We have developed a fast and accurate LRP-based phasing method, Eagle, and demonstrated that LRP can be effective in a cohort representing a small fraction of a large outbred population. Ever since Kong et al.13 established the efficacy of LRP in the Icelandic population—speculating that “having as little as 1% of a population genotyped may be adequate for the method to yield useful results”—the extension of LRP to more general settings has been eagerly anticipated but up to now unrealized1. We have successfully applied Eagle to phase 0.2% of the UK population and demonstrated its utility for enhancing the accuracy of downstream imputation. We note that LRP in 0.2% of the UK population cannot match the accuracy that was achieved in 11% of the Icelandic population13,15 (which further improved with genotyping of >30% of the Icelandic population25); however, these results give reason for optimism that LRP-based phasing accuracy in the UK (and other large outbred populations) will continue to improve as more individuals are genotyped.
