A catalog of ancient proxies for modern genetic variants.

The ability to observe the genomes of past human populations using ancient DNA provides an extraordinary perspective on many fundamental questions in human genetics, including understanding the evolutionary history of variants that underlie human disease and other phenotypes. However, ancient DNA is often damaged and degraded, yielding low-coverage of most nucleotides. Further, many publicly available genotypes for ancient humans are limited to ~1.23 million specific loci. Thus, variants of interest often fall outside these specific positions, limiting the ability of ancient DNA to shed light on many loci. Here, we address this challenge by quantifying linkage disequilibrium (LD) between modern variants and ancient genotyped variants (AGVs) to generate a catalog enabling rapid identification of proxy variants. We identified 260,732,675 pairs of AGVs and modern variants with a minimum LD threshold hold of