Additional file 1: of PRS-on-Spark (PRSoS): a novel, efficient and flexible approach for generating polygenic risk scores

Supplementary Methods and Data Analysis. Additional information on the MAVAN cohort. Genetic data quality control and supplementary data analyses are provided. (Additional file 4: Figure S3, Additional file 5: Figure S4). (PDF 142 kb

Additional file 3: of PRS-on-Spark (PRSoS): a novel, efficient and flexible approach for generating polygenic risk scores

Figure S2. PRSice v1.25, PRSice-2, and PRSoS performance across datasets. Bar plot shows the results of the performance test comparing running PRSice v1.25, PRSice-2, and PRSoS across the datasets. Processing time (y-axis) uses a log base 10 scale. Error bars indicate standard deviations. Numbers in boxed inserts indicate the size of the genotype data input. †Note that the file sizes used for the Imputed PP are same for PRSice v1.25 and PRSoS, thus illustrating the processing speed difference with same file size input. Genotype input formats are different across all three software for the other performance tests. Imputed PP = imputed posterior probabilities, Imputed HC = imputed posterior probabilities converted to “hard calls”, Array Data = observed genotypes. (PDF 34 kb

Additional file 5: of PRS-on-Spark (PRSoS): a novel, efficient and flexible approach for generating polygenic risk scores

Figure S4. Software performance between datasets across number of PRS p-value thresholds to generate in a single run. Imputed HC = imputed posterior probabilities converted to “hard calls”, Array Data = observed genotypes. (PDF 5 kb

Additional file 2: of PRS-on-Spark (PRSoS): a novel, efficient and flexible approach for generating polygenic risk scores

Figure S1. PRSice v1.25 and PRSoS performance across the number of cores used to generate PRS and five thresholds using the Imputed Hard Call dataset. PRSice v1.25 could only run on 1 core. PRSoS performance was tested with 1, 4, 12, 20, and 24 cores on a Linux CentOS 7, 24-core Intel Xeon server. Error bars indicate standard deviations. (PDF 4 kb