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Scientific Reports May 2020Precious 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...
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.
Topics: Animals; Anthozoa; Commerce; Coral Reefs; DNA; DNA Fingerprinting; Internationality; Jewelry; Phylogeny; Sequence Analysis, DNA
PubMed: 32427854
DOI: 10.1038/s41598-020-64582-4 -
Genes Nov 2023In forensic investigations, DNA profiles are routinely obtained from firearms evidence and alternative hypotheses may be proposed for consideration on the activity...
In forensic investigations, DNA profiles are routinely obtained from firearms evidence and alternative hypotheses may be proposed for consideration on the activity level. DNA profiles found to be consistent with the DNA profile of a specific individual could be a result of directly handling the firearm or other modes of transfer of DNA. Sixteen law-enforcement-owned firearms were evaluated with samples collected from the frame and slide area, the trigger and trigger guard area, and the front and rear sights after brief handling by laboratory personnel. Twenty-two out of forty-eight samples resulted in DNA profiles suitable for comparison, of which six resulted in likelihood ratios (LR) that demonstrated support for the hypothesis that included the brief handler as a contributor to the DNA profile obtained from the sample. Five of these samples were obtained from the frame and slide and one was from the trigger and trigger guard area. None of the DNA profiles obtained from the sights supported the inclusion of the brief handler as a contributor to the DNA profile. Gaining knowledge and supporting data on the nature of DNA profiles typically obtained from both owners and brief handlers can be useful for the purposes of evaluative reporting when considering results obtained from firearm evidence.
Topics: Firearms; DNA Fingerprinting; DNA
PubMed: 38136949
DOI: 10.3390/genes14122127 -
Forensic Science International Jul 2023Extracting DNA from degraded human remains poses a challenge for any forensic genetics laboratory, as it requires efficient high-throughput methods. While little...
Extracting DNA from degraded human remains poses a challenge for any forensic genetics laboratory, as it requires efficient high-throughput methods. While little research has compared different techniques, silica in suspension has been identified in the literature as the best method for recovering small fragments, which are often present in these types of samples. In this study, we tested five DNA extraction protocols on 25 different degraded skeletal remains. Including the humerus, ulna, tibia, femur, and petrous bone. The five protocols were organic extraction by phenol/chloroform/isoamyl alcohol, silica in suspension, High Pure Nucleic Acid Large Volume silica columns (Roche), InnoXtract™ Bone (InnoGenomics), and PrepFiler™ BTA with AutoMate™ Express robot (ThermoFisher). We analysed five DNA quantification parameters (small human target quantity, large human target quantity, human male target quantity, degradation index, and internal PCR control threshold), and five DNA profile parameters (number of alleles with peak height higher than analytic and stochastic threshold, average relative fluorescence units (RFU), heterozygous balance, and number of reportable loci) were analysed. Our results suggest that organic extraction by phenol/chloroform/isoamyl alcohol was the best performing method in terms of both quantification and DNA profile results. However, Roche silica columns were found to be the most efficient method.
Topics: Humans; Male; Body Remains; Chloroform; DNA Fingerprinting; Microsatellite Repeats; DNA; Phenol; Silicon Dioxide
PubMed: 37224759
DOI: 10.1016/j.forsciint.2023.111730 -
Genes Apr 2023Microhaplotypes (MHs) are widely accepted as powerful markers in forensic studies. They have the advantage of both short tandem repeats (STRs) and single nucleotide...
Microhaplotypes (MHs) are widely accepted as powerful markers in forensic studies. They have the advantage of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), with no stutter and amplification bias, short fragments and amplicons, low mutation and recombination rates, and high polymorphisms. In this study, we constructed a panel of 50 MHs that are distributed on 21 chromosomes and analyzed them using the Multiseq multiple polymerase chain reaction (multi-PCR) targeted capture sequencing protocol based on the massively parallel sequencing (MPS) platform. The sizes of markers and amplicons ranged between 11-81 bp and 123-198 bp, respectively. The sensitivity was 0.25 ng, and the calling results were consistent with Sanger sequencing and the Integrative Genomics Viewer (IGV). It showed measurable polymorphism among sequenced 137 Southwest Chinese Han individuals. No significant deviations in the Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium (LD) were found at all MHs after Bonferroni correction. Furthermore, the specificity was 1:40 for simulated two-person mixtures, and the detection rates of highly degraded single samples and mixtures were 100% and 93-100%, respectively. Moreover, animal DNA testing was incomplete and low depth. Overall, our MPS-based 50-plex MH panel is a powerful forensic tool that provides a strong supplement and enhancement for some existing panels.
Topics: Animals; DNA Fingerprinting; Polymorphism, Single Nucleotide; Polymerase Chain Reaction; DNA; High-Throughput Nucleotide Sequencing
PubMed: 37107623
DOI: 10.3390/genes14040865 -
Journal of Epidemiology and Community... Sep 2005Paternal discrepancy (PD) occurs when a child is identified as being biologically fathered by someone other than the man who believes he is the father. This paper... (Review)
Review
Paternal discrepancy (PD) occurs when a child is identified as being biologically fathered by someone other than the man who believes he is the father. This paper examines published evidence on levels of PD and its public health consequences. Rates vary between studies from 0.8% to 30% (median 3.7%, n = 17). Using information from genetic and behavioural studies, the article identifies those who conceive younger, live in deprivation, are in long term relationships (rather than marriages), or in certain cultural groups are at higher risk. Public health consequences of PD being exposed include family break up and violence. However, leaving PD undiagnosed means cases having incorrect information on their genetics and fathers continuing to suspect that children may not be theirs. Increasing paternity testing and use of DNA techniques in clinical and judicial procedures means more cases of PD will be identified. Given developing roles for individual's genetics in decisions made by health services, private services (for example, insurance), and even in personal lifestyle decisions, the dearth of intelligence on how and when PD should be exposed urgently needs addressing.
Topics: Child; DNA Fingerprinting; Extramarital Relations; Family; Female; Genetic Techniques; Health Services Accessibility; Humans; Incidental Findings; Male; Paternity; Prevalence; Public Health; Risk Factors; Socioeconomic Factors; Tissue and Organ Procurement
PubMed: 16100312
DOI: 10.1136/jech.2005.036517 -
Genes Oct 2021The top challenges of adopting new methods to forensic DNA analysis in routine laboratories are often the capital investment and the expertise required to implement and... (Review)
Review
The top challenges of adopting new methods to forensic DNA analysis in routine laboratories are often the capital investment and the expertise required to implement and validate such methods locally. In the case of next-generation sequencing, in the last decade, several specifically forensic commercial options became available, offering reliable and validated solutions. Despite this, the readily available expertise to analyze, interpret and understand such data is still perceived to be lagging behind. This review gives an introductory overview for the forensic scientists who are at the beginning of their journey with implementing next-generation sequencing locally and because most in the field do not have a bioinformatics background may find it difficult to navigate the new terms and analysis options available. The currently available open-source and commercial software for forensic sequencing data analysis are summarized here to provide an accessible starting point for those fairly new to the forensic application of massively parallel sequencing.
Topics: Computational Biology; DNA Fingerprinting; Data Interpretation, Statistical; Forensic Genetics; High-Throughput Nucleotide Sequencing; Humans; Microsatellite Repeats; Sequence Analysis, DNA; Software
PubMed: 34828345
DOI: 10.3390/genes12111739 -
Genes Mar 2023In 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...
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 × 10 (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.
Topics: Pregnancy; Humans; Female; Aged; Forensic Genetics; DNA Fingerprinting; DNA, Mitochondrial; Polymerase Chain Reaction; Body Remains
PubMed: 37107609
DOI: 10.3390/genes14040851 -
International Journal of Legal Medicine Sep 2023The combined approach of classical fingerprinting and DNA profiling is a powerful tool in forensic investigations of latent "touch" traces. However, little attention has...
The combined approach of classical fingerprinting and DNA profiling is a powerful tool in forensic investigations of latent "touch" traces. However, little attention has been paid to the organic solvents frequently used in dactyloscopic laboratories to facilitate the separation of adhesive evidence prior to fingerprint development and downstream effects on subsequent DNA profiling. In the present study, we tested a selection of adhesive removers (n = 9) and assessed their potential impact on DNA recovery and amplification by PCR. Thereby, we identified and characterized novel PCR inhibitors. All investigated chemicals contain volatile organic compounds that evaporate under normal indoor atmospheric conditions. Exposure to certain solvents resulted in increased DNA degradation, but only if evaporation was prevented. A series of adhesive-removal experiments were conducted with prepared mock evidence (self-adhesive postage stamps affixed to paper envelope) to investigate the impact of treatment time and the location of applied traces on DNA recovery and dactyloscopy, respectively. Due to the early onset of print decomposition, we found that only a short treatment time was compatible with the development of fingerprints on the adhesive side of a stamp. Solvents also removed DNA from the adhesive surface, thus resulting in a marked shift in the substrate distribution of recovered DNA from the stamp to the envelope, but not in the reverse direction. Furthermore, we observed that treatment with conventional fingerprint reagents lead to a significant reduction in the amounts of DNA recovered from stamps, while the additional use of adhesive removers did not significantly enhance this effect.
Topics: Humans; Dermatoglyphics; Adhesives; DNA Fingerprinting; Solvents; DNA
PubMed: 37402011
DOI: 10.1007/s00414-023-03042-w -
Current Biology : CB Feb 2011
Topics: DNA Fingerprinting; Evolution, Molecular; Forensic Sciences; Genetics, Population; Humans; Publishing
PubMed: 21391314
DOI: 10.1016/j.cub.2010.12.041 -
Croatian Medical Journal Feb 2017To select appropriate preprocessing methods for different substrates by comparing the effects of four different preprocessing methods on touch DNA samples and to...
AIM
To select appropriate preprocessing methods for different substrates by comparing the effects of four different preprocessing methods on touch DNA samples and to determine the effect of various storage times on the results of touch DNA sample analysis.
METHOD
Hand touch DNA samples were used to investigate the detection and inspection results of DNA on different substrates. Four preprocessing methods, including the direct cutting method, stubbing procedure, double swab technique, and vacuum cleaner method, were used in this study. DNA was extracted from mock samples with four different preprocessing methods. The best preprocess protocol determined from the study was further used to compare performance after various storage times. DNA extracted from all samples was quantified and amplified using standard procedures.
RESULTS
The amounts of DNA and the number of alleles detected on the porous substrates were greater than those on the non-porous substrates. The performances of the four preprocessing methods varied with different substrates. The direct cutting method displayed advantages for porous substrates, and the vacuum cleaner method was advantageous for non-porous substrates. No significant degradation trend was observed as the storage times increased.
CONCLUSION
Different substrates require the use of different preprocessing method in order to obtain the highest DNA amount and allele number from touch DNA samples. This study provides a theoretical basis for explorations of touch DNA samples and may be used as a reference when dealing with touch DNA samples in case work.
Topics: Alleles; DNA; DNA Fingerprinting; Hand; Humans; Specimen Handling; Touch
PubMed: 28252870
DOI: 10.3325/cmj.2017.58.4