Oxford University Press (OUP)
SCOPUS (2012-2023)SCIE-ISI
2047-217X
Cơ quản chủ quản: Oxford University Press , OXFORD UNIV PRESS
Lĩnh vực:
Computer Science ApplicationsHealth Informatics
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SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
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PRSice-2: Polygenic Risk Score software for biobank-scale dataAbstract
Background
Polygenic risk score (PRS) analyses have become an integral part of biomedical research, exploited to gain insights into shared aetiology among traits, to control for genomic profile in experimental studies, and to strengthen causal inference, among a range of applications. Substantial efforts are now devoted to biobank projects to collect large genetic and phenotypic data, providing unprecedented opportunity for genetic discovery and applications. To process the large-scale data provided by such biobank resources, highly efficient and scalable methods and software are required.
Results
Here we introduce PRSice-2, an efficient and scalable software program for automating and simplifying PRS analyses on large-scale data. PRSice-2 handles both genotyped and imputed data, provides empirical association P-values free from inflation due to overfitting, supports different inheritance models, and can evaluate multiple continuous and binary target traits simultaneously. We demonstrate that PRSice-2 is dramatically faster and more memory-efficient than PRSice-1 and alternative PRS software, LDpred and lassosum, while having comparable predictive power.
Conclusion
PRSice-2's combination of efficiency and power will be increasingly important as data sizes grow and as the applications of PRS become more sophisticated, e.g., when incorporated into high-dimensional or gene set–based analyses. PRSice-2 is written in C++, with an R script for plotting, and is freely available for download from http://PRSice.info.
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The role of reporting standards for metabolite annotation and identification in metabolomic studies
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The 3,000 rice genomes project: new opportunities and challenges for future rice research
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