A rapid column‐based ancient DNA extraction method for increased sample throughput

@article{Rohland2010ARC,
  title={A rapid column‐based ancient DNA extraction method for increased sample throughput},
  author={Nadin Rohland and Heike Siedel and Michael Hofreiter},
  journal={Molecular Ecology Resources},
  year={2010},
  volume={10}
}
Genetic analyses using museum specimens and ancient DNA from fossil samples are becoming increasingly important in phylogenetic and especially population genetic studies. Recent progress in ancient DNA sequencing technologies has substantially increased DNA sequence yields and, in combination with barcoding methods, has enabled large‐scale studies using any type of DNA. Moreover, more and more studies now use nuclear DNA sequences in addition to mitochondrial ones. Unfortunately, nuclear DNA is… 
View on Wiley
genetics.med.harvard.edu
173 Citations
Highly Influential Citations
4
Background Citations
21
Methods Citations
52
Results Citations
2

173 Citations

Citation Type

Citation Type

Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age
TLDR
This work compares an ancient DNA extraction protocol (Dabney) with a bone extraction method (Loreille) typically used in forensics and suggests that the choice of extraction method needs to be based on available sample, degradation state, and targeted genotyping method.
Analysis of Whole Mitogenomes from Ancient Samples.
TLDR
This protocol was designed for enrichment of mitochondrial DNA in ancient or other degraded samples, and can be easily adapted for using for building libraries for shotgun-sequencing of whole genomes, or enrichment of other genomic regions.
Technical Advances and Challenges in Genome-Scale Analysis of Ancient DNA
TLDR
In this chapter, an overview of some of the major technical advances and challenges in aDNA and paleogenomic research is provided.
One of the key characteristics of ancient DNA, low copy number, may be a product of its extraction
Preamplification Procedure for the Analysis of Ancient DNA Samples
TLDR
Data show that the TaqMan PreAmp procedure may improve the sensitivity of qPCR analysis, for the first time in ancient DNA, and a comparison between results obtained from nonpreamplified and preamplified samples is reported.
Museum genomics: low‐cost and high‐accuracy genetic data from historical specimens
TLDR
A low‐cost approach using high‐throughput next‐generation sequencing is described to obtain reliable genome‐scale sequence data from a traditionally preserved mammal skin and skull using a simple extraction protocol and it is shown that single‐nucleotide polymorphisms from the genome sequences obtained independently from the skin and from the skull are highly repeatable compared to a reference genome.
An optimized DNA extraction protocol for wood DNA barcoding of Pterocarpus erinaceus
TLDR
The protocol developed in this study shortens the period of DNA extraction from wood tissues by approximately 58% and the amplicon yields obtained indicate good extraction efficiency, and the wood samples sent for certification were identified as Pterocarpus erinaceus using the barcode combination matK+ndhF-rpl32+ITS2.
Progress in forensic bone DNA analysis: Lessons learned from ancient DNA.
Massive influence of DNA isolation and library preparation approaches on palaeogenomic sequencing data
TLDR
It is found that alternative methodologies can significantly and substantially affect total DNA yield, the mean length and length distribution of recovered fragments, nucleotide composition, and the total amount of usable data generated.
Extending the spectrum of DNA sequences retrieved from ancient bones and teeth.
TLDR
It is shown that much shorter DNA fragments are present in ancient skeletal remains but lost during DNA extraction, and the combination of DNA extraction and library preparation techniques described here substantially increases the yield of DNA sequences from ancient remains and provides access to a yet unexploited source of highly degraded DNA fragments.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 40 REFERENCES
Comparison and optimization of ancient DNA extraction.
TLDR
This optimized method uses a buffer consisting solely of EDTA and proteinase K for bone digestion and binding DNA to silica via guanidinium thiocyanate for DNA purification, and outperforms all other methods in terms of DNA yields as measured using quantitative PCR.
Direct multiplex sequencing (DMPS)--a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA.
TLDR
A novel and highly sensitive method for targeted sequencing of ancient and degraded DNA, which couples multiplex PCR directly with sample barcoding and high-throughput sequencing, and which opens up the opportunity to simultaneously generate many kilobases of overlapping sequence data from large sets of difficult samples.
Ancient DNA extraction from bones and teeth
TLDR
The purification step removes most of the various types of PCR inhibitors present in ancient bone samples, thereby optimizing the amount of ancient DNA available for subsequent enzymatic manipulation, such as PCR amplification.
Is amino acid racemization a useful tool for screening for ancient DNA in bone?
TLDR
It is concluded that Asx d/l is not a useful screening technique for ancient DNA from bone because aspartic acid is retained in the bone within the constrained environment of the collagen triple helix, where it cannot racemize for steric reasons.
Two‐step multiplex polymerase chain reaction improves the speed and accuracy of genotyping using DNA from noninvasive and museum samples
TLDR
A two‐step multiplex PCR procedure that allows rapid genotyping using at least 19 different microsatellite loci was applied to quantified amounts of noninvasive DNAs from western chimpanzee, western gorilla, mountain gorilla and black and white colobus faecal samples, as well as to DNA from ~100‐year‐old gorilla teeth from museums.
Genetic analyses from ancient DNA.
TLDR
The precautions and criteria necessary to ascertain to the greatest extent possible that results represent authentic ancient DNA sequences are discussed, which highlight some significant results and areas of promising future research.
Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts
TLDR
The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature.
High efficiency DNA extraction from bone by total demineralization.
Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology
TLDR
To gain maximal access to the historical record contained within chloroplast genomes, multiplex sequencing-by-synthesis (MSBS) is adapted to simultaneously sequence multiple genomes using the Illumina Genome Analyzer.
New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains
TLDR
The initial DNA concentration in the bone tissue is found to be as relevant for the total accessible mitochondrial DNA as the extent of DNA degradation post-mortem, and there is evidence suggesting that mitochondrial DNA is better preserved than nuclear DNA in ancient permafrost samples.
...
1
2
3
4
...