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: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.本RDS文件包含一系列数据框，对应9种性状的多基因风险评分（Polygenic Risk Scores，PRS）权重表。基于单核苷酸多态性（Single Nucleotide Polymorphism，SNP）的PRS通过Illumina GSA芯片（v2版）获取的数据计算得到，同时剔除了链向不明的SNP位点。遗传数据使用Minimac4工具，以HRC r1.1（欧洲人群参考面板）进行基因型填充。针对精神分裂症（Trubetskoy等，2022）、双相情感障碍（包含I型与II型亚型，Mullins等，2021）、孤独症（Grove等，2019）、癫痫（局灶性癫痫及全面性遗传性癫痫，国际抗癫痫联盟，2022）、注意缺陷多动障碍（ADHD，Demontis等，2019）以及身高（Yengo等，2018）的PRS，均通过R包"bigsnpr"（v1.12.2）中内置的LDpred2-auto工具（Privé等，2020）构建得到，我们严格遵循了该方法作者发布的指南（https://privefl.github.io/bigsnpr/articles/LDpred2.html）。本研究采用的连锁不平衡（Linkage Disequilibrium，LD）参考样本，由心理健康研究中心临床遗传学实验室采集，为莫斯科地区斯拉夫裔人群为主的内部队列（n=1638）。所有样本均来自无亲缘关系的个体，PRS计算过程未引入任何协变量。精神分裂症患者样本与对照样本在性别分布与种族构成上匹配一致。本研究使用的数据来源：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及V. E. Golimbet，2023年，《通过综合病例研究评估新发SLC6A1基因突变对精神分裂症的影响》，《精神病学研究》327卷（7月）：115399，DOI: 10.1016/j.psychres.2023.115399。