PRS Weight Tables for Nine Traits using LDpred2-auto

The rds file contains a list of data frames, corresponding to PRS weight tables for nine traits.Single nucleotide polymorphism (SNP)-based Polygenic Risk Scores (PRS) were calculated with data obtained from Illumina GSA chip (v2), ambiguously oriented SNPs were excluded. Genetic data were imputed by the Minimac4 tool with the HRC r1.1 (European panel). PRS for schizophrenia (Trubetskoy et al. 2022), bipolar disorder (including separately type I and type II, Mullins et al. 2021), autism (Grove et al. 2019), epilepsy (focal and GGE, ILAEC 2022), ADHD (Demontis et al. 2019), and height (Yengo et al. 2018) were inferred with LDpred2-auto tool (Privé et al. 2020) available in the R package “bigsnpr” (v1.12.2). We followed a guide from the method’s author (https://privefl.github.io/bigsnpr/articles/LDpred2.html). An in-house sample (n=1638) collected in the laboratory of Clinical Genetics, Mental Health Research Center, predominantly consisting of individuals of Slavic descent from the Moscow region, was employed as the LD reference. All samples consisted of unrelated individuals. No covariates were incorporated into the PRS calculations. Both control and SZ patient samples were similar in terms of gender and ethnicity.The data used in this publication:<br>Kondratyev, N. V., M. V. Alfimova, V. G. Kaleda, T. V. Lezheiko, V. A. Mikhailova, D. S. Karpov, M. V. Ublinsky, V. L. Ushakov, I. S. Lebedeva, and V. E. Golimbet. 2023. “Assessing the Impact of the de Novo SLC6A1 Mutation in Schizophrenia through a Comprehensive Case Study.” Psychiatry Research 327 (July): 115399. https://doi.org/10.1016/j.psychres.2023.115399.