PGS Catalog - PGS000664 / Rapid decline of glomerular filtration rate (GFR) (Polygenic Score)

Polygenic Score (PGS) ID: PGS000664

Predicted Trait
Reported Trait	Rapid decline of glomerular filtration rate (GFR)
Mapped Trait(s)	GFR change measurement (EFO_0006829)

Released in PGS Catalog: Jan. 7, 2021

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Score Details

Score Construction
PGS Name	GRS7_GFR
Development Method
Name	Genome-wide significant SNPs, candidate gene based approach
Parameters	p<5e-10 within ±500kB of lead variant
Variants
Original Genome Build	GRCh37
Number of Variants	7
Effect Weight Type	Unweighted

PGS Source
PGS Catalog Publication (PGP) ID	PGP000124
Citation (link to publication)	Gorski M et al. Kidney Int (2020)

Ancestry Distribution
Source of Variant Associations (GWAS)	European: 51.5% Multi-ancestry (including European): 30.6% European African Hispanic or Latin American South Asian East Asian: 15% African: 1.3% South Asian: 1.2% Hispanic or Latin American: 0.4% 1,102,457 individuals (100%)
PGS Evaluation	European: 100% 3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)

Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)
Europe PMC: 33137338	141,964 individuals [ 34,874 cases , 107,090 controls ]	European, African American or Afro-Caribbean, Hispanic or Latin American, South Asian	26 cohorts ADVANCE ,ARIC ,ASPS ,BioMe ,CHS ,DIACORE ,FINCAVAS ,GCKD ,JHS ,KORA ,LifeLines ,MESA ,MyCode ,NESDA ,POPGEN ,PREVEND ,RS ,SHIP ,SIMES ,SINDI ,SOLID-TIMI_52 ,STABILITY ,UKB ,Vanderbilt ,YFS ,deCODE
Europe PMC: 33137338	195,145 individuals [ 19,901 cases , 175,244 controls ]	European, African American or Afro-Caribbean, Hispanic or Latin American	19 cohorts ADVANCE ,AFTER_EU ,ARIC ,BioMe ,DIACORE ,ESTHER ,FHS ,GCKD ,JHS ,KORA ,LifeLines ,MDC-CC ,MESA ,MyCode ,SOLID-TIMI_52 ,STABILITY ,UKB ,Vanderbilt ,deCODE
GWAS Catalog: GCST008058 Europe PMC: 31152163	13,359 individuals	South Asian	82 cohorts AA-DHS ,ADVANCE ,AFTER_EU ,AGES ,AMISH ,ARIC ,ASPS ,Airwave ,BBJ ,BES ,BioMe ,CHNS ,CHRIS ,CHS ,CROATIA-KORCULA ,CROATIA-SPLIT ,CROATIA-VIS ,Cilento ,CoLaus ,Czech_post-MONICA ,DC ,DIACORE ,EGCUT ,ERF ,ESTHER ,FHS ,FINCAVAS ,FINRISK ,FamHS ,GCKD ,GS:SFHS ,GSK ,Generation_R ,HANDLS ,HYPERGENES ,INGI-Carlantino ,INGI-FVG ,INGI-Val_Borbera ,INTERVAL ,JHS ,JUPITER ,KORA ,LIFE-Adult ,LIFE-Child ,LIFE-HEART ,LLFS ,LOLIPOP ,LURIC ,LifeLines ,Living-Biobank ,MDC-CC ,MESA ,METSIM ,MICROS ,MyCode ,NEO ,NESDA ,OGP ,ORCADES ,PIVUS ,POPGEN ,PREVEND ,QIMR ,RS ,SCES ,SCHS ,SHIP ,SIMES ,SINDI ,SKIPOGH ,SOLID-TIMI_52 ,SORBS ,SP2 ,STABILITY ,TRAILS ,TwinGene ,ULSAM ,VIKING ,Vanderbilt ,WGHS ,YFS ,deCODE
GWAS Catalog: GCST008058 Europe PMC: 31152163	567,460 individuals	European	82 cohorts AA-DHS ,ADVANCE ,AFTER_EU ,AGES ,AMISH ,ARIC ,ASPS ,Airwave ,BBJ ,BES ,BioMe ,CHNS ,CHRIS ,CHS ,CROATIA-KORCULA ,CROATIA-SPLIT ,CROATIA-VIS ,Cilento ,CoLaus ,Czech_post-MONICA ,DC ,DIACORE ,EGCUT ,ERF ,ESTHER ,FHS ,FINCAVAS ,FINRISK ,FamHS ,GCKD ,GS:SFHS ,GSK ,Generation_R ,HANDLS ,HYPERGENES ,INGI-Carlantino ,INGI-FVG ,INGI-Val_Borbera ,INTERVAL ,JHS ,JUPITER ,KORA ,LIFE-Adult ,LIFE-Child ,LIFE-HEART ,LLFS ,LOLIPOP ,LURIC ,LifeLines ,Living-Biobank ,MDC-CC ,MESA ,METSIM ,MICROS ,MyCode ,NEO ,NESDA ,OGP ,ORCADES ,PIVUS ,POPGEN ,PREVEND ,QIMR ,RS ,SCES ,SCHS ,SHIP ,SIMES ,SINDI ,SKIPOGH ,SOLID-TIMI_52 ,SORBS ,SP2 ,STABILITY ,TRAILS ,TwinGene ,ULSAM ,VIKING ,Vanderbilt ,WGHS ,YFS ,deCODE
GWAS Catalog: GCST008058 Europe PMC: 31152163	4,961 individuals	Hispanic or Latin American	82 cohorts AA-DHS ,ADVANCE ,AFTER_EU ,AGES ,AMISH ,ARIC ,ASPS ,Airwave ,BBJ ,BES ,BioMe ,CHNS ,CHRIS ,CHS ,CROATIA-KORCULA ,CROATIA-SPLIT ,CROATIA-VIS ,Cilento ,CoLaus ,Czech_post-MONICA ,DC ,DIACORE ,EGCUT ,ERF ,ESTHER ,FHS ,FINCAVAS ,FINRISK ,FamHS ,GCKD ,GS:SFHS ,GSK ,Generation_R ,HANDLS ,HYPERGENES ,INGI-Carlantino ,INGI-FVG ,INGI-Val_Borbera ,INTERVAL ,JHS ,JUPITER ,KORA ,LIFE-Adult ,LIFE-Child ,LIFE-HEART ,LLFS ,LOLIPOP ,LURIC ,LifeLines ,Living-Biobank ,MDC-CC ,MESA ,METSIM ,MICROS ,MyCode ,NEO ,NESDA ,OGP ,ORCADES ,PIVUS ,POPGEN ,PREVEND ,QIMR ,RS ,SCES ,SCHS ,SHIP ,SIMES ,SINDI ,SKIPOGH ,SOLID-TIMI_52 ,SORBS ,SP2 ,STABILITY ,TRAILS ,TwinGene ,ULSAM ,VIKING ,Vanderbilt ,WGHS ,YFS ,deCODE
GWAS Catalog: GCST008058 Europe PMC: 31152163	165,726 individuals	East Asian	82 cohorts AA-DHS ,ADVANCE ,AFTER_EU ,AGES ,AMISH ,ARIC ,ASPS ,Airwave ,BBJ ,BES ,BioMe ,CHNS ,CHRIS ,CHS ,CROATIA-KORCULA ,CROATIA-SPLIT ,CROATIA-VIS ,Cilento ,CoLaus ,Czech_post-MONICA ,DC ,DIACORE ,EGCUT ,ERF ,ESTHER ,FHS ,FINCAVAS ,FINRISK ,FamHS ,GCKD ,GS:SFHS ,GSK ,Generation_R ,HANDLS ,HYPERGENES ,INGI-Carlantino ,INGI-FVG ,INGI-Val_Borbera ,INTERVAL ,JHS ,JUPITER ,KORA ,LIFE-Adult ,LIFE-Child ,LIFE-HEART ,LLFS ,LOLIPOP ,LURIC ,LifeLines ,Living-Biobank ,MDC-CC ,MESA ,METSIM ,MICROS ,MyCode ,NEO ,NESDA ,OGP ,ORCADES ,PIVUS ,POPGEN ,PREVEND ,QIMR ,RS ,SCES ,SCHS ,SHIP ,SIMES ,SINDI ,SKIPOGH ,SOLID-TIMI_52 ,SORBS ,SP2 ,STABILITY ,TRAILS ,TwinGene ,ULSAM ,VIKING ,Vanderbilt ,WGHS ,YFS ,deCODE
GWAS Catalog: GCST008058 Europe PMC: 31152163	13,842 individuals	African American or Afro-Caribbean	82 cohorts AA-DHS ,ADVANCE ,AFTER_EU ,AGES ,AMISH ,ARIC ,ASPS ,Airwave ,BBJ ,BES ,BioMe ,CHNS ,CHRIS ,CHS ,CROATIA-KORCULA ,CROATIA-SPLIT ,CROATIA-VIS ,Cilento ,CoLaus ,Czech_post-MONICA ,DC ,DIACORE ,EGCUT ,ERF ,ESTHER ,FHS ,FINCAVAS ,FINRISK ,FamHS ,GCKD ,GS:SFHS ,GSK ,Generation_R ,HANDLS ,HYPERGENES ,INGI-Carlantino ,INGI-FVG ,INGI-Val_Borbera ,INTERVAL ,JHS ,JUPITER ,KORA ,LIFE-Adult ,LIFE-Child ,LIFE-HEART ,LLFS ,LOLIPOP ,LURIC ,LifeLines ,Living-Biobank ,MDC-CC ,MESA ,METSIM ,MICROS ,MyCode ,NEO ,NESDA ,OGP ,ORCADES ,PIVUS ,POPGEN ,PREVEND ,QIMR ,RS ,SCES ,SCHS ,SHIP ,SIMES ,SINDI ,SKIPOGH ,SOLID-TIMI_52 ,SORBS ,SP2 ,STABILITY ,TRAILS ,TwinGene ,ULSAM ,VIKING ,Vanderbilt ,WGHS ,YFS ,deCODE

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)	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
PPM016131	PSS010042\| European Ancestry\| 1,601 individuals	PGP000396 \| Koraishy FM et al. BMC Nephrol (2022) \|Ext.	Reported Trait: Baseline eGFR	β: -1.0 [-1.59, -0.41]	—	—	Age, gender, education, the first ten genetic principal components, exposure severity	—
PPM001371	PSS000600\| European Ancestry\| 11,440 individuals	PGP000124 \| Gorski M et al. Kidney Int (2020)	Reported Trait: Rapid decline of glomerular filtration rate estimated from creatinine (CKDi25)	—	—	Odds Ratio (OR, high vs. low risk): 1.29 [1.06, 1.57]	Age, sex and baseline eGFRcrea	—
PPM001372	PSS000599\| European Ancestry\| 3,447 individuals	PGP000124 \| Gorski M et al. Kidney Int (2020)	Reported Trait: Acute kidney injury	—	—	Odds Ratio (OR, high vs. low risk): 1.2 [1.08, 1.33]	Matching variables (age-group and sex), quantitative age	—
PPM016132	PSS010042\| European Ancestry\| 1,601 individuals	PGP000396 \| Koraishy FM et al. BMC Nephrol (2022) \|Ext.	Reported Trait: Chronic kidney disease stage	OR: 1.18 [1.05, 1.32]	—	—	Age, gender, education, the first ten genetic principal components, exposure severity	—
PPM016133	PSS010042\| European Ancestry\| 1,601 individuals	PGP000396 \| Koraishy FM et al. BMC Nephrol (2022) \|Ext.	Reported Trait: eGFR Decline (<= -1.00 ml/min/1.73m2/year)	OR: 1.14 [1.01, 1.28]	—	—	Age, gender, education, the first ten genetic principal components, exposure severity	—

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
PSS000600	CKDi25 cases defined as >25% eGFRcrea decline during follow-up together with a movement from eGFRcrea≥60 mL/min/1.73m^2 at baseline to eGFR<60 mL/min/1.73m^2 at follow up compared to CKDi25 controls defined as eGFRcrea≥60 mL/min/1.73m^2. High risk groups had 8-14 adverse alleles. Low risk groups had 0-5 adverse alleles.	—	11,440 individuals [ 448 cases , 10,992 controls ]	—	European	—	DIACORE, KORA, UKB	87.61% overlap between the CKDi25 GWAS cohort and this dataset.
PSS010042	—	—	1,601 individuals, 93.0 % Male samples	Mean = 54.12 years	European	—	NR	WTC
PSS000599	Cases: ICD 10 code N17. Controls: no ICD10 code N17, frequency-matched by age-group and sex	—	3,447 individuals [ 1,013 cases , 2,434 controls ]	—	European	—	UKB	Possible overlap between GWAS cohorts and this dataset.