Comparison of nuclear DNA yield and STR typing success in Second World War petrous bones and metacarpals III

Pajnič, Irena Zupanič; Inkret, Jezerka; Zupanc, Tomaž; Podovšovnik, Eva

doi:10.1016/j.fsigen.2021.102578

Cited by 11 publications

(16 citation statements)

References 44 publications

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“…Our study supports the idea that higher DNA yields are obtained from petrous bone, whereas this kind of remain shows high variability in terms of degradation index (as stated before [38]). Nevertheless, there is a certain variability among the different studies that can be found in literature that may be explained by the sampling technique, as it has been stated that DNA is not evenly distributed around the skeletal remain [39, 40].…”

Section: Resultssupporting

confidence: 91%

A comparison between petrous bone and tooth, femur and tibia DNA analysis from degraded skeletal remains

et al. 2023

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Skeletal remains are the only biological material that remains after long periods; however, environmental conditions such as temperature, humidity, and pH affect DNA preservation, turning skeletal remains into a challenging sample for DNA laboratories. Sample selection is a key factor, and femur and tooth have been traditionally recommended as the best substrate of genetic material. Recently, petrous bone (cochlear area) has been suggested as a better option due to its DNA yield. This research aims to evaluate the efficiency of petrous bone compared to other cranium samples (tooth) and postcranial long bones (femur and tibia). A total amount of 88 samples were selected from 38 different individuals. The samples were extracted by using an organic extraction protocol, DNA quantification by Quantifiler Trio kit and amplified with GlobalFiler kit. Results show that petrous bone outperforms other bone remains in quantification data, yielding 15–30 times more DNA than the others. DNA profile data presented likeness between petrous bone and tooth regarding detected alleles; however, the amount of DNA extracted in petrous bones allowed us to obtain more informative DNA profiles with superior quality. In conclusion, petrous bone or teeth sampling is recommended if DNA typing is going to be performed with environmentally degraded skeletal remains.

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Section: Resultssupporting

confidence: 91%

A comparison between petrous bone and tooth, femur and tibia DNA analysis from degraded skeletal remains

et al. 2023

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“…However, the temporal bone is not always available for genetic testing because of historical interest or of practical or ethical reasons [ 35 ]. In such cases, other bones have to be selected for the genetic testing of aged skeletons; long bones (mainly femur) are preferred for analyses [ 4 ], while metacarpal and other short bone elements provide promising or even better results [ 36 ]. Therefore, several bones from the same skeleton should be collected whenever possible [ 4 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 ].…”

Section: Discussionmentioning

confidence: 99%

“…Therefore, our results support previous data showing that the compact cortical bone has to be preferred in genetic studies [ 4 , 16 , 21 , 22 , 23 , 24 , 26 , 27 , 28 ]. However, we strongly recommend that more than one bone sample, including the temporal [ 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 ] and the metatarsals [ 36 ] bones, should be collected if available, both in forensic and archaeological casework. It is likely that even the magnetic bead-based protocol [ 47 ] we used for DNA purification in 2022 contributed to the successful outcome.…”

Section: Discussionmentioning

confidence: 99%

“…Although high-throughput shotgun sequencing and the analysis of genome-wide data have largely replaced current PCR-based methods in ancient DNA (aDNA) analysis [ 1 , 2 , 13 ], there are many aspects that aDNA analysis and forensic DNA analysis have in common; for instance, the use of limited amounts of degraded DNA, the precautions adopted to prevent contamination, and the use of authenticity criteria [ 14 , 15 , 16 , 17 , 18 , 19 , 20 ]. In addition, both disciplines have developed strategies to select the skeletal element which provides, a priori, the highest probabilities of positive outcomes [ 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 ].…”

Section: Introductionmentioning

confidence: 99%

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The Baron Pasquale Revoltella’s Will in the Forensic Genetics Era

Fattorini

Previderé

Bonin

et al. 2023

Genes

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In this article, we describe multiple analytical strategies that were first developed for forensic purposes, on a set of three bone samples collected in 2011. We analyzed a single bone sample (patella) collected from the artificially mummified body of the Baron Pasquale Revoltella (1795–1869), as well two femurs which allegedly belonged to the Baron’s mother (Domenica Privato Revoltella, 1775–1830). Likely due to the artificial mummification procedures, the inner part of the Baron’s patella allowed the extraction of high-quality DNA yields, which were successfully used for PCR-CE and PCR-MPS typing of autosomal, Y-specific, and mitochondrial markers. The samples extracted from the trabecular inner part of the two femurs yielded no typing results by using the SNP identity panel, whereas the samples extracted from the compact cortical part of the same bone samples allowed genetic typing, even by the employment of PCR-CE technology. Altogether, 10/15 STR markers, 80/90 identity SNP markers, and HVR1, HVR2, and HVR3 regions of the mtDNA were successfully typed from the Baron’s mother’s remains by the combined use of PCR-CE and PCR-MPS technologies. The kinship analysis showed a likelihood ratio of at least 9.1 × 106 (corresponding to a probability of maternity of 99.9999999%), and thus confirmed the identity of the skeletal remains as those of the Baron’s mother. This casework represented a challenging trial for testing forensic protocols on aged bones samples. It highlighted the importance of accurately sampling from the long bones, and that DNA degradation is not blocked by freezing at −80 °C.

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“…Generally, the mitogenome CN is tissue-specific [ 14 ], and bone tissue requires special attention when determining the correct mtDNA NGS input quantity if one takes into account the findings on the preservation of DNA in old bones. For aged bones, high nDNA degradation has been observed [ 30 , 31 ], and there is a great variability in the preservation of DNA between different types of bones [ 31 – 34 ] within each bone [ 35 – 37 ] and between individuals [ 30 , 31 ]. This represents the extraordinary complexity of old bone tissue, which most likely also reflects the differences in mtDNA preservation and its quantity and quality.…”

Section: Introductionmentioning

confidence: 99%

Measure quantity of mitochondrial DNA in aged bones or calculate it from nuclear DNA quantitative PCR results?

Obal,

Zupanc,

Zupanič Pajnič

2023

Int J Legal Med

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Mitochondrial DNA (mtDNA) is of great value in forensics to procure information about a person when a next of kin, personal belongings, or other sources of nuclear DNA (nDNA) are unavailable, or nDNA is lacking in quality and quantity. The quality and reliability of the results depend greatly on ensuring optimal conditions for the given method, for instance, the optimal input of the copy number (CN) in next-generation sequencing (NGS) methods. The unavailability of commercial quantitative PCR (qPCR) methods to determine mtDNA CN creates the necessity to rely on recommendations to infer mtDNA CN from nDNA yield. Because nDNA yield varies between individuals, tissues, parts of the same tissue, and because mtDNA CN varies between tissues, such assumptions must be examined for a specific context, rather than be generalized. This study compares mtDNA CN calculated from nDNA yield and qPCR measured mtDNA CN. Seventy-five femurs from the Second World War victims were used as samples; they were cut below the greater trochanter, surface contaminants were removed by mechanical and chemical cleaning, samples were fully demineralized, and DNA was isolated. PowerQuant® Kit (Promega) was used to analyze DNA yield. An in-house method was used to determine mtDNA CN. Comparison of mtDNA CN from nDNA derived calculations and measured mtDNA CN highlighted vast differences. The results emphasize the need to perform qPCR to assess mtDNA CN before NGS analyses of aged bones’ mitogenomes rather than estimating mtDNA CN from nDNA yield to ensure the quality and reliability of the results of NGS analysis.

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Comparison of nuclear DNA yield and STR typing success in Second World War petrous bones and metacarpals III

Cited by 11 publications

References 44 publications

A comparison between petrous bone and tooth, femur and tibia DNA analysis from degraded skeletal remains

A comparison between petrous bone and tooth, femur and tibia DNA analysis from degraded skeletal remains

The Baron Pasquale Revoltella’s Will in the Forensic Genetics Era

Measure quantity of mitochondrial DNA in aged bones or calculate it from nuclear DNA quantitative PCR results?

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