Extraction of high quality DNA from biological materials and calcified tissues

Stray, James E.; Holt, Allison; Brevnov, Maxim G.; Calandro, Lisa M.; Furtado, Manohar R.; Shewale, Jaiprakash G.

doi:10.1016/j.fsigss.2009.08.086

Cited by 15 publications

(11 citation statements)

References 3 publications

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“…). In general, the DNA yields in this study are comparable or higher than reported for similar skeletal remains in previous studies (). Variation in DNA quantity between the technical replicates was observed (Table ).…”

Section: Resultssupporting

confidence: 86%

“…Bone preparation consists of cleaning the external surface of the bone (via washing, UV radiation, and/or sanding), cutting the bone into smaller pieces (if necessary), and crushing the bone into a powder with liquid nitrogen in a blender cup or a freezer mill (4,5,(14)(15)(16)(17)(18). While finely ground bone powder generally yields type-able amounts of DNA (4,5,7,12,13,(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28), it destroys the sample, increases the risk of contamination, and creates a potential hazard to the processor from airborne powder (4,17,27). Therefore, several studies have explored nondestructive extraction methods from whole bone and teeth (14,16,23,27).…”

mentioning

confidence: 99%

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Evaluation Of A Powder‐Free DNA Extraction Method For Skeletal Remains

Harrel

Mayes

Gangitano

et al. 2018

Journal of Forensic Sciences

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Bones are often recovered in forensic investigations, including missing persons and mass disasters. While traditional DNA extraction methods rely on grinding bone into powder prior to DNA purification, the TBone Ex buffer (DNA Chip Research Inc.) digests bone chips without powdering. In this study, six bones were extracted using the TBone Ex kit in conjunction with the PrepFiler® BTA™ DNA extraction kit (Thermo Fisher Scientific) both manually and via an automated platform. Comparable amounts of DNA were recovered from a 50 mg bone chip using the TBone Ex kit and 50 mg of powdered bone with the PrepFiler® BTA™ kit. However, automated DNA purification decreased DNA yield (p < 0.05). Nevertheless, short tandem repeat (STR) success was comparable across all methods tested. This study demonstrates that digestion of whole bone fragments is an efficient alternative to powdering bones for DNA extraction without compromising downstream STR profile quality.

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Section: Resultssupporting

confidence: 86%

mentioning

confidence: 99%

Evaluation Of A Powder‐Free DNA Extraction Method For Skeletal Remains

Harrel

Mayes

Gangitano

et al. 2018

Journal of Forensic Sciences

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“…Using a set of 25 worked coral samples, we evaluated which one of five candidate DNA extraction protocols is most suited to retrieve DNA from worked precious coral samples. Each of the five tested methods (abbreviated as "W", "F", "B", "E", "Y") have earlier proven to be useful in extracting DNA from biomineralized material 29,[39][40][41][42][43][44][45][46][47][48] . DNA was extracted from each of the 25 worked coral skeletal samples with all five techniques, and DNA purity and quantity were assessed using real-time quantitative PCR (qPCR) technology.…”

Section: Resultsmentioning

confidence: 99%

“…The lengths of the concatenated LR and MSH sequences were between 264 base-pairs (bp) and 290 bp long per coral sample (Supplementary Results S2). Bayesian phylogenetic analysis identified 10 samples (11,14,19,22,23,31,34,38,41,45) as Corallium rubrum, of which nine had sequences identical to either of two the reference C. rubrum sequences, and one (11) had a single variable site (Fig. 4).…”

Section: Resultsmentioning

confidence: 99%

DNA fingerprinting: an effective tool for taxonomic identification of precious corals in jewelry

Lendvay

Cartier

Gysi

et al. 2020

Sci Rep

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Precious coral species have been used to produce jewelry and ornaments since antiquity. Due to the high value and demand for corals, some coral beds have been heavily fished over past centuries. Fishing and international trade regulations were put in place to regulate fishing practices in recent decades. To this date, the control of precious coral exploitation and enforcement of trade rules have been somewhat impaired by the fact that different species of worked coral samples can be extremely difficult to distinguish, even for trained experts. Here, we developed methods to use DNA recovered from precious coral samples worked for jewelry to identify their species. We evaluated purity and quantity of DNA extracted using five different techniques. Then, a minimally invasive sampling protocol was tested, which allowed genetic analysis without compromising the value of the worked coral objects.The best performing DNA extraction technique applies decalcification of the skeletal material with EDTA in the presence of laurylsarcosyl and proteinase, and purification of the DNA with a commercial silica membrane. This method yielded pure DNA in all cases using 100 mg coral material and in over half of the cases when using "quasi non-destructive" sampling with sampled material amounts as low as 2.3 mg. Sequence data of the recovered DNA gave an indication that the range of precious coral species present in the trade is broader than previously anticipated. Precious corals are among the most appreciated and oldest known gems. They are valued for their color, texture and workability (polishing, carving), and have thus been collected and used for adornment for millennia 1-3. Growing demand, particularly in Asia in recent years, has led to an increase in prices of precious corals used in jewelry 4-6. The most valuable precious coral species belong to the Coralliidae family within the Octocorallia subclass of the Anthozoa. The precious coral material used for jewelry is the worked (i.e. cut, carved and polished) hard coral skeletal axis, which is a biogenic material created by a biomineralization process 7. In this process, closely packed magnesium-rich calcite crystals are secreted by coral polyps (1-2 mm in size) to build up a skeleton over decades. The polyps can thrive on the surface of the skeleton as colonies connected and surrounded by a 0.5-1 mm thick surface tissue (coenenchyme) 8. The Coral Commission of The World Jewellery Confederation (CIBJO) lists eight Coralliidae species as significant in the precious coral jewelry industry 9,10. Precious coral products are sold worldwide, with production centers located in Italy, Japan and Taiwan and large-scale trade of raw material between these areas 5,6,11. Until recent decades, the populations of these highly coveted marine animals experienced exploitation in boom and bust cycles where the discovery of precious coral beds led to rushes by coral fishers and these beds were exploited as long as it remained economically feasible 12,13. Local and international regulations were put...

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“…Nevertheless, an effective system to extract DNA rapidly from a limited calcified tissue source with removal of PCR inhibitors is offered in the Prepfiler BTA Kit from Applied Biosystems. Based on sophisticated magnetic bead chemistry and an innovative BTA® (bone, teeth, adhesive) lysis buffer provides a system that is now automated for DNA extraction from these challenging sources (Stray et al 2009;Applied Biosystems, 2012;Davis et al 2012).…”

Section: 2) Techniques To Remove Pcr Inhibitors From Buried Skeletamentioning

confidence: 99%

The validation of forensic DNA extraction systems to utilize soil contaminated biological evidence

Kasu

Shires

2015

Legal Medicine

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The production of full DNA profiles from biological evidence found in soil has a high failure rate due largely to the inhibitory substance humic acid (HA). Abundant in various natural soils, HA co-extracts with DNA during extraction and inhibits DNA profiling by binding to the molecular components of the genotyping assay. To successfully utilize traces of soil contaminated evidence, such as that found at many murder and rape crime scenes in South Africa, a reliable HA removal extraction system would often be selected based on previous validation studies. However, for many standard forensic DNA extraction systems, peer-reviewed publications detailing the efficacy on soil evidence is either lacking or is incomplete. Consequently, these sample types are often not collected or fail to yield suitable DNA material due to the use of unsuitable methodology. The aim of this study was to validate the common forensic DNA collection and extraction systems used in South Africa, namely DNA IQ, FTA elute and Nucleosave for processing blood and saliva contaminated with HA. A forensic appropriate volume of biological evidence was spiked with HA (0, 0.5, 1.5 and 2.5 mg/ml) and processed through each extraction protocol for the evaluation of HA removal using QPCR and STR-genotyping. The DNA IQ magnetic bead system effectively removed HA from highly contaminated blood and saliva, and generated consistently acceptable STR profiles from both artificially spiked samples and crude soil samples. This system is highly recommended for use on soil-contaminated evidence over the cellulose card-based systems currently being preferentially used for DNA sample collection.

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Extraction of high quality DNA from biological materials and calcified tissues

Cited by 15 publications

References 3 publications

Evaluation Of A Powder‐Free DNA Extraction Method For Skeletal Remains

Evaluation Of A Powder‐Free DNA Extraction Method For Skeletal Remains

DNA fingerprinting: an effective tool for taxonomic identification of precious corals in jewelry

The validation of forensic DNA extraction systems to utilize soil contaminated biological evidence

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