Repository logo
 
Publication

Quincunx: an R package to query, download and wrangle PGS catalog data

2022-01-01Journal article Open Access
Simple item page
dc.contributor.authorMagno, Ramiro
dc.contributor.authorDuarte, Isabel
dc.contributor.authorMaia, Ana-Teresa
dc.date.accessioned2022-01-14T15:06:35Z
dc.date.available2022-01-14T15:06:35Z
dc.date.issued2022-01-01
dc.description.abstractFor two decades, GWAS identified individual variants associated with risk for complex diseases. These associations can be combined into polygenic scores (PGS) aiming at quantifying an individual’s risk to disease, inform on prognosis and even treatment response (Lambert et al., 2019). Broadly, PGS use summary statistics produced by GWAS to calculate a weighted sum of trait-associated alleles carried by each individual, in which the weights correspond to the per-allele size effects. Initially used to validate associations with disease and uncover interactions between variants, PGS have been more challenging to implement in the clinic. In 2020, over 1400 publications on PGS appeared in PubMed, raising the need for a standardized distribution of studies’ key data, assuring their wide evaluation and accurate use. The Polygenic Score (PGS) Catalog, created in 2019, is a publicly available, manually curated database of PGS and relevant metadata, that responds to this need (Lambert et al., 2020). Its current release [date 2021-02-03] includes data from 133 publications and 721 PGS associated with 194 traits. Currently, data is accessed via three ways: (i) the web graphical user interface (GUI); (ii) by downloading database dumps; and (iii) the recent PGS Catalog representational state transfer (REST) application programming interface (API), the preferred method for batch analyses.pt_PT
dc.description.sponsorshipPOCI-01-0145-FEDER-022184; ALG-01-0145-FEDER31477
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.doi10.1093/bioinformatics/btab522pt_PT
dc.identifier.eissn1460-2059
dc.identifier.urihttp://hdl.handle.net/10400.1/17482
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherOxford university presspt_PT
dc.relationCenter for Health Technology and Services Research
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.titleQuincunx: an R package to query, download and wrangle PGS catalog datapt_PT
dc.title.alternativeQuincunx: um pacote R para consultar, baixar e wrangle dados do catálogo PGSpt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleCenter for Health Technology and Services Research
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F04255%2F2020/PT
oaire.citation.endPage296pt_PT
oaire.citation.issue1pt_PT
oaire.citation.startPage294pt_PT
oaire.citation.titleBioinformaticspt_PT
oaire.citation.volume38pt_PT
oaire.fundingStream6817 - DCRRNI ID
person.familyNameMagno
person.familyNamedos Santos Duarte
person.familyNameMaia
person.givenNameRamiro
person.givenNameGuilhermina Isabel
person.givenNameAna-Teresa
person.identifier.ciencia-idED15-7F67-7B64
person.identifier.orcid0000-0001-5226-3441
person.identifier.orcid0000-0003-0060-2936
person.identifier.orcid0000-0002-0454-9207
person.identifier.ridF-4404-2012
person.identifier.scopus-author-id14319300100
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
relation.isAuthorOfPublication17a3525a-04ce-46b3-9ee1-267916bd28ca
relation.isAuthorOfPublication6e1e1dd4-e2b4-4dfa-b7d7-f7990e9bd179
relation.isAuthorOfPublication229d470e-6eb8-4144-a68a-5e0d5bec8a2c
relation.isAuthorOfPublication.latestForDiscovery6e1e1dd4-e2b4-4dfa-b7d7-f7990e9bd179
relation.isProjectOfPublication58b2d36c-a8f1-4f5c-8512-a501deb47eb8
relation.isProjectOfPublication.latestForDiscovery58b2d36c-a8f1-4f5c-8512-a501deb47eb8

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
quincunx -an R package to query, download and wrangle.pdf
Size:
273.07 KB
Format:
Adobe Portable Document Format
Download

Collections

FCB2-Artigos (em revistas ou actas indexadas)