Improved DNA extraction from ancient bones using silica‐based spin columns

Yang, Dongya; Waye, John S.; Dudar, J. Christopher; Saunders, Shelley R.

doi:10.1002/(sici)1096-8644(199804)105:4<539::aid-ajpa10>3.3.co;2-2

Cited by 168 publications

(198 citation statements)

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“…Silica-based methods use a bindrelease mechanism which has been shown to eliminate some inhibitors during purification (Yang et al, 1998). In this kit the purification reagents are in single-sample, self-contained cartridges.…”

Section: Discussionmentioning

confidence: 99%

Technical note: Bone DNA extraction and purification using silica‐coated paramagnetic beads

Dukes¹,

Williams

Massey

et al. 2012

American J Phys Anthropol

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The goal of this study was to develop a simple method to improve DNA recovery from challenging bone samples. To this end, an optimized procedure was developed that combined the demineralization and DNA extraction into a single step, followed by DNA purification using an automated silica-coated paramagnetic bead procedure. This method replaced a previous silica-membrane-based procedure, which was able to recover sufficient DNA to obtain full autosomal and Y chromosome STR profiles from greater than 90% of the samples, including samples greater than 20 years old. The development process began with the evaluation of buffer and demineralization systems to determine the best reagent combination. During the developmental process, we observed that the addition of EDTA and DTT affected silica-based DNA purification methods by raising the pH of the digest buffer. The protocols with buffer ATL, PK, EDTA, and DTT followed by lowering the pH with sodium acetate just before purification resulted in the best yields. The method reduced the extraction volume from 10 to 1.5 ml and used commercially available reagents already being utilized in forensic DNA casework. Because of the simplicity and small volume needed for the procedure, many steps where contamination could be introduced have been eliminated or minimized. This study demonstrated a new method of recovering DNA from bone samples capable of extracting trace quantities of DNA, removing potential inhibitors, and minimizing the potential for exogenous DNA contamination.

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Section: Discussionmentioning

confidence: 99%

Technical note: Bone DNA extraction and purification using silica‐coated paramagnetic beads

Dukes¹,

Williams

Massey

et al. 2012

American J Phys Anthropol

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“…These primers were designed to eliminate bias by amplifying all Botrytis species, including any Botrytis DNA present in the herbarium sample, instead of targeting individual species. The need to amplify short DNA fragments (200-350 bp) was likely due to the low concentration and poor condition of the DNA that is recovered from archival or herbarium tissue samples (Yang et al 1998). Rogers and Bendich (1985) reported that 400 bp was the average size of DNA extracted from herbarium specimens.…”

Section: Discussionmentioning

confidence: 99%

DNA sequence analysis of herbarium specimens facilitates the revival of Botrytis mali, a postharvest pathogen of apple

O’Gorman

Sholberg²,

Stokes³

et al. 2008

Mycologia

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The fungus Botrytis cinerea has been widely accepted as the species responsible for causing gray mold decay of apple, although a second species causing apple decay, B. mali, was reported in 1931. Botrytis mali was validly published in 1931, nevertheless it has always been considered a doubtful species. To study the relationship of Botrytis isolates causing gray mold on apple, DNA sequence analysis was employed. Twenty-eight Botrytis isolates consisting of 10 species were sampled, including two B. mali herbarium specimens from apple originally deposited in 1932. The DNA sequence analysis of the beta-tubulin and glyceraldehyde-3-phosphate dehydrogenase (G3PDH) genes placed the isolates into groupings with defined species boundaries that generally reflected the morphologically based model for Botrytis classification. The B. cinerea isolates from apple and other host plants were placed in a single clade. The B. mali herbarium specimens however always fell well outside that clade. The DNA sequence analysis reported in this study support the initial work by Ruehle (1931) describing the apple pathogen B. mali as a unique species.

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“…DNA was extracted using urea‐based extraction buffer combined with silica‐based spin column purification—MinElute PCR Purification Kit (Qiagen), according to the manufactures protocols (Malmström et al, 2009; Yang, Eng, Waye, Dudar, & Saunders, 1998). The obtained DNA extracts were used for preparation of blunt‐end Illumina genomic libraries (Meyer & Kircher, 2010).…”

Section: Methodsmentioning

confidence: 99%

A female Viking warrior confirmed by genomics

Hedenstierna-Jonson

Kjellström

Zachrisson

et al. 2017

American J Phys Anthropol

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ObjectivesThe objective of this study has been to confirm the sex and the affinity of an individual buried in a well‐furnished warrior grave (Bj 581) in the Viking Age town of Birka, Sweden. Previously, based on the material and historical records, the male sex has been associated with the gender of the warrior and such was the case with Bj 581. An earlier osteological classification of the individual as female was considered controversial in a historical and archaeological context. A genomic confirmation of the biological sex of the individual was considered necessary to solve the issue.Materials and methodsGenome‐wide sequence data was generated in order to confirm the biological sex, to support skeletal integrity, and to investigate the genetic relationship of the individual to ancient individuals as well as modern‐day groups. Additionally, a strontium isotope analysis was conducted to highlight the mobility of the individual.ResultsThe genomic results revealed the lack of a Y‐chromosome and thus a female biological sex, and the mtDNA analyses support a single‐individual origin of sampled elements. The genetic affinity is close to present‐day North Europeans, and within Sweden to the southern and south‐central region. Nevertheless, the Sr values are not conclusive as to whether she was of local or nonlocal origin.DiscussionThe identification of a female Viking warrior provides a unique insight into the Viking society, social constructions, and exceptions to the norm in the Viking time‐period. The results call for caution against generalizations regarding social orders in past societies.

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Improved DNA extraction from ancient bones using silica‐based spin columns

Cited by 168 publications

References 1 publication

Technical note: Bone DNA extraction and purification using silica‐coated paramagnetic beads

Technical note: Bone DNA extraction and purification using silica‐coated paramagnetic beads

DNA sequence analysis of herbarium specimens facilitates the revival of Botrytis mali, a postharvest pathogen of apple

A female Viking warrior confirmed by genomics

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