ArticleGenes2022
Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA.
Article in Genes, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
11 citing papers in PubMed, 26 citations in OpenAlex.
- Detrimental effect of metal contaminants on forensic DNA analysis and strategies for mitigation.International journal of legal medicine · 2026Review
- Article
- Two worlds beneath: Distinct microbial strategies of the rock-attached and planktonic subsurface biosphere.Microbiome · 2026Article
- Genome Shows no Recent Inbreeding in Near-Extinction Woolly Rhinoceros Sample Found in Ancient Wolf's Stomach.Genome biology and evolution · 2026Article
- Genomic formation of lower Yellow River populations in the Han dynasty.BMC biology · 2025Article
- A High-Throughput Ancient DNA Extraction Method for Large-Scale Sample Screening.Molecular ecology resources · 2025Article
- A Million Years of Mammoth Mitogenome Evolution.Molecular biology and evolution · 2025Article
- Heterochronous mitogenomes shed light on the Holocene history of the Scandinavian brown bear.Scientific reports · 2024Article
- Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.Cell · 2024Article
- Ancient reindeer mitogenomes reveal island-hopping colonisation of the Arctic archipelagos.Scientific reports · 2024Article
- Article
Corrections and comments
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Authors and funding
8 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rapid and cost-effective retrieval of endogenous DNA from ancient specimens remains a limiting factor in palaeogenomic research. Many methods have been developed to increase ancient DNA yield, but modifications to existing protocols are often based on personal experience rather than systematic testing. Here, we present a new silica column-based extraction protocol, where optimizations were tested in controlled experiments. Using relatively well-preserved permafrost samples, we tested the efficiency of pretreatment of bone and tooth powder with a bleach wash and a predigestion step. We also tested the recovery efficiency of MinElute and QIAquick columns, as well as Vivaspin columns with two molecular weight cut-off values. Finally, we tested the effect of uracil-treatment with two different USER enzyme concentrations. We find that neither bleach wash combined with a predigestion step, nor predigestion by itself, significantly increased sequencing efficiency. Initial results, however, suggest that MinElute columns are more efficient for ancient DNA extractions than QIAquick columns, whereas different molecular weight cut-off values in centrifugal concentrator columns did not have an effect. Uracil treatments are effective at removing DNA damage even at concentrations of 0.15 U/µL (as compared to 0.3 U/µL) of ancient DNA extracts.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.