Efficient blockLASSO for polygenic scores with applications to all of us and UK Biobank.

Timothy G Raben¹, Louis Lello^2,3, Erik Widen^2,3, Stephen D H Hsu^2,3

¹Department of Physics and Astronomy, Michigan State University, East Lansing, USA. rabentim@msu.edu.

²Department of Physics and Astronomy, Michigan State University, East Lansing, USA.

³Genomic Prediction, Inc., North Brunswick, NJ, USA.

PubMed PMC DOI PDF

Abstract

We develop a "block" LASSO (blockLASSO) approach for training polygenic scores (PGS) and demonstrate its use in All of Us (AoU) and the UK Biobank (UKB). blockLASSO utilizes the approximate block diagonal structure (due to chromosomal partition of the genome) of linkage disequilibrium (LD). The new implementation can be used for exploratory and methods research where repeated PGS training is neces…

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