Optimized in-solution enrichment of over a million ancient human SNPs
Abstract Background In-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 chal...
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2025-07-01
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| Online Access: | https://doi.org/10.1186/s13059-025-03622-6 |
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| author | Roberta Davidson Xavier Roca-Rada Shyamsundar Ravishankar Leonard Taufik Christian Haarkötter Evelyn Collen Matthew P. Williams Peter Webb M. Irfan Mahmud Erlin Novita Idje Djami Gludhug A. Purnomo Cristina Santos Assumpció Malgosa Linda R. Manzanilla Ana Maria Silva Sofia Tereso Vítor Matos Pedro C. Carvalho Teresa Fernandes Anne-France Maurer João C. Teixeira Raymond Tobler Lars Fehren-Schmitz Bastien Llamas |
| author_facet | Roberta Davidson Xavier Roca-Rada Shyamsundar Ravishankar Leonard Taufik Christian Haarkötter Evelyn Collen Matthew P. Williams Peter Webb M. Irfan Mahmud Erlin Novita Idje Djami Gludhug A. Purnomo Cristina Santos Assumpció Malgosa Linda R. Manzanilla Ana Maria Silva Sofia Tereso Vítor Matos Pedro C. Carvalho Teresa Fernandes Anne-France Maurer João C. Teixeira Raymond Tobler Lars Fehren-Schmitz Bastien Llamas |
| author_sort | Roberta Davidson |
| collection | DOAJ |
| description | Abstract Background In-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. Results We 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. Conclusions In 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. |
| format | Article |
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| institution | Kabale University |
| issn | 1474-760X |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
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| series | Genome Biology |
| spelling | doaj-art-d15ca8b66b17460c9a3ccdacbc5ac8fc2025-08-20T03:38:18ZengBMCGenome Biology1474-760X2025-07-0126112010.1186/s13059-025-03622-6Optimized in-solution enrichment of over a million ancient human SNPsRoberta Davidson0Xavier Roca-Rada1Shyamsundar Ravishankar2Leonard Taufik3Christian Haarkötter4Evelyn Collen5Matthew P. Williams6Peter Webb7M. Irfan Mahmud8Erlin Novita Idje Djami9Gludhug A. Purnomo10Cristina Santos11Assumpció Malgosa12Linda R. Manzanilla13Ana Maria Silva14Sofia Tereso15Vítor Matos16Pedro C. Carvalho17Teresa Fernandes18Anne-France Maurer19João C. Teixeira20Raymond Tobler21Lars Fehren-Schmitz22Bastien Llamas23Australian Centre for Ancient DNA, The Environment Institute, School of Biological Sciences, The University of AdelaideAustralian Centre for Ancient DNA, The Environment Institute, School of Biological Sciences, The University of AdelaideAustralian Centre for Ancient DNA, The Environment Institute, School of Biological Sciences, The University of AdelaideAustralian Centre for Ancient DNA, The Environment Institute, School of Biological Sciences, The University of AdelaideLaboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of GranadaAustralian Centre for Ancient DNA, The Environment Institute, School of Biological Sciences, The University of AdelaideDepartment of Biology, The Pennsylvania State UniversityAustralian Centre for Ancient DNA, The Environment Institute, School of Biological Sciences, The University of AdelaideResearch Center for Prehistoric and Historic Archaeology, National Research and Innovation Agency (BRIN)Research Center for Prehistoric and Historic Archaeology, National Research and Innovation Agency (BRIN)Australian Centre for Ancient DNA, The Environment Institute, School of Biological Sciences, The University of AdelaideGrup de Recerca en Antropologia Biològica (GREAB), Unitat d’Antropologia Biològica, Universitat Autònoma de BarcelonaGrup de Recerca en Antropologia Biològica (GREAB), Unitat d’Antropologia Biològica, Universitat Autònoma de BarcelonaInstituto de Investigaciones Antropológicas, Universidad Nacional Autónoma de MéxicoCIAS, Research Centre for Anthropology and Health, Department of Life Sciences, University of CoimbraCIAS, Research Centre for Anthropology and Health, Department of Life Sciences, University of CoimbraCIAS, Research Centre for Anthropology and Health, Department of Life Sciences, University of CoimbraFaculty of Arts and Humanities, University of CoimbraCIAS, Research Centre for Anthropology and Health, Department of Life Sciences, University of CoimbraHERCULES Laboratory and IN2PAST, University of ÉvoraAustralian Centre for Ancient DNA, The Environment Institute, School of Biological Sciences, The University of AdelaideAustralian Centre for Ancient DNA, The Environment Institute, School of Biological Sciences, The University of AdelaideDepartment of Anthropology, UCSC Paleogenomics, University of CaliforniaAustralian Centre for Ancient DNA, The Environment Institute, School of Biological Sciences, The University of AdelaideAbstract Background In-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. Results We 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. Conclusions In 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.https://doi.org/10.1186/s13059-025-03622-6Ancient DNAEnrichmentPopulation geneticsHuman paleogenomics |
| spellingShingle | Roberta Davidson Xavier Roca-Rada Shyamsundar Ravishankar Leonard Taufik Christian Haarkötter Evelyn Collen Matthew P. Williams Peter Webb M. Irfan Mahmud Erlin Novita Idje Djami Gludhug A. Purnomo Cristina Santos Assumpció Malgosa Linda R. Manzanilla Ana Maria Silva Sofia Tereso Vítor Matos Pedro C. Carvalho Teresa Fernandes Anne-France Maurer João C. Teixeira Raymond Tobler Lars Fehren-Schmitz Bastien Llamas Optimized in-solution enrichment of over a million ancient human SNPs Genome Biology Ancient DNA Enrichment Population genetics Human paleogenomics |
| title | Optimized in-solution enrichment of over a million ancient human SNPs |
| title_full | Optimized in-solution enrichment of over a million ancient human SNPs |
| title_fullStr | Optimized in-solution enrichment of over a million ancient human SNPs |
| title_full_unstemmed | Optimized in-solution enrichment of over a million ancient human SNPs |
| title_short | Optimized in-solution enrichment of over a million ancient human SNPs |
| title_sort | optimized in solution enrichment of over a million ancient human snps |
| topic | Ancient DNA Enrichment Population genetics Human paleogenomics |
| url | https://doi.org/10.1186/s13059-025-03622-6 |
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