ArticleGenome biology2025
Optimized in-solution enrichment of over a million ancient human SNPs.
Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Ancient DNA reveals a family ossuary and long-distance migration on the Pacific coast before the Inca Empire.Nature communications · 2026Article
- Subsistence transition preceded population turnover in the eastern Colombian Andes.bioRxiv : the preprint server for biology · 2026Article
- Article
- Lessons learned: Recommendations for reproducible paleogenomic data analyses.American journal of human genetics · 2025Review
- The genetic history of Portugal over the past 5,000 years.Genome biology · 2025Article
- Genetic transitions in the Neolithic and Bronze Age at Mas d'en Boixos (Catalonia, Spain).iScience · 2025Article
- The genomic footprints of migration: how ancient DNA reveals our history of mobility.Genome biology · 2025Review
- Estimating effective population size trajectories from time-series identity-by-descent segments.Genetics · 2025Article
- Article
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Authors and funding
24 authors.
Funding
Abstract
backgroundIn-solution hybridization enrichment of genetic markers is a method of choice in paleogenomic studies, where the DNA of interest is generally heavily fragmented and contaminated with environmental DNA, and where the retrieval of genetic data comparable between individuals is challenging. Here, we benchmark the commercial "Twist Ancient DNA" reagent from Twist Biosciences using sequencing libraries from ancient human samples of diverse demographic origin with low to high endogenous DNA content (0.1-44%). For each library, we tested one and two rounds of enrichment and assessed performance compared to deep shotgun sequencing.
resultsWe find that the "Twist Ancient DNA" assay provides robust enrichment of approximately 1.2M target SNPs without introducing allelic bias that may interfere with downstream population genetics analyses. Additionally, we show that pooling up to 4 sequencing libraries and performing two rounds of enrichment is both reliable and cost-effective for libraries with less than 27% endogenous DNA content. Above 38% endogenous content, a maximum of one round of enrichment is recommended for cost-effectiveness and to preserve library complexity.
conclusionsIn conclusion, we provide researchers in the field of human paleogenomics with a comprehensive understanding of the strengths and limitations of different sequencing and enrichment strategies, and our results offer practical guidance for optimizing experimental protocols.
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