One of the key characteristics of ancient DNA, low copy number, may be a product of its extraction

Barta, Jodi Lynn; Monroe, Cara; Teisberg, Justin E.; Winters, Misa; Flanigan, Kelli; Kemp, Brian M.

doi:10.1016/j.jas.2014.03.030

Cited by 35 publications

(27 citation statements)

References 88 publications

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“…Because inhibition and other sources of sporadic inefficiency (e.g., pipetting errors or saturation of reactions with excessive amounts of DNA) are sample-dependent, we recommend the spike-in strategy as a general means of quality control in library preparation. When applying a similar control strategy to silica-based DNA extraction, we found that recovery rates are much less variable compared to library preparation; in fact, at between 80 and 90%, they are consistently higher than reported in a previous study (Barta et al 2014). Unlike in library preparation, we therefore consider spike-in controls unnecessary in DNA extraction.…”

Section: Genome Research 1233mentioning

confidence: 43%

Extending the spectrum of DNA sequences retrieved from ancient bones and teeth

Glocke

Meyer

2017

Genome Res.

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The number of DNA fragments surviving in ancient bones and teeth is known to decrease with fragment length. Recent genetic analyses of Middle Pleistocene remains have shown that the recovery of extremely short fragments can prove critical for successful retrieval of sequence information from particularly degraded ancient biological material. Current sample preparation techniques, however, are not optimized to recover DNA sequences from fragments shorter than ∼35 base pairs (bp). Here, we show that much shorter DNA fragments are present in ancient skeletal remains but lost during DNA extraction. We present a refined silica-based DNA extraction method that not only enables efficient recovery of molecules as short as 25 bp but also doubles the yield of sequences from longer fragments due to improved recovery of molecules with singlestrand breaks. Furthermore, we present strategies for monitoring inefficiencies in library preparation that may result from co-extraction of inhibitory substances during DNA extraction. 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. Our work may thus open the door for genetic analyses on even older material.

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Section: Genome Research 1233mentioning

confidence: 43%

Extending the spectrum of DNA sequences retrieved from ancient bones and teeth

Glocke

Meyer

2017

Genome Res.

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“…; Barta et al . ). If specifically short DNA fragments had been lost in the DNA extractions using modified protocols, this would explain both the lower yield and higher quality.…”

Section: Discussionmentioning

confidence: 97%

“…), specifically regarding the analysis of nuclear DNA (Barta et al . ). Different methods provide highly variable yields of DNA, in particular for short (under 200 bp) DNA segments (Dabney et al .…”

Section: Introductionmentioning

confidence: 97%

Extracting DNA from ‘jaws’: high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material

Nielsen

Morgan

Maher

et al. 2016

Molecular Ecology Resources

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Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so‐called bio‐swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high‐yield sources of DNA for genomic‐scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield.

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“…DNA extraction methods, including commercial kits, may leave behind some residual inhibitors and often result in loss of sample DNA (Shipley et al 2012;Monroe et al 2013;Barta et al 2014;Kemp et al 2014), which increases the chance of sample cross-contamination (Frickhofen and Young 1991;Queipo-Ortuño et al 2008).…”

Section: Introductionmentioning

confidence: 99%

A fast and accurate method of detecting Aleutian mink disease virus in blood and tissues of chronically infected mink

Farid

Rupasinghe

2017

Can. J. Microbiol.

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this article has been changed to the CC BY 4.0 license. The PDF and HTML versions of the article have been modified accordingly. Abstract:The objective of this study was to assess the sensitivity of the Omni Klentaq-LA DNA polymerase for detecting Aleutian mink disease virus (AMDV) in mink blood and tissues by PCR without DNA extraction. The presence of AMDV DNA was directly tested by Klentaq in the plasma, serum, whole blood, and spleen homogenates of 188 mink 4 and 16 months after inoculation with the virus. Samples from bone marrow, small intestine, liver, lungs, kidneys, and lymph nodes of 20 of the same mink were also tested by Klentaq. DNA was extracted from paired samples of plasma and the aforesaid tissues by a commercial nucleic acid extraction kit (Dynabeads Silane) and tested by PCR. Compared with the extracted DNA, Klentaq detected a significantly greater number of samples in the whole blood, serum, plasma, spleen, and small intestine. It was concluded that Klentaq is a preferred system for directly detecting AMDV DNA in mink blood and tissues. The lower success rate of extracted DNA compared with Klentaq could be the result of DNA losses during the extraction process. This is an important factor in chronically infected mink, which have a low AMDV copy number in the bloodstream. Direct AMDV detection also reduces the cost of PCR amplification and lowers the risk of sample contamination.

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One of the key characteristics of ancient DNA, low copy number, may be a product of its extraction

Cited by 35 publications

References 88 publications

Extending the spectrum of DNA sequences retrieved from ancient bones and teeth

Extending the spectrum of DNA sequences retrieved from ancient bones and teeth

Extracting DNA from ‘jaws’: high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material

A fast and accurate method of detecting Aleutian mink disease virus in blood and tissues of chronically infected mink

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