Work

Matched full-UDG and non-UDG ancient DNA libraries reveal trade-offs in post-mortem damage correction for imputation and kinship inference

Year: 2026

Type: preprint

Abstract: Ancient DNA studies increasingly combine full uracil-DNA glycosylase-treated, full-UDG, and non-UDG libraries, but which computational damage correction to apply before imputation and kinship analysis remains unsettled. We compared terminal trimming, base-quality rescaling and known-SNP masking in matched full-UDG and non-UDG libraries from the same extracts of two medieval Mongolian individuals. All methods reduced or reversed the difference in mean alternative-allele fraction between damage-prone and transversion SNPs but retained different proportions of covered sites. In non-UDG libraries, masking and rescaling within five bases of each fragment end produced similar cross-library non-reference discordance, NRD, while retaining 92% and 99.3% of covered sites, respectively. In these 3′-biased libraries, ten-base 3′-only trimming retained more covered sites at lower observed discordance than five-base-per- end symmetric trimming. ancIBD inferred widespread sharing of one identity-by-descent chromosome copy, IBD1, across correction methods. Uncorrected non-UDG data shifted TKGWV2 toward second-degree estimates, whereas corrected mixed-library comparisons supported first-degree relatedness. READv2 and the low rate of opposite-homozygote sites, IBS0, supported a parent-offspring relationship. Mitochondrial data and genetic sex favoured ORT16 as mother and ORT15 as son. No method performed best across all measures, so the choice depends on whether residual damage, site retention or the downstream analysis matters most.

Source: bioRxiv (Cold Spring Harbor Laboratory)

DOI: 10.64898/2026.09.07.749785

Authors: Odongoo Ravdandorj, Chuluun Sampildondov, Khulan Janchiv, Takashi Gakuhari

Institutions: Kanazawa University, Sapiens Life Sciences, Evolution and Medicine Research Center, Institute for the Study of Ancient Civilizations and Cultural Resources, Kanazawa University, National University of Mongolia

Language: English

Topic: Forensic and Genetic Research

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funder: Japan Society for the Promotion of Science

Awards: "Shin" Paleogenomics Creates New Perspectives on the Utilization of Museum Materials, Paleogenomic and Paleoepigenomic Analysis of Mandibular Tori in a Medieval M ongolian Population, In pursuit of the real image of Chinggis Khan - Interdisciplinary research based on excavation of mausoleum ruins, The integrated study for the SDM region on ancient DNA preservation