PGS Publication: PGP000249

Publication Information (EuropePMC)
Title Generalizability of Polygenic Risk Scores for Breast Cancer Among Women With European, African, and Latinx Ancestry.
PubMed ID 34347061(Europe PMC)
doi 10.1001/jamanetworkopen.2021.19084
Publication Date Aug. 2, 2021
Journal JAMA Netw Open
Author(s) Liu C, Zeinomar N, Chung WK, Kiryluk K, Gharavi AG, Hripcsak G, Crew KD, Shang N, Khan A, Fasel D, Manolio TA, Jarvik GP, Rowley R, Justice AE, Rahm AK, Fullerton SM, Smoller JW, Larson EB, Crane PK, Dikilitas O, Wiesner GL, Bick AG, Terry MB, Weng C.
Released in PGS Catalog: Nov. 4, 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)
PGS000317
(PRS180)
 PGP000094 |
Shieh Y et al. J Natl Cancer Inst (2020)
 Breast cancer breast carcinoma 180
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000317/ScoringFiles/PGS000317.txt.gz
PGS000015
(GPS_BC)
 PGP000006 |
Khera AV et al. Nat Genet (2018)
 Breast cancer breast carcinoma 5,218
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000015/ScoringFiles/PGS000015.txt.gz - Check Terms/Licenses
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
PGS000007
(PRS3820_BC)
 PGP000002 |
Mavaddat N et al. Am J Hum Genet (2018)
 Breast cancer breast carcinoma 3,820
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000007/ScoringFiles/PGS000007.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
PPM005169 PGS000007
(PRS3820_BC)
 PSS003599|
European Ancestry|
33,954 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer — AUROC: 0.59 [0.58, 0.6] R²: 0.021 — —
PPM005170 PGS000015
(GPS_BC)
 PSS003599|
European Ancestry|
33,954 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer — AUROC: 0.61 [0.6, 0.62] R²: 0.017 — —
PPM005171 PGS000004
(PRS313_BC)
 PSS003598|
African Ancestry|
3,801 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer — AUROC: 0.55 [0.51, 0.58] R²: 0.0003 — —
PPM005172 PGS000007
(PRS3820_BC)
 PSS003598|
African Ancestry|
3,801 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer — AUROC: 0.53 [0.5, 0.57] R²: 0.0002 — —
PPM005167 PGS000317
(PRS180)
 PSS003600|
Hispanic or Latin American Ancestry|
2,196 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer OR: 1.2 [1.0, 1.46] — — Age, family history, study site, 3 ancestry-specific PCs —
PPM005168 PGS000004
(PRS313_BC)
 PSS003599|
European Ancestry|
33,954 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer — AUROC: 0.6 [0.59, 0.61] R²: 0.025 — —
PPM005176 PGS000317
(PRS180)
 PSS003600|
Hispanic or Latin American Ancestry|
2,196 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer — AUROC: 0.54 [0.47, 0.62] R²: 0.05 — —
PPM005159 PGS000004
(PRS313_BC)
 PSS003599|
European Ancestry|
33,954 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer OR: 1.4 [1.35, 1.45] — — Age, family history, study site, 3 ancestry-specific PCs —
PPM005160 PGS000007
(PRS3820_BC)
 PSS003599|
European Ancestry|
33,954 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer OR: 1.36 [1.31, 1.41] — — Age, family history, study site, 3 ancestry-specific PCs —
PPM005161 PGS000015
(GPS_BC)
 PSS003599|
European Ancestry|
33,954 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer OR: 1.46 [1.41, 1.51] — Odds Ratio (OR, top 1% vs middle 20%): 2.48 [1.89, 3.25] Age, family history, study site, 3 ancestry-specific PCs —
PPM005162 PGS000004
(PRS313_BC)
 PSS003598|
African Ancestry|
3,801 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer OR: 1.26 [1.1, 1.44] — — Age, family history, study site, 3 ancestry-specific PCs —
PPM005163 PGS000007
(PRS3820_BC)
 PSS003598|
African Ancestry|
3,801 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer OR: 1.21 [1.06, 1.39] — — Age, family history, study site, 3 ancestry-specific PCs —
PPM005164 PGS000015
(GPS_BC)
 PSS003598|
African Ancestry|
3,801 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer OR: 1.24 [1.08, 1.43] — — Age, family history, study site, 3 ancestry-specific PCs —
PPM005165 PGS000004
(PRS313_BC)
 PSS003600|
Hispanic or Latin American Ancestry|
2,196 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer OR: 1.3 [1.08, 1.57] — — Age, family history, study site, 3 ancestry-specific PCs —
PPM005166 PGS000015
(GPS_BC)
 PSS003600|
Hispanic or Latin American Ancestry|
2,196 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer OR: 1.35 [1.11, 1.64] — — Age, family history, study site, 3 ancestry-specific PCs —
PPM005173 PGS000015
(GPS_BC)
 PSS003598|
African Ancestry|
3,801 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer — AUROC: 0.55 [0.52, 0.59] R²: 0.0004 — —
PPM005174 PGS000004
(PRS313_BC)
 PSS003600|
Hispanic or Latin American Ancestry|
2,196 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer — AUROC: 0.55 [0.5, 0.6] R²: 0.0008 — —
PPM005175 PGS000015
(GPS_BC)
 PSS003600|
Hispanic or Latin American Ancestry|
2,196 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer — AUROC: 0.56 [0.51, 0.6] R²: 0.001 — —

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
PSS003598 Cases were individuals with breast cancer. Breast cancer cases were defined by at least one occurrence of the following ICD10CM female breast cancer diagnostic codes: C50.01, C50.011, C50.012, C50.019, C50.1, C50.11, C50.111, C50.112, C50.119, C50.2, C50.21, C50.211, C50.212, C50.219, C50.3, C50.31, C50.311, C50.312, C50.319, C50.4, C50.41, C50.411, C50.412, C50.419, C50.5, C50.51, C50.511, C50.512, C50.519, C50.6, C50.61, C50.611, C50.612, C50.619, C50.81, C50.811, C50.812, C50.819, C50.91, C50.911, C50.912, C50.919, D05, D05.1, D05.10, D05.11, D05.12, D05.8, D05.81, D05.82, D05.9, D05.90, D05.91, D05.92, Z85.3,Z86.000 and ICD9CM female breast cancer diagnostic codes: 174, 174, 174.1, 174.2, 174.3, 174.4, 174.5, 174.6, 174.8, 174.9, 233, V10.3. Alternatively breast cancer cases were defined by at least two occurrences (from distinct calendar days) of breast cancer history from the following ICD10CM codes: Z85.3, Z86.000 and ICD9CM code: V10.3, if she had no breast cancer diagnostic codes. —
[
  • 274 cases
  • , 3,527 controls
]
,
0.0 % Male samples
 Mean = 59.6 years
Sd = 16.5 years		 African unspecified — eMERGE —
PSS003599 Cases were individuals with breast cancer. Breast cancer cases were defined by at least one occurrence of the following ICD10CM female breast cancer diagnostic codes: C50.01, C50.011, C50.012, C50.019, C50.1, C50.11, C50.111, C50.112, C50.119, C50.2, C50.21, C50.211, C50.212, C50.219, C50.3, C50.31, C50.311, C50.312, C50.319, C50.4, C50.41, C50.411, C50.412, C50.419, C50.5, C50.51, C50.511, C50.512, C50.519, C50.6, C50.61, C50.611, C50.612, C50.619, C50.81, C50.811, C50.812, C50.819, C50.91, C50.911, C50.912, C50.919, D05, D05.1, D05.10, D05.11, D05.12, D05.8, D05.81, D05.82, D05.9, D05.90, D05.91, D05.92, Z85.3,Z86.000 and ICD9CM female breast cancer diagnostic codes: 174, 174, 174.1, 174.2, 174.3, 174.4, 174.5, 174.6, 174.8, 174.9, 233, V10.3. Alternatively breast cancer cases were defined by at least two occurrences (from distinct calendar days) of breast cancer history from the following ICD10CM codes: Z85.3, Z86.000 and ICD9CM code: V10.3, if she had no breast cancer diagnostic codes. —
[
  • 3,960 cases
  • , 29,994 controls
]
,
0.0 % Male samples
 Mean = 66.1 years
Sd = 17.7 years		 European — eMERGE —
PSS003600 Cases were individuals with breast cancer. Breast cancer cases were defined by at least one occurrence of the following ICD10CM female breast cancer diagnostic codes: C50.01, C50.011, C50.012, C50.019, C50.1, C50.11, C50.111, C50.112, C50.119, C50.2, C50.21, C50.211, C50.212, C50.219, C50.3, C50.31, C50.311, C50.312, C50.319, C50.4, C50.41, C50.411, C50.412, C50.419, C50.5, C50.51, C50.511, C50.512, C50.519, C50.6, C50.61, C50.611, C50.612, C50.619, C50.81, C50.811, C50.812, C50.819, C50.91, C50.911, C50.912, C50.919, D05, D05.1, D05.10, D05.11, D05.12, D05.8, D05.81, D05.82, D05.9, D05.90, D05.91, D05.92, Z85.3,Z86.000 and ICD9CM female breast cancer diagnostic codes: 174, 174, 174.1, 174.2, 174.3, 174.4, 174.5, 174.6, 174.8, 174.9, 233, V10.3. Alternatively breast cancer cases were defined by at least two occurrences (from distinct calendar days) of breast cancer history from the following ICD10CM codes: Z85.3, Z86.000 and ICD9CM code: V10.3, if she had no breast cancer diagnostic codes. —
[
  • 147 cases
  • , 2,049 controls
]
,
0.0 % Male samples
 Mean = 59.9 years
Sd = 19.4 years		 Hispanic or Latin American — eMERGE —