Derivation and validation of genome-wide polygenic score for urinary tract stone diagnosis.

Genetic Predisposition to Disease Genome-Wide Association Study Humans Multifactorial Inheritance Polymorphism, Single Nucleotide United Kingdom / epidemiology Urinary Calculi
genomics nephrolithiasis personalized medicine polygenic risk score urinary tract stone

Journal

Kidney international
ISSN: 1523-1755
Titre abrégé: Kidney Int
Pays: United States
ID NLM: 0323470

Informations de publication

Date de publication:
11 2020
Historique:
received: 21 12 2019
revised: 30 03 2020
accepted: 16 04 2020
pubmed: 17 6 2020
medline: 22 6 2021
entrez: 17 6 2020
Statut: ppublish

Résumé

Urinary tract stones have high heritability indicating a strong genetic component. However, genome-wide association studies (GWAS) have uncovered only a few genome wide significant single nucleotide polymorphisms (SNPs). Polygenic risk scores (PRS) sum cumulative effect of many SNPs and shed light on underlying genetic architecture. Using GWAS summary statistics from 361,141 participants in the United Kingdom Biobank, we generated a PRS and determined association with stone diagnosis in 28,877 participants in the Mount Sinai BioMe Biobank. In BioMe (1,071 cases and 27,806 controls), for every standard deviation increase, we observed a significant increment in adjusted odds ratio of a factor of 1.2 (95% confidence interval 1.13-1.26). In comparison, a risk score comprised of GWAS significant SNPs was not significantly associated with diagnosis. After stratifying individuals into low and high-risk categories on clinical risk factors, there was a significant increment in adjusted odds ratio of 1.3 (1.12-1.6) in the low- and 1.2 (1.1-1.2) in the high-risk group for every standard deviation increment in PRS. In a 14,348-participant validation cohort (Penn Medicine Biobank), every standard deviation increment was associated with a significant adjusted odds ratio of 1.1 (1.03 - 1.2). Thus, a genome-wide PRS is associated with urinary tract stones overall and in the absence of known clinical risk factors and illustrates their complex polygenic architecture.

Identifiants

DOI: 10.1016/j.kint.2020.04.055 PMID: 32540406 PMC: PMC7606592
pubmed: 32540406
pii: S0085-2538(20)30641-4
doi: 10.1016/j.kint.2020.04.055
pmc: PMC7606592
mid: NIHMS1603591
pii:
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

1323-1330

Subventions

Organisme : NHLBI NIH HHS
ID : R01 HL085757
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM124836
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG009610
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL139865
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG007278
Pays : United States
Organisme : CSRD VA
ID : IK2 CX001780
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM007205
Pays : United States
Organisme : NIDDK NIH HHS
ID : R01 DK108803
Pays : United States
Organisme : NIDDK NIH HHS
ID : U01 DK116100
Pays : United States
Organisme : ACL HHS
ID : U01OH011326
Pays : United States
Organisme : NIOSH CDC HHS
ID : U01 OH011326
Pays : United States
Organisme : NIDDK NIH HHS
ID : R01 DK112258
Pays : United States
Organisme : NIDDK NIH HHS
ID : K23 DK107908
Pays : United States

Commentaires et corrections

Type : CommentIn
Type : CommentIn

Informations de copyright

Copyright © 2020 International Society of Nephrology. All rights reserved.

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Auteurs

Ishan Paranjpe (I)

The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York, USA; The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA; The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

Noah Tsao (N)

Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

Renae Judy (R)

Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

Manish Paranjpe (M)

Division of Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts, USA.

Kumardeep Chaudhary (K)

The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA; The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

Derek Klarin (D)

Malcolm Randall Veterans Affairs Medical Center, Gainesville, Florida, USA; Division of Vascular Surgery and Endovascular Therapy, University of Florida College of Medicine, Gainesville, Florida, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

Iain Forrest (I)

The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

Ross O'Hagan (R)

The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA; The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

Arjun Kapoor (A)

Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

John Pfail (J)

Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

Suraj Jaladanki (S)

The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA; The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

Fayzan Chaudhry (F)

The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

Akhil Vaid (A)

The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

Phan Q Duy (PQ)

Medical Scientist Training Program, Yale University School of Medicine, New Haven, Connecticut, USA.
The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
Regeneron Genetics Center, Tarrytown, New York, USA.

John Cijiang He (JC)

Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Renal Program, James J Peters Veterans Affairs Medical Center at Bronx, New York, New York, USA.

Benjamin S Glicksberg (BS)

The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

Steven G Coca (SG)

Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

Mantu Gupta (M)

Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

Ron Do (R)

The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

Scott M Damrauer (SM)

Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

Girish N Nadkarni (GN)

The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA; The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Renal Program, James J Peters Veterans Affairs Medical Center at Bronx, New York, New York, USA. Electronic address: girish.nadkarni@mountsinai.org.

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Génotype › Prédisposition génétique à une maladie › Derivation and validation of genome-wide...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Épidémiologie moléculaire › Étude d'association pangénomique › Derivation and validation of genome-wide...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Derivation and validation of genome-wide...
questionsmedicales.fr › Phénomènes génétiques › Modes de transmission héréditaire › Hérédité multifactorielle › Derivation and validation of genome-wide...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Polymorphisme génétique › Polymorphisme de nucléotide simple › Derivation and validation of genome-wide...
questionsmedicales.fr › Régions géographiques › Europe › Royaume-Uni › Derivation and validation of genome-wide...
questionsmedicales.fr › États, signes et symptômes pathologiques › États anatomopathologiques › Calculs › Calculs urinaires › Derivation and validation of genome-wide...