<p class="first" id="d12921660e222">During the past few years, various novel statistical
methods have been developed for
fine-mapping with the use of summary statistics from genome-wide association studies
(GWASs). Although these approaches require information about the linkage disequilibrium
(LD) between variants, there has not been a comprehensive evaluation of how estimation
of the LD structure from reference genotype panels performs in comparison with that
from the original individual-level GWAS data. Using population genotype data from
Finland and the UK Biobank, we show here that a reference panel of 1,000 individuals
from the target population is adequate for a GWAS cohort of up to 10,000 individuals,
whereas smaller panels, such as those from the 1000 Genomes Project, should be avoided.
We also show, both theoretically and empirically, that the size of the reference panel
needs to scale with the GWAS sample size; this has important consequences for the
application of these methods in ongoing GWAS meta-analyses and large biobank studies.
We conclude by providing software tools and by recommending practices for sharing
LD information to more efficiently exploit summary statistics in genetics research.