Nondestructive extraction DNA method from bones or teeth, true or false?

Gomes, Cláudia; Palomo-Díez, Sara; Roig, J.; López-Parra, A.M.; Baeza-Richer, Carlos; Arroyo, Ángel Esparza; Gibaja, Juan Francisco; Arroyo-Pardo, Eduardo

doi:10.1016/j.fsigss.2015.09.111

Cited by 19 publications

(18 citation statements)

References 6 publications

(7 reference statements)

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“…After the same cleaning process, the samples were separated to proceed with the two types of extraction: the DNA from samples 1PC 3 , 2PC 3 and 3PC 3 was extracted according to Rohland and Hofreiter [4], and samples 1PC 4 , 2PC 4 and 3PC 4 according to Gomes and Palomo-Díez [5]. However, in both cases, the incubation time with the "Extraction Buffer", was extended to 48 h. On the other hand, the pH of all buffers from both extractions was corrected to pH = 8 [6].…”

Section: Extraction Methods Bmentioning

confidence: 99%

“…After the external cleaning of the samples (1PC 1-2 ; 2PC 1-2 ; 3PC 1-2 ) with Aluminium oxide, one of the samples was pulverized (1PC 1 , 2PC 1 and 3PC 1 ), and the extraction protocol was followed according to the described by Rohland and Hofreiter [4]. The other samples (1PC 2 , 2PC 2 and 3PC 2 ) were not submitted to the destruction process, being the DNA directly extracted according to Gomes and Palomo-Díez [5].…”

Section: Samplingmentioning

confidence: 99%

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“Inhibiting inhibitors”: Preliminary results of a new “DNA extraction-amplification” disinhibition technique in critical human samples

Gomes

Alonso

Marquina

et al. 2017

Forensic Science International: Genetics Supplement Series

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The present study focused on the genetic analysis of a presumptive Bronze Age family burial, with at least six skeletons (Plana Castell, Barcelona, Spain). In order to investigate the individuals' biological affiliation, a molecular study was undertaken, but it was impossible to obtain a positive DNA amplification. The excavation data indicated that the skeletons were buried in an old location used as a dumping ground, being very likely the presence of biological and/or chemical contaminants. To overcome this difficulty, we undertook several modifications both in the extraction as in the amplification protocol, like MgCl2 concentration, or the inclusion of Bovine Serum Albumin (BSA). Despite their antiquity, the preliminary results indicate that all samples were effectively inhibited, and for the first time we were able to obtain mtDNA results, specifically, for the Hypervariable mitochondrial region 1. It also allowed us to infer that our protocol performance increased considerable, mainly the amplification modifications. In general, the best results were obtained with MgCl2 0,6 μL (20 mM) and BSA 2 mg/mL per sample. Our result is quite important in a forensic analysis, mainly in cases where corpse/s is/are buried directly in the soil.

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Section: Extraction Methods Bmentioning

confidence: 99%

Section: Samplingmentioning

confidence: 99%

“Inhibiting inhibitors”: Preliminary results of a new “DNA extraction-amplification” disinhibition technique in critical human samples

Gomes

Alonso

Marquina

et al. 2017

Forensic Science International: Genetics Supplement Series

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“…Non-destructive and non-invasive sampling methodologies are increasingly being demanded by museums and archives in order to preserve the integrity of unique accessions and maintain sufficient material for future analyses [ 250 , 251 , 252 ]. A variety of studies have developed novel biomolecular sampling techniques for bones and teeth [ 253 , 254 ], insects [ 170 , 255 , 256 ], shells [ 152 ], books and parchment [ 249 , 257 ], and fluid-preserved specimens [ 198 ] which do not require invasive sampling. As both our extraction techniques and bioinformatic approaches improve, potentially greater amounts of information may be achieved from minute samples.…”

Section: Moving Forwardmentioning

confidence: 99%

Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles

Green

Speller

2017

Genes

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Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively “novel”. Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.

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“…One of the samples from each individual was pulverized in a freezer mill filled with liquid Nitrogen, and then, the extraction protocol was followed according to the described by Rohland and Hofreiter [4]. The other sample was not submitted to the destruction process, being the DNA directly extracted according to Gomes and Palomo-Díez et al [5].…”

Section: Pretreatment and Dna Extractionmentioning

confidence: 99%

Biological kinship analysis in extremely critical samples: The case of a Spanish Neolithic necropolis

Gomes

Gibaja²,

Buxó

et al. 2017

Forensic Science International: Genetics Supplement Series

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It is common in archeology and some forensic cases to make assumptions about the relationship between persons buried in the same grave, or in distinct burials but in the same cemetery. However, there is no objective criterion to make such suppositions. This study aims to investigate the biological relationship among six Neolithic individuals (4200-3400 cal BC) from the Can Gambús-1 necropolis (Barcelona, Spain) as well as, their possible mitochondrial ancestry. From at least 47 tombs, six skeletons were selected, from six individual graves, selecting from each one three integral teeth, without cavities or caries. To carry out this study, the samples were analyzed by two distinct extraction methods, one destructive and other non-destructive, and to determine a presumptive (biological) kinship between the buried individuals, small length nuclear DNA markers were considered, as well as a mitochondrial DNA analysis, in order to determine their maternal lineage. The samples were extremely degraded, requiring several attempts to achieve sequences with a standard quality, without double peaks or other artefacts. Despite the degraded state of the samples, it has been possible to analyze the mitochondrial information and to determine that the studied individuals had a European ancestry, and were not maternally related, since they did not share the same mitochondrial haplotype.

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Nondestructive extraction DNA method from bones or teeth, true or false?

Cited by 19 publications

References 6 publications

“Inhibiting inhibitors”: Preliminary results of a new “DNA extraction-amplification” disinhibition technique in critical human samples

“Inhibiting inhibitors”: Preliminary results of a new “DNA extraction-amplification” disinhibition technique in critical human samples

Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles

Biological kinship analysis in extremely critical samples: The case of a Spanish Neolithic necropolis

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