LDpred2: better, faster, stronger

MOTIVATION: Polygenic scores have become a central tool in human genetics research. LDpred is a popular method for deriving polygenic scores based on summary statistics and a matrix of correlation between genetic variants. However, LDpred has limitations that may reduce its predictive performance. RESULTS: Here, we present LDpred2, a new version of LDpred that addresses these issues. We also provide two new options in LDpred2: a 'sparse' option that can learn effects that are exactly 0, and an 'auto' option that directly learns the two LDpred parameters from data. We benchmark predictive performance of LDpred2 against the previous version on simulated and real data, demonstrating substantial improvements in…

• AU
  Aarhus Universitet

  Award: 58024
• NR
  National Research Foundation
• DG
  Danmarks Grundforskningsfond
• L
  Lundbeckfonden

  Award: R248-2017-2003
• HL
  H. Lundbeck A/S