)|
19,264 individuals
 PGP000171 |
Fahed AC et al. Nat Commun (2020)
|Ext.		 Reported Trait: Breast cancer in non-carriers of a hereditary breast and ovarian cancer variant OR: 1.57 [1.49, 1.65] — — Age, PCs (1-4) —
PPM001960 PGS000004
(PRS313_BC)
 PSS000980|
Multi-ancestry (including European)|
26,595 individuals
 PGP000171 |
Fahed AC et al. Nat Commun (2020)
|Ext.		 Reported Trait: Prevalent breast cancer OR: 1.61 [1.52, 1.7] — — Age, PCs (1-4) —
PPM001961 PGS000765
(PRS_CRC95)
 PSS000981|
Multi-ancestry (including European)|
48,807 individuals
 PGP000171 |
Fahed AC et al. Nat Commun (2020)
|Ext.		 Reported Trait: Prevalent colorectal cancer OR: 1.65 [1.48, 1.85] — — Age, sex, PCs (1-4) —

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
PSS000979 Cases were individuals with breast cancer based on self-reporting at the time of enrollment. Out of the total 19,264 individuals, 845 individuals were carriers of a hereditary breast and ovarian cancer (HBOC) variant. Of the 845 individuals, 174 had breast cancer. —
[
  • 1,375 cases
  • , 12,365 controls
]
,
0.0 % Male samples
 — European — CG —
PSS000979 Cases were individuals with breast cancer based on self-reporting at the time of enrollment. Out of the total 19,264 individuals, 845 individuals were carriers of a hereditary breast and ovarian cancer (HBOC) variant. Of the 845 individuals, 174 had breast cancer. —
[
  • 30 cases
  • , 410 controls
]
,
0.0 % Male samples
 — African unspecified — CG —
PSS000979 Cases were individuals with breast cancer based on self-reporting at the time of enrollment. Out of the total 19,264 individuals, 845 individuals were carriers of a hereditary breast and ovarian cancer (HBOC) variant. Of the 845 individuals, 174 had breast cancer. —
[
  • 83 cases
  • , 695 controls
]
,
0.0 % Male samples
 — Asian unspecified — CG —
PSS000979 Cases were individuals with breast cancer based on self-reporting at the time of enrollment. Out of the total 19,264 individuals, 845 individuals were carriers of a hereditary breast and ovarian cancer (HBOC) variant. Of the 845 individuals, 174 had breast cancer. —
[
  • 432 cases
  • , 3,874 controls
]
,
0.0 % Male samples
 — Not reported — CG —
PSS000980 Cases were individuals with breast cancer based on self-reporting at the base line (Data code: 1002), primary diagnoses (ICD-10) from hospitalization records (Data codes: C50,C500,C501,C502,C503,C504,C505,C506,C508,C509,D05,D050,D051,D057,D059,D486,Z853), primary diagnoses (ICD-9) from hospitalization records (Data codes: 174,174,1740,1743,1744,1745,1748,1749,2330,2383,2393), secondary disgnoses (ICD-10) from hopsitalization records (Data codes: C50,C500,C501,C502,C503,C504,C505,C506,C508,D05,D050,D051,D057,D 059,D486,Z853), secondary diagnoses (ICD-9) from hopsitalization records (Data codes: 174,1749,2330,V103), cancer registry data specifying the type of cancer (ICD-10) from the cancer registry (Data codes: C50,C500,C501,C502,C503,C504,C506,C508,C509,D050,D051,D057,D059,174,175,1740,1741,1742,1743,1744,1745,1746,1748,1749,2330,2383), primary cause of death (ICD-10) from the death registry (Data codes: C50,C500,C501,C502,C503,C504,C505,C506,C508) and secondary cause of death (ICD-10) from the death registry (Data codes: C50,C500,C501,C502,C503,C504,C505,C506,C508) . Of the total number of cases and controls, 115 were carriers of a pathogenic or likely pathogenic variant. Of the total number of cases and controls, 115 were carriers of a pathogenic or likely pathogenic variant. —
[
  • 1,276 cases
  • , 23,442 controls
]
,
0.0 % Male samples
 — European — UKB —
PSS000980 Cases were individuals with breast cancer based on self-reporting at the base line (Data code: 1002), primary diagnoses (ICD-10) from hospitalization records (Data codes: C50,C500,C501,C502,C503,C504,C505,C506,C508,C509,D05,D050,D051,D057,D059,D486,Z853), primary diagnoses (ICD-9) from hospitalization records (Data codes: 174,174,1740,1743,1744,1745,1748,1749,2330,2383,2393), secondary disgnoses (ICD-10) from hopsitalization records (Data codes: C50,C500,C501,C502,C503,C504,C505,C506,C508,D05,D050,D051,D057,D 059,D486,Z853), secondary diagnoses (ICD-9) from hopsitalization records (Data codes: 174,1749,2330,V103), cancer registry data specifying the type of cancer (ICD-10) from the cancer registry (Data codes: C50,C500,C501,C502,C503,C504,C506,C508,C509,D050,D051,D057,D059,174,175,1740,1741,1742,1743,1744,1745,1746,1748,1749,2330,2383), primary cause of death (ICD-10) from the death registry (Data codes: C50,C500,C501,C502,C503,C504,C505,C506,C508) and secondary cause of death (ICD-10) from the death registry (Data codes: C50,C500,C501,C502,C503,C504,C505,C506,C508) . Of the total number of cases and controls, 115 were carriers of a pathogenic or likely pathogenic variant. Of the total number of cases and controls, 115 were carriers of a pathogenic or likely pathogenic variant. —
[
  • 12 cases
  • , 612 controls
]
,
0.0 % Male samples
 — African unspecified — UKB —
PSS000980 Cases were individuals with breast cancer based on self-reporting at the base line (Data code: 1002), primary diagnoses (ICD-10) from hospitalization records (Data codes: C50,C500,C501,C502,C503,C504,C505,C506,C508,C509,D05,D050,D051,D057,D059,D486,Z853), primary diagnoses (ICD-9) from hospitalization records (Data codes: 174,174,1740,1743,1744,1745,1748,1749,2330,2383,2393), secondary disgnoses (ICD-10) from hopsitalization records (Data codes: C50,C500,C501,C502,C503,C504,C505,C506,C508,D05,D050,D051,D057,D 059,D486,Z853), secondary diagnoses (ICD-9) from hopsitalization records (Data codes: 174,1749,2330,V103), cancer registry data specifying the type of cancer (ICD-10) from the cancer registry (Data codes: C50,C500,C501,C502,C503,C504,C506,C508,C509,D050,D051,D057,D059,174,175,1740,1741,1742,1743,1744,1745,1746,1748,1749,2330,2383), primary cause of death (ICD-10) from the death registry (Data codes: C50,C500,C501,C502,C503,C504,C505,C506,C508) and secondary cause of death (ICD-10) from the death registry (Data codes: C50,C500,C501,C502,C503,C504,C505,C506,C508) . Of the total number of cases and controls, 115 were carriers of a pathogenic or likely pathogenic variant. Of the total number of cases and controls, 115 were carriers of a pathogenic or likely pathogenic variant. —
[
  • 25 cases
  • , 597 controls
]
,
0.0 % Male samples
 — Asian unspecified — UKB —
PSS000980 Cases were individuals with breast cancer based on self-reporting at the base line (Data code: 1002), primary diagnoses (ICD-10) from hospitalization records (Data codes: C50,C500,C501,C502,C503,C504,C505,C506,C508,C509,D05,D050,D051,D057,D059,D486,Z853), primary diagnoses (ICD-9) from hospitalization records (Data codes: 174,174,1740,1743,1744,1745,1748,1749,2330,2383,2393), secondary disgnoses (ICD-10) from hopsitalization records (Data codes: C50,C500,C501,C502,C503,C504,C505,C506,C508,D05,D050,D051,D057,D 059,D486,Z853), secondary diagnoses (ICD-9) from hopsitalization records (Data codes: 174,1749,2330,V103), cancer registry data specifying the type of cancer (ICD-10) from the cancer registry (Data codes: C50,C500,C501,C502,C503,C504,C506,C508,C509,D050,D051,D057,D059,174,175,1740,1741,1742,1743,1744,1745,1746,1748,1749,2330,2383), primary cause of death (ICD-10) from the death registry (Data codes: C50,C500,C501,C502,C503,C504,C505,C506,C508) and secondary cause of death (ICD-10) from the death registry (Data codes: C50,C500,C501,C502,C503,C504,C505,C506,C508) . Of the total number of cases and controls, 115 were carriers of a pathogenic or likely pathogenic variant. Of the total number of cases and controls, 115 were carriers of a pathogenic or likely pathogenic variant. —
[
  • 24 cases
  • , 607 controls
]
,
0.0 % Male samples
 — Not reported — UKB —
PSS000981 Cases were individuals with colorectal cancer based on self-reporting at the baseline (Coding IDs: 10,221,023), primary cause of death (ICD-10) from the death registry (Coding IDsC180,C182,C183,C184,C185,C186,C187,C188,C189), secondary cause of death (ICD-10) from the death registry (Coding IDs: C180,C182,C183,C184,C185,C186,C187,C188,C189), type of cancer (ICD-10) from the cancer registry (Coding IDs: C18,C180,C181,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375, 153,154,1530,1531,1532,1533,1534,1535,1536,1537,1538,1539,1540,1541,1 548,2303,2304), primary diagnoses (ICD-10) from hospitalization records (Coding IDs: C18,C180,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375), primary diagnoses (ICD-9) from hopsitalization records (Coding IDs: 153,154,1530,1532,1533,1534,1536,1537,1539,1540,1541), secondary diagnoses (ICD-10) from hospitalization records (Coding IDs: C18,C180,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375), secondary diagnoses (ICD-9) from hospitialization records (Coding IDs: 153,153,154,1532,1533,1541). Of the total number of cases and controls, 76 were carriers of a pathogenic or likely pathogenic variant in any of the following genes: MLH1, MSH2, MSH6 and PMS2. —
[
  • 303 cases
  • , 45,233 controls
]
 — European — UKB —
PSS000981 Cases were individuals with colorectal cancer based on self-reporting at the baseline (Coding IDs: 10,221,023), primary cause of death (ICD-10) from the death registry (Coding IDsC180,C182,C183,C184,C185,C186,C187,C188,C189), secondary cause of death (ICD-10) from the death registry (Coding IDs: C180,C182,C183,C184,C185,C186,C187,C188,C189), type of cancer (ICD-10) from the cancer registry (Coding IDs: C18,C180,C181,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375, 153,154,1530,1531,1532,1533,1534,1535,1536,1537,1538,1539,1540,1541,1 548,2303,2304), primary diagnoses (ICD-10) from hospitalization records (Coding IDs: C18,C180,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375), primary diagnoses (ICD-9) from hopsitalization records (Coding IDs: 153,154,1530,1532,1533,1534,1536,1537,1539,1540,1541), secondary diagnoses (ICD-10) from hospitalization records (Coding IDs: C18,C180,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375), secondary diagnoses (ICD-9) from hospitialization records (Coding IDs: 153,153,154,1532,1533,1541). Of the total number of cases and controls, 76 were carriers of a pathogenic or likely pathogenic variant in any of the following genes: MLH1, MSH2, MSH6 and PMS2. —
[
  • 6 cases
  • , 993 controls
]
 — African unspecified — UKB —
PSS000981 Cases were individuals with colorectal cancer based on self-reporting at the baseline (Coding IDs: 10,221,023), primary cause of death (ICD-10) from the death registry (Coding IDsC180,C182,C183,C184,C185,C186,C187,C188,C189), secondary cause of death (ICD-10) from the death registry (Coding IDs: C180,C182,C183,C184,C185,C186,C187,C188,C189), type of cancer (ICD-10) from the cancer registry (Coding IDs: C18,C180,C181,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375, 153,154,1530,1531,1532,1533,1534,1535,1536,1537,1538,1539,1540,1541,1 548,2303,2304), primary diagnoses (ICD-10) from hospitalization records (Coding IDs: C18,C180,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375), primary diagnoses (ICD-9) from hopsitalization records (Coding IDs: 153,154,1530,1532,1533,1534,1536,1537,1539,1540,1541), secondary diagnoses (ICD-10) from hospitalization records (Coding IDs: C18,C180,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375), secondary diagnoses (ICD-9) from hospitialization records (Coding IDs: 153,153,154,1532,1533,1541). Of the total number of cases and controls, 76 were carriers of a pathogenic or likely pathogenic variant in any of the following genes: MLH1, MSH2, MSH6 and PMS2. —
[
  • 3 cases
  • , 1,216 controls
]
 — Asian unspecified — UKB —
PSS000981 Cases were individuals with colorectal cancer based on self-reporting at the baseline (Coding IDs: 10,221,023), primary cause of death (ICD-10) from the death registry (Coding IDsC180,C182,C183,C184,C185,C186,C187,C188,C189), secondary cause of death (ICD-10) from the death registry (Coding IDs: C180,C182,C183,C184,C185,C186,C187,C188,C189), type of cancer (ICD-10) from the cancer registry (Coding IDs: C18,C180,C181,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375, 153,154,1530,1531,1532,1533,1534,1535,1536,1537,1538,1539,1540,1541,1 548,2303,2304), primary diagnoses (ICD-10) from hospitalization records (Coding IDs: C18,C180,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375), primary diagnoses (ICD-9) from hopsitalization records (Coding IDs: 153,154,1530,1532,1533,1534,1536,1537,1539,1540,1541), secondary diagnoses (ICD-10) from hospitalization records (Coding IDs: C18,C180,C182,C183,C184,C185,C186,C187,C188,C189,C19,C20,D010,D011,D012,D374,D375), secondary diagnoses (ICD-9) from hospitialization records (Coding IDs: 153,153,154,1532,1533,1541). Of the total number of cases and controls, 76 were carriers of a pathogenic or likely pathogenic variant in any of the following genes: MLH1, MSH2, MSH6 and PMS2. —
[
  • 3 cases
  • , 1,050 controls
]
 — Not reported — UKB —