Journal: medRxiv

Article Title: Selection, optimization, and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse populations

doi: 10.1101/2023.05.25.23290535

Figure Lengend Snippet: Performance measures from the PRS pipeline validation study at the clinical laboratory. PRS pipeline accuracy is assessed as the Pearson correlation between scores derived from PCR-free 30X WGS and those derived from imputed genotyping data (GDA) in the same 70 specimens. Pearson correlation shown in the mean correlation across all ancestry groups tested. PRS pipeline precision (repeatability) is the measure of concordance in PRS scores calculated from the same 70 specimens, run through the pipeline 10 times over the course of two weeks. PRS pipeline precision (reproducibility) is assessed using three samples, each run 6 times end-to-end and then compared in a pairwise manner. The z-score standard deviation is used as a measure of variability. PRS site missingness is the percentage of genomics sites in the original score that are missing from the final imputed dataset. Odds Ratios for high PRS vs Not high pRS are derived from the condition-specific cohorts and calculated by each condition lead group across the ancestries available. Odds ratio information for Obesity/BMI is in preparation for publication by the GIANT consortium.

Article Snippet: Infinium genotyping data is compared to this fingerprint as a primary check of sample chain-of-custody fidelity and to preclude sample or plate swaps during lab processing.

Techniques: Biomarker Discovery, Derivative Assay, Standard Deviation