Evaluating genotype imputation pipeline for ultra-low coverage ancient genomes

Abstract

Although ancient DNA data have become increasingly more important in studies about past populations, it is often not feasible or practical to obtain high coverage genomes from poorly preserved samples. While methods of accurate genotype imputation from > 1 × coverage data have recently become a routine, a large proportion of ancient samples remain unusable for downstream analyses due to their low coverage. Here, we evaluate a two-step pipeline for the imputation of common variants in ancient genomes at 0.05–1 × coverage. We use the genotype likelihood input mode in Beagle and filter for confident genotypes as the input to impute missing genotypes. This procedure, when tested on ancient genomes, outperforms a single-step imputation from genotype likelihoods, suggesting that current genotype callers do not fully account for errors in ancient sequences and additional quality controls can be beneficial. We compared the effect of various genotype likelihood calling methods, post-calling, pre-imputation and post-imputation filters, different reference panels, as well as different imputation tools. In a Neolithic Hungarian genome, we obtain ~ 90% imputation accuracy for heterozygous common variants at coverage 0.05 × and > 97% accuracy at coverage 0.5 ×. We show that imputation can mitigate, though not eliminate reference bias in ultra-low coverage ancient genomes.

Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula

“…To distinguish relationship type within degree (e.g., first degree, full siblings versus parent-offspring), we used IBD analysis as implemented in Plink-1.9 59 on imputed genotypes (STAR Methods). Genotypes were imputed using a pipeline detailed in Hui et al 60 and STAR Methods, and in the case of close (1 to 2) degrees of relationship, both methods provided consistent results (Table 2).…”

Inferring population histories for ancient genomes using genome-wide genealogies

“…ancients and moderns) (Wohns et al 2021). A possibility for making lower coverage ancient genomes, or indeed hybrid capture array data, accessible to these methods is imputation (Rubinacci et al 2020; Hui et al 2020). A potential concern is that imputation may introduce biases, particularly in ancient genomes with ancestries that are not well reflected in modern groups.…”

Genetic ancestry changes in Stone to Bronze Age transition in the East European plain

“…Similarly, to analyze the other phenotype-informative markers (diet, immunity, and diseases), 2 Mb around each variant was selected, and the overlapping regions were merged, for a total of 47 regions (45 regions in 17 autosomes and 2 regions on chrX). For the local imputation, we used a two-step pipeline ( 97 ) as follows: (i) variant calling, (ii) first imputation step using a reference panel as much similar as possible to the target samples, (iii) variant filtering, (iv) second imputation step using a larger worldwide reference panel, and (v) final variant filtering. This pipeline has been validated by randomly downsampling a high-coverage Neolithic sample (NE1) ( 98 ) to 0.05× and comparing the imputed variants in the low-coverage version with the called variants from the original genome.…”