PRSice: Polygenic Risk Score software

Jack Euesden; Cathryn M Lewis; Paul F O'Reilly

doi:10.1093/bioinformatics/btu848

PRSice: Polygenic Risk Score software

Jack Euesden, Cathryn M Lewis, Paul F O'Reilly

Research output: Contribution to journal › Article › peer-review

865 Citations (Scopus)

245 Downloads (Pure)

Abstract

A polygenic risk score (PRS) is a sum of trait-associated alleles across many genetic loci, typically weighted by effect sizes estimated from a genome-wide association study (GWAS). The application of PRS has grown in recent years as their utility for detecting shared genetic aetiology among traits has become appreciated; PRS can also be used to establish the presence of a genetic signal in underpowered studies, infer the genetic architecture of a trait, for screening in clinical trials, and can act as a biomarker for a phenotype. Here we present the first dedicated PRS software, PRSice ('precise'), for calculating, applying, evaluating and plotting the results of polygenic risk scores. PRSice can calculate PRS at a large number of thresholds ("high resolution") to provide the best-fit PRS, as well as provide results calculated at broad P-value thresholds, can thin SNPs according to linkage disequilibrium and P-value or use all SNPs, handles genotyped and imputed data, can calculate and incorporate ancestry-informative variables, and can apply PRS across multiple traits in a single run. We exemplify the use of PRSice via application to data on Schizophrenia, Major Depressive Disorder and Smoking, illustrate the importance of identifying the best-fit PRS, and estimate a P-value significance threshold for high-resolution PRS studies. Availability: PRSice is written in R, including wrappers for bash data management scripts and PLINK-1.9 to minimise computational time. PRSice runs as a command-line program with a variety of user-options, and is freely available for download from http://PRSice.info

CONTACT: [email protected]; [email protected]

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original language	English
Pages (from-to)	1466–1468
Journal	BIOINFORMATICS
Volume	31
Issue number	9
Early online date	29 Dec 2014
DOIs	https://doi.org/10.1093/bioinformatics/btu848
Publication status	Published - 1 May 2015

Access to Document

10.1093/bioinformatics/btu848Licence: CC BY

PRSice- Polygenic Risk Score software_LEWIS_Publishedonline24December2014_GOLD VoR (CC BY)Final published version, 278 KBLicence: CC BY

Cite this

@article{4b1575a67fa64ea89e53aae4717a6610,

title = "PRSice: Polygenic Risk Score software",

abstract = "A polygenic risk score (PRS) is a sum of trait-associated alleles across many genetic loci, typically weighted by effect sizes estimated from a genome-wide association study (GWAS). The application of PRS has grown in recent years as their utility for detecting shared genetic aetiology among traits has become appreciated; PRS can also be used to establish the presence of a genetic signal in underpowered studies, infer the genetic architecture of a trait, for screening in clinical trials, and can act as a biomarker for a phenotype. Here we present the first dedicated PRS software, PRSice ('precise'), for calculating, applying, evaluating and plotting the results of polygenic risk scores. PRSice can calculate PRS at a large number of thresholds ({"}high resolution{"}) to provide the best-fit PRS, as well as provide results calculated at broad P-value thresholds, can thin SNPs according to linkage disequilibrium and P-value or use all SNPs, handles genotyped and imputed data, can calculate and incorporate ancestry-informative variables, and can apply PRS across multiple traits in a single run. We exemplify the use of PRSice via application to data on Schizophrenia, Major Depressive Disorder and Smoking, illustrate the importance of identifying the best-fit PRS, and estimate a P-value significance threshold for high-resolution PRS studies. Availability: PRSice is written in R, including wrappers for bash data management scripts and PLINK-1.9 to minimise computational time. PRSice runs as a command-line program with a variety of user-options, and is freely available for download from http://PRSice.info CONTACT: [email protected]; [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.",

author = "Jack Euesden and Lewis, {Cathryn M} and O'Reilly, {Paul F}",

year = "2015",

month = may,

day = "1",

doi = "10.1093/bioinformatics/btu848",

language = "English",

volume = "31",

pages = "1466–1468",

journal = "BIOINFORMATICS",

issn = "1367-4803",

publisher = "Oxford University Press (OUP)",

number = "9",

}

TY - JOUR

T1 - PRSice

T2 - Polygenic Risk Score software

AU - Euesden, Jack

AU - Lewis, Cathryn M

AU - O'Reilly, Paul F

PY - 2015/5/1

Y1 - 2015/5/1

N2 - A polygenic risk score (PRS) is a sum of trait-associated alleles across many genetic loci, typically weighted by effect sizes estimated from a genome-wide association study (GWAS). The application of PRS has grown in recent years as their utility for detecting shared genetic aetiology among traits has become appreciated; PRS can also be used to establish the presence of a genetic signal in underpowered studies, infer the genetic architecture of a trait, for screening in clinical trials, and can act as a biomarker for a phenotype. Here we present the first dedicated PRS software, PRSice ('precise'), for calculating, applying, evaluating and plotting the results of polygenic risk scores. PRSice can calculate PRS at a large number of thresholds ("high resolution") to provide the best-fit PRS, as well as provide results calculated at broad P-value thresholds, can thin SNPs according to linkage disequilibrium and P-value or use all SNPs, handles genotyped and imputed data, can calculate and incorporate ancestry-informative variables, and can apply PRS across multiple traits in a single run. We exemplify the use of PRSice via application to data on Schizophrenia, Major Depressive Disorder and Smoking, illustrate the importance of identifying the best-fit PRS, and estimate a P-value significance threshold for high-resolution PRS studies. Availability: PRSice is written in R, including wrappers for bash data management scripts and PLINK-1.9 to minimise computational time. PRSice runs as a command-line program with a variety of user-options, and is freely available for download from http://PRSice.info CONTACT: [email protected]; [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

AB - A polygenic risk score (PRS) is a sum of trait-associated alleles across many genetic loci, typically weighted by effect sizes estimated from a genome-wide association study (GWAS). The application of PRS has grown in recent years as their utility for detecting shared genetic aetiology among traits has become appreciated; PRS can also be used to establish the presence of a genetic signal in underpowered studies, infer the genetic architecture of a trait, for screening in clinical trials, and can act as a biomarker for a phenotype. Here we present the first dedicated PRS software, PRSice ('precise'), for calculating, applying, evaluating and plotting the results of polygenic risk scores. PRSice can calculate PRS at a large number of thresholds ("high resolution") to provide the best-fit PRS, as well as provide results calculated at broad P-value thresholds, can thin SNPs according to linkage disequilibrium and P-value or use all SNPs, handles genotyped and imputed data, can calculate and incorporate ancestry-informative variables, and can apply PRS across multiple traits in a single run. We exemplify the use of PRSice via application to data on Schizophrenia, Major Depressive Disorder and Smoking, illustrate the importance of identifying the best-fit PRS, and estimate a P-value significance threshold for high-resolution PRS studies. Availability: PRSice is written in R, including wrappers for bash data management scripts and PLINK-1.9 to minimise computational time. PRSice runs as a command-line program with a variety of user-options, and is freely available for download from http://PRSice.info CONTACT: [email protected]; [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

U2 - 10.1093/bioinformatics/btu848

DO - 10.1093/bioinformatics/btu848

M3 - Article

C2 - 25550326

SN - 1367-4803

VL - 31

SP - 1466

EP - 1468

JO - BIOINFORMATICS

JF - BIOINFORMATICS

IS - 9

ER -

PRSice: Polygenic Risk Score software

Abstract

Access to Document

Fingerprint

Cite this