TY - JOUR
T1 - Optimized in-solution enrichment of over a million ancient human SNPs
AU - Davidson, Roberta
AU - Roca-Rada, Xavier
AU - Ravishankar, Shyamsundar
AU - Taufik, Leonard
AU - Haarkötter, Christian
AU - Collen, Evelyn
AU - Williams, Matthew P.
AU - Webb, Peter
AU - Mahmud, M. Irfan
AU - Djami, Erlin Novita Idje
AU - Purnomo, Gludhug A.
AU - Santos, Cristina
AU - Malgosa, Assumpció
AU - Manzanilla, Linda R.
AU - Silva, Ana Maria
AU - Tereso, Sofia
AU - Matos, Vítor
AU - Carvalho, Pedro C.
AU - Fernandes, Teresa
AU - Maurer, Anne France
AU - Teixeira, João C.
AU - Tobler, Raymond
AU - Fehren-Schmitz, Lars
AU - Llamas, Bastien
N1 - Publisher Copyright:
© The Author(s) 2025.
PY - 2025/7/3
Y1 - 2025/7/3
N2 - 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.
AB - 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.
KW - Ancient DNA
KW - Enrichment
KW - Human paleogenomics
KW - Population genetics
KW - High-Throughput Nucleotide Sequencing/methods
KW - Gene Library
KW - Humans
KW - DNA, Ancient/analysis
KW - Polymorphism, Single Nucleotide
KW - Genome, Human
KW - Sequence Analysis, DNA/methods
UR - https://www.scopus.com/pages/publications/105010169065
UR - https://portalrecerca.uab.cat/en/publications/7a71a3e8-14b6-408c-b4b3-6626ad5d230e
UR - https://www.mendeley.com/catalogue/ade90f3b-4469-3321-b71c-796128107dd0/
U2 - 10.1186/s13059-025-03622-6
DO - 10.1186/s13059-025-03622-6
M3 - Article
C2 - 40611166
AN - SCOPUS:105010169065
SN - 1474-7596
VL - 26
JO - Genome Biology
JF - Genome Biology
IS - 1
M1 - 190
ER -