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Scientific Reports Jul 2021We address computational and statistical aspects of DNA-based identification of victims in the aftermath of disasters. Current methods and software for such...
We address computational and statistical aspects of DNA-based identification of victims in the aftermath of disasters. Current methods and software for such identification typically consider each victim individually, leading to suboptimal power of identification and potential inconsistencies in the statistical summary of the evidence. We resolve these problems by performing joint identification of all victims, using the complete genetic data set. Individual identification probabilities, conditional on all available information, are derived from the joint solution in the form of posterior pairing probabilities. A closed formula is obtained for the a priori number of possible joint solutions to a given DVI problem. This number increases quickly with the number of victims and missing persons, posing computational challenges for brute force approaches. We address this complexity with a preparatory sequential step aiming to reduce the search space. The examples show that realistic cases are handled efficiently. User-friendly implementations of all methods are provided in the R package dvir, freely available on all platforms.
Topics: DNA Fingerprinting; Disaster Victims; Female; Humans; Male; Pedigree; Probability; Software
PubMed: 34211052
DOI: 10.1038/s41598-021-93071-5 -
Journal of Forensic Sciences Jul 2022The prevalence of sexual assault cases and increasingly sensitive DNA analysis methods have resulted in sexual assault kit backlogs in the United States. Although...
The prevalence of sexual assault cases and increasingly sensitive DNA analysis methods have resulted in sexual assault kit backlogs in the United States. Although traditional DNA extraction and purification utilizing detergents, proteinase K, and DTT have been the primary technique for lysing sperm cell fractions from these samples, it is labor-intensive and inefficient regarding time and sperm DNA recovery - hindering the ability of forensic analysts to keep pace with evidence submissions. Thus, this study examined seven alternative sperm cell lysis techniques to develop a method that could efficiently lyse sperm and consistently generate high-quality profiles while also reducing time, labor, and cost requirements. Microscopic examination of lysates indicated only Casework Direct and alkaline techniques could lyse all spermatozoa within samples, while quantification results demonstrated all methods performed comparably to the control method of forensicGEM™ Sperm (p > 0.06). Amplification with 0.25 ng DNA revealed that unpurified lysates from Casework Direct, alkaline, and NP-40 techniques produced DNA profiles with acceptable mean STR peak heights and interlocus balance, both of which were similar to or better than the control. Overall, this study demonstrated the ability of Casework Direct, alkaline, and NP-40 methods to efficiently lyse spermatozoa and provide high-quality STR profiles despite the absence of a purification step. Ultimately, based on the data reported herein, alkaline lysis is the recommended alternative sperm lysis approach given its ability to generate high-quality profiles, save time, and decrease the cost per reaction when compared to traditional sperm cell lysis methods.
Topics: DNA; DNA Fingerprinting; Humans; Male; Microsatellite Repeats; Semen; Sex Offenses; Specimen Handling; Spermatozoa
PubMed: 35285573
DOI: 10.1111/1556-4029.15027 -
Scientific Reports Jul 2019Variability in efficacy and safety is a worldwide concern with commercial probiotics for their growing and inevitable use in food and health sectors. Here, we introduce...
Variability in efficacy and safety is a worldwide concern with commercial probiotics for their growing and inevitable use in food and health sectors. Here, we introduce a probiotic thermophysical fingerprinting methodology using a coupling thermogravimetry and differential scanning calorimetry. Qualitative and quantitative information on the material decomposition and transition phases is provided under heating conditions. By monitoring the changes in both mass and internal energy over temperature and time, a couple of thermal data at the maximum decomposition steps allow the creation of a unique and global product identity, depending on both strain and excipient components. We demonstrate that each powder formulation of monostrain and multistrain from different lots and origins have a unique thermophysical profile. Our approach also provides information on the formulation thermostability and additive/excipient composition. An original fingerprint form is proposed by converting the generated thermal data sequence into a star-like pattern for a perspective library construction.
Topics: Biometric Identification; Calorimetry, Differential Scanning; DNA Fingerprinting; Excipients; Phenotype; Powders; Probiotics; Thermodynamics; Thermogravimetry
PubMed: 31292519
DOI: 10.1038/s41598-019-46469-1 -
Electrophoresis Nov 2018DNA sequencing, starting with Sanger's chain termination method in 1977 and evolving into the next generation sequencing (NGS) techniques of today that employ massively... (Review)
Review
DNA sequencing, starting with Sanger's chain termination method in 1977 and evolving into the next generation sequencing (NGS) techniques of today that employ massively parallel sequencing (MPS), has become essential in application areas such as biotechnology, virology, and medical diagnostics. Reflected by the growing number of articles published over the last 2-3 years, these techniques have also gained attention in the forensic field. This review contains a brief description of first, second, and third generation sequencing techniques, and focuses on the recent developments in human DNA analysis applicable in the forensic field. Relevance to the forensic analysis is that besides generation of standard STR-profiles, DNA repeats can also be sequenced to look for polymorphisms. Furthermore, additional SNPs can be sequenced to acquire information on ancestry, paternity or phenotype. The current MPS systems are also very helpful in cases where only a limited amount of DNA or highly degraded DNA has been secured from a crime scene. If enough autosomal DNA is not present, mitochondrial DNA can be sequenced for maternal lineage analysis. These developments clearly demonstrate that the use of NGS will grow into an indispensable tool for forensic science.
Topics: DNA; DNA Fingerprinting; Forensic Genetics; High-Throughput Nucleotide Sequencing; Humans; Microsatellite Repeats; Polymorphism, Single Nucleotide
PubMed: 30101986
DOI: 10.1002/elps.201800082 -
Frontiers in Bioscience (Landmark... Sep 2022As we continually reflect on the wars of the 20th century, identification of the remains of victims takes an increasingly prominent position in ongoing research.... (Review)
Review
As we continually reflect on the wars of the 20th century, identification of the remains of victims takes an increasingly prominent position in ongoing research. Existing work on the identification of human remains from 20th century wars primarily covers the determination of phenotypic characteristics, kinship and geographic origins, supporting the establishment of genetic information databases. Compared with standard forensic methods, DNA analyses have revealed greater effectiveness. The process of DNA analysis includes DNA extraction, genetic marker testing and data analysis. Protocols from ancient DNA research can be applied to degraded remains, and next-generation sequencing (NGS) techniques can compensate for shortcomings in the most commonly-used PCR-capillary electrophoresis typing. As it stands, wide-ranging inter-governmental and inter-institutional collaboration is necessary in order to set up NGS-based public databases, and thereby promote the identification of human remains and archaeological forensics.
Topics: Body Remains; DNA Fingerprinting; DNA, Ancient; Genetic Markers; High-Throughput Nucleotide Sequencing; Humans; Microsatellite Repeats
PubMed: 36224018
DOI: 10.31083/j.fbl2709271 -
The International Journal of Biological... Dec 2013Standard operating procedures (SOPs) optimization for nucleic acid extraction from stored samples is of crucial importance in a biological repository, considering the...
Standard operating procedures (SOPs) optimization for nucleic acid extraction from stored samples is of crucial importance in a biological repository, considering the large number of collected samples and their future downstream molecular and biological applications. However, the validity of molecular studies using stored specimens depends not only on the integrity of the biological samples, but also on the procedures that ensure the traceability of the same sample, certifying its uniqueness, and ensuring the identification of potential sample contaminations. With this aim, we have developed a rapid, reliable, low-cost, and simple DNA fingerprinting tool for a routine use in quality control of biorepositories samples. The method consists of a double ALU insertion/deletion genotyping panel suitable for uniqueness, identification of sample contaminations, and gender validation. Preliminary data suggest that this easy-to-use DNA fingerprinting protocol could routinely provide assurances of DNA identity and quality in a biorepository setting.
Topics: DNA; DNA Fingerprinting; Electrophoresis, Agar Gel; Humans; Pilot Projects; Reproducibility of Results; Specimen Handling
PubMed: 23873620
DOI: 10.5301/JBM.5000044 -
Archives of Pathology & Laboratory... Nov 1999This article reviews the history of DNA-based human identification from its inception in 1985. Since the development of the technology, experts called for setting of... (Review)
Review
This article reviews the history of DNA-based human identification from its inception in 1985. Since the development of the technology, experts called for setting of standards and use of proficiency tests for quality assurance measures. The response of the National Institute of Standards and Technology to DNA forensic standards needs was catalyzed by the Technical Working Group on DNA Analysis Methods, sponsored by the Federal Bureau of Investigation with funding provided by the National Institute of Justice. Standard reference materials were developed for the original technologies used in DNA identification and for the newer polymerase chain reaction-based technologies. Adoption of recommended standards developed through the Federal Bureau of Investigation-commissioned DNA Advisory Board show the acceptance of National Institute of Standards and Technology standards for calibration of laboratory protocols. New technologies will require a process of validation and continued testing through the use of proficiency tests, such as those provided through the College of American Pathologists. Robotics and parallel processing of samples will lead to increased efficiency in DNA testing. The use of DNA data banks of convicted felons will increase dramatically with the the Federal Bureau of Investigation's national implementation of a computerized identification system known as the Combined DNA Index System. This system that will make major use of short, tandem, repeat genetic systems and will be the major driver of technology for the next 5 to 10 years. Finally, sample collection and training are of major concern for those who look at the long-term impact of DNA testing in forensic laboratories.
Topics: DNA; DNA Fingerprinting; Databases, Factual; Female; Forensic Medicine; Humans; Male; Reference Standards; United States
PubMed: 10539909
DOI: 10.5858/1999-123-1063-IODTOS -
BioTechniques Apr 2008Forensic samples that contain too little template DNA or are too degraded require alternate genetic marker analyses or approaches to what is currently used for routine... (Review)
Review
Forensic samples that contain too little template DNA or are too degraded require alternate genetic marker analyses or approaches to what is currently used for routine casework. Single nucleotide polymorphisms (SNPs) offer promise to support forensic DNA analyses because of an abundance of potential markers, amenability to automation, and potential reduction in required fragment length to only 60-80 bp. The SNP markers will serve an important role in analyzing challenging forensic samples, such as those that are very degraded, for augmenting the power of kinship analyses and family reconstructions for missing persons and unidentified human remains, as well as for providing investigative lead value in some cases without a suspect (and no genetic profile match in CODIS). The SNPs for forensic analyses can be divided into four categories: identity-testing SNPs; lineage informative SNPs; ancestry informative SNPs; and phenotype informative SNPs. In addition to discussing the applications of these different types of SNPs, this article provides some discussion on privacy issues so that society and policymakers can be more informed.
Topics: Confidentiality; DNA Fingerprinting; DNA Mutational Analysis; Forensic Genetics; Genetic Linkage; Humans; Internationality; Polymorphism, Single Nucleotide
PubMed: 18474034
DOI: 10.2144/000112806 -
Scientific Reports Dec 2023DNA analysis-based identification is by far the gold standard in forensic genetics and it should be performed in every case involving human remains or unidentified...
DNA analysis-based identification is by far the gold standard in forensic genetics and it should be performed in every case involving human remains or unidentified bodies. Bones and teeth are the preferred source of human DNA for genetic analysis. However, there are cases where the nature of the proceedings and historical significance prevent the disruption of skeletal structure. The remains may also be heavily degraded. In such situations, forensic geneticists seek alternative sources of human DNA. Teeth calculus has proven to be a viable source of DNA for identification purposes. The aim of this study was to assess the concentration of human DNA in teeth calculus and evaluate the usefulness of teeth calculus as a DNA source in the identification process. Teeth calculus was collected from skeletons exhumed between 2021 and 2022 by the PBGOT (Polish Genetic Database of Victims of Totalitarianism) team from the former Stalag IID prisoner-of-war camp in Stargard. Genetic analyses included the determination of autosomal and Y-STR markers. The total concentration of human DNA was also evaluated in samples from teeth calculus and teeth taken from the same individuals. The pilot study included 22 skeletons with a sufficient amount of calculus for isolation (specified in the protocol). Samples were taken from the largest areas of calculus deposited on lingual surfaces of mandibular incisors. The prepared samples underwent DNA extraction. Our study demonstrated that teeth calculus is a source of human DNA for remains from the World War II period. The obtained DNA concentration allowed for the determination of STR markers. It was shown that teeth calculus contains human DNA in an amount suitable for preliminary identification analyses.
Topics: Humans; Dental Calculus; Pilot Projects; DNA Fingerprinting; Microsatellite Repeats; DNA; Incisor
PubMed: 38066060
DOI: 10.1038/s41598-023-48761-7 -
Genes Mar 2020The high variability and somatic stability of DNA fingerprints can be used to identify individuals, which is of great value in plant breeding. DNA fingerprint databases...
The high variability and somatic stability of DNA fingerprints can be used to identify individuals, which is of great value in plant breeding. DNA fingerprint databases are essential and important tools for plant molecular research because they provide powerful technical and information support for crop breeding, variety quality control, variety right protection, and molecular marker-assisted breeding. Building a DNA fingerprint database involves the production of large amounts of heterogeneous data for which storage, analysis, and retrieval are time and resource consuming. To process the large amounts of data generated by laboratories and conduct quality control, a database management system is urgently needed to track samples and analyze data. We developed the plant international DNA-fingerprinting system (PIDS) using an open source web server and free software that has automatic collection, storage, and efficient management functions based on merging and comparison algorithms to handle massive microsatellite DNA fingerprint data. PIDS also can perform genetic analyses. This system can match a corresponding capillary electrophoresis image on each primer locus as fingerprint data to upload to the server. PIDS provides free customization and extension of back-end functions to meet the requirements of different laboratories. This system can be a significant tool for plant breeders and can be applied in forensic science for human fingerprint identification, as well as in virus and microorganism research.
Topics: Algorithms; DNA Fingerprinting; DNA, Plant; Database Management Systems; Microsatellite Repeats; Plants; Software
PubMed: 32235513
DOI: 10.3390/genes11040373