ApplyPolygenicScore functionality. Application of ApplyPolygenicScore functions demonstrated in a case study of 1071 individuals from the TCGA database, diagnosed with bladder (BLCA), liver (LIHC), or uterine (UCEC) cancer. A. Recommended workflow when implementing functions provided by ApplyPolygenicScore . A set of preprocessing functions convert polygenic risk score model (PGM) weight files into BED-formatted genomic coordinate files for suggested use in filtering VCF genotype data to desired coordinates. PGM application functions facilitate genetic data importation and weighted sum computation. Visualization functions provide summary information on computed PGSs and phenotype data. Solid arrows indicate required inputs and dotted arrows indicate optional inputs. B. BMI PGS densities, cohort-wide and by categorical phenotypes, computed in the case study cohort and automatically plotted by the create.pgs.density.plot function. C. Correlations of PGSs from (B) with continuous phenotypes automatically plotted by the create.pgs.with.continuous.phenotype.plot function. D. Receiver-operator curves plotted by the analyze.pgs.binary.predictiveness function depicting the performance of the PGSs from (B) to predict obesity status as a sole predictor (top) and with covariates age at diagnosis, sex, and the first 10 principal components of genetic ancestry (bottom). Positive obesity status is defined as BMI ≥ 30. E. From top to bottom: percentile rank of PGSs from (B) for each individual in ascending order, decile and quartile covariate bars, categorical phenotype covariate bars, and continuous phenotype heatmaps.
Nicole Zeltser; Rachel M.A. Dang; Rupert Hugh-White; Daniel Knight; Jaron Arbet; Paul C.
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🚀 ApplyPolygenicScore encourages the research community to extend the findings of the statistical genetics niche, facilitating broader use of PGSs and subsequent novel discovery: bit.ly/41jRDnS
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