Forensic genetics derives from a late offshoot of the big tree resulting from the conjunction between legal medicine and criminalistics (for the distinction between forensic genetics and other forensic sciences, see [1-3]).Its historical evolution shows substantial theoretical and technological developments and has, meanwhile, turned this discipline into a broad and independent . A few panels of autosomal SNPs have also been developed for individual identification in different animal species [111117]. Such investigations are relevant for guaranteeing consumer choices according to health concerns (e.g., sensitivities or allergies), dietary preferences (e.g., vegetarian, nongenetically modified organisms), religious beliefs (e.g., halal and kosher specifications), and to detect fraudulent substitution of a given species by a similar one with lower economic value [198, 199]. Stoeckle MY, Gamble CC, Kirpekar R, Young G, Ahmed S, Little DP. Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection. Evolutionary Biology: Biodiversification from Genotype to Phenotype. Gonzalez-Candelas F, Bracho MA, Wrobel B, Moya A. Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source, Molecular epidemiology and forensic genetics: application to a hepatitis C virus transmission event at a hemodialysis unit. Basic Principles In: Siegel JA, Saukko PJ, editors. More conclusive results in forensic testing are now a practical reality thanks to advances in genomics. Chemical elemental distribution and soil DNA fingerprints provide the critical evidence in murder case investigation. Menotti-Raymond M, David VA, Stephens JC, Lyons LA, O'Brien SJ. It involves cases related with breed, variety, or populations such as was the attack perpetrated by a dog or by a wolf?, The coming paradigm shift in forensic identification science. Heating Up Cold Cases: An Interview with Bruce Budowle on Human Bazakos C, Dulger AO, Uncu AT, Spaniolas S, Spano T, Kalaitzis P. A SNP-based PCR-RFLP capillary electrophoresis analysis for the identification of the varietal origin of olive oils. Molecular genetic characterization of animal genetic resources. Here, we overview the use of nonhuman genetic material (NHGM) as ancillary evidence to solve classical forensic problems and in cases that fall outside the civil and criminal human authorship or responsibility. The current state of GMO governance: are we ready for GM animals? The identification of individuals can be achieved using a number of markers sufficient to provide high power of discrimination. PCR analysis of tissue samples from the 1979 Sverdlovsk anthrax victims: the presence of multiple Bacillus anthracis strains in different victims, Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Moreover, current MPS technologies still present relatively high sequencing errors [e.g., 266] which, although could be assumed for other disciplines, may not meet forensic standards [267]. Xanthopoulou A, Ganopoulos I, Kalivas A, Osathanunkul M, Chatzopoulou P, Tsaftaris A, et al. Historically, the first contributions correspond to situations in which NHGM is used as a silent witness resulting from involuntary transfer and leading to the so-called transfer or associative evidence. 1 While genetics is the study of heredity, genomics is defined as the study of genes and their functions, and . Handbook of Forensic Genetics: Biodiversity and Heredity in Civil and Criminal Investigation, Food and forensic molecular identification: update and challenges, Identity, traceability, acceptability and substantial equivalence of food, Food forensics: methods for determining the authenticity of foodstuffs. DNA Barcoding analysis of seafood accuracy in Washington, D.C. restaurants, Next generation sequencing and its applications in forensic genetics. van Asch B, Pinheiro R, Pereira R, Alves C, Pereira V, Pereira F, et al. Berger B, Berger C, Hecht W, Hellmann A, Rohleder U, Schleenbecker U, et al. Genome is a fancy word for all your DNA. The genetic information obtained is then compared with other genetic information (i.e., derived from reliable databases [e.g., 10] or reference sample[s]) considering statistical analyses. From potatoes to puppies, all living organisms have their own genome. Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain, 2 Sukrong S, Zhu S, Ruangrungsi N, Phadungcharoen T, Palanuvej C, Komatsu K. Molecular analysis of the genus Mitragyna existing in Thailand based on rDNA ITS sequences and its application to identify a narcotic species: Mitragyna speciosa. Later, a more advanced post-PCR technique, high-resolution DNA melting (HRM) analysis, which is based on the detection of small differences in amplicon melting (dissociation) curves, was also considered for NHFG [e.g., 19]. Forensic Genomics | Mary Ann Liebert, Inc., publishers Wasser SK, Joseph Clark W, Drori O, Stephen Kisamo E, Mailand C, Mutayoba B, et al. Although microbes have long been recognized as important players in our daily life, present in areas such as medicine and public health, ecology, and in industrial applications, microbial forensics (MF) is still a relatively recent scientific field [168, 169]. Genomics - World Health Organization (WHO) Different mtDNA regions have been tested and validated for use in a forensic context, including CYTB [125127], COI [128130], and rRNA genes [131, 132]. van de Goor LH, Panneman H, van Haeringen WA. Validation of the barcoding gene COI for use in forensic genetic species identification. Heaton MP, Leymaster KA, Kalbfleisch TS, Kijas JW, Clarke SM, McEwan J, et al. Kanthaswamy S, Tom BK, Mattila AM, Johnston E, Dayton M, Kinaga J, et al. In this module, you will learn about how genomics is used to estimate ancestry and predict physical appearance or traits in criminal investigations, and review the current evidentiary standards for utilizing genetic evidence. Dawnay N, Ogden R, Wetton JH, Thorpe RS, McEwing R. Genetic data from 28 STR loci for forensic individual identification and parentage analyses in 6 bird of prey species. Importantly, the same mtDNA sequence can be found in many individuals of a population and therefore cannot be used for individual identification. MA was also supported by the Ramn y Cajal grant RYC-2015-18241 from the Spanish Government. The genetic information is then compared with reference databases and the results are described in a written report (red boxes). Species identification of rhinoceros horns using the cytochrome b gene. Genetic profiles and sex identification of found-dead wolves determined by the use of an 11-loci PCR multiplex, Inference of population structure using multilocus genotype data, Molecular clocks ticking in the court room. Dormontt EE, Boner M, Braun B, Breulmann G, Degen B, Espinoza E, et al. You will also examine the scientific viability of using genomics to estimate phenotypic traits . Although culture in selective growth media remains as the preferred standard for characterization of microbial agents at the resolution of genus/species level, complementary detection methods based on diverse molecular markers are increasingly applied [170]. sharing sensitive information, make sure youre on a federal Honjo M, Ueno S, Tsumura Y, Handa T, Washitani I, Ohsawa R. Tracing the origins of stocks of the endangered species Primula sieboldii using nuclear microsatellites and chloroplast DNA, Where did they come from? Cardoso HF, Santos A, Dias R, Garcia C, Pinto M, Sergio C, et al. Developing Story: Forensic Genomics, Surveillance, and Ethics Development of a set of SNP markers present in expressed genes of the apple. The International Society for Forensic Genetics (ISFG) has drafted a guide to the forensic validation of STR kits, and this guide provides excellent standards and guidance for the forensic application of STR kits. One of the main constraints associated with the use of MF is the lack of standards and guidelines, although phylogenetic analyses have supported associations and have successfully been admitted as evidence in legal criminal cases [196]. Introduction. Genomic, transcriptomic, and epigenomic principles, data, and technologies are applied to identify and analyze useful DNA and RNA markers to address various forensic questions that cannot be answered, or only in a limited way, via genetic or other approaches. Koser CU, Holden MT, Ellington MJ, Cartwright EJ, Brown NM, Ogilvy-Stuart AL, et al. Jackson PJ, Hugh-Jones ME, Adair DM, Green G, Hill KK, Kuske CR, et al. Nevertheless, the most successful use of mtDNA in forensic zoology has been in species identification. What Forensic Science Is and How to Become a Forensic Scientist Bethesda, MD 20894, Web Policies Some well-known cases of the epidemiological studies are the swine-origin influenza A virus (H1N1; 2009) [175], the Haitian cholera (2010) [176], the haemolytic-uremic syndrome (Escherichia coli O104:H4; 2011) [177], the Coronavirus Middle East respiratory syndrome (2012) [178], the avian-origin Influenza A virus (H7N9; 2013) [179], the West African Ebola virus (2013/2015) [180], the Middle Eastern poliomyelitis (2014) [181], the Portuguese Legionnaires disease (2014) [182], and the Zika virus outbreaks [183]. The procedure usually involves the sequencing of a variable region amplified with conserved PCR primers followed by database searches and phylogenetic analyses. DNA: Promise and peril. Liron JP, Ripoli MV, Garcia PP, Giovambattista G. Assignment of paternity in a judicial dispute between two neighbor Holstein dairy farmers. Kitpipit T, Thongjued K, Penchart K, Ouithavon K, Chotigeat W. Mini-SNaPshot multiplex assays authenticate elephant ivory and simultaneously identify the species origin. Forensic Genomics. Budowle B, Connell ND, Bielecka-Oder A, Colwell RR, Corbett CR, Fletcher J, et al. An assessment of the utility of universal and specific genetic markers for opium poppy identification. Building microbial forensics as a response to bioterrorism. However, our understanding of the genetics underlying such complex traits is still very limited, although significant progress is expected [149]. Menotti-Raymond MA, David VA, Wachter LL, Butler JM, O'Brien SJ. Concerning the latter, we want to highlight the application of forensic genetics to the illegal wildlife trade (IWT), since this is one of the biggest threats to a variety of species and habitats, with a consequent loss of biodiversity [100, 101]. The lack of knowledge in the population structure and sampling errors obviously has a serious impact on the confidence of the parameter estimates. About the Publisher. Population genetic parameters include measures of genetic diversity, genetic differentiation, and demographics. Caratti S, Rossi L, Sona B, Origlia S, Viara S, Martano G, et al. Data was collected to better understand the impact of FGG on a number of metrics relating to substantive, procedural, and distributive justice. The first studies performed in the 90s resorted to classical techniques (i.e., RADP and ISSR) but nowadays, real-time PCR [204], HRM [205207], and MPS [208] are widely applied for food traceability with the advantage of quantifying each particular component in a faster and affordable procedure. Note that most of the cases indicated above applied NGS approaches to identify and study the different biological agents. government site. Nucleic acid amplification: Alternative methods of polymerase chain reaction. Indeed, a substitution model of evolution that fits the data best should be selected and considered in sophisticated phylogenetic inferences (i.e., based on maximum-likelihood or Bayesian approaches) [61, 65]. Martins-Lopes P, Gomes S, Pereira L, Guedes-Pinto H. Pereira L, Gomes S, Castro C, Eiras-Dias JE, Brazao J, Graca A, et al. Brooks A, Creighton EK, Gandolfi B, Khan R, Grahn RA, Lyons LA. Regarding scenario C, the selection of the genetic marker depends on the investigated species. Linacero R, Ballesteros I, Sanchiz A, Prieto N, Iniesto E, Martinez Y, et al. Forensic zoology often has to deal with degraded samples. They have also been employed in resolving criminal and civil cases, such as dog or bear attacks [37, 38, 92], silent witnesses of crimes [6], identification of samples from sport horses [41, 93], and in wildlife crime investigations (wildlife forensics), including big cats [94], mouflons [95, 96], wild boars [97, 98], and elephants [99], among others. The development and validation of a single SNaPshot multiplex for tiger species and subspecies identificationimplications for forensic purposes. The experimental workflow ends with a report describing the technical procedures applied and the answers to the question(s) of the request. An STR forensic typing system for genetic individualization of domestic cat (Felis catus) samples. Therefore, some of these STR kits are still a few steps behind those developed for human identification. This makes relevant parameters difficult to estimate with acceptable accuracy and thus inhibits solid statistical evaluation of the evidence [255]. A few multiplex PCR/primer extension assays to genotype mtDNA SNPs have also been developed for species and subspecies identification (i.e., tiger [49], elephant [145], and other animals [146, 147]). Forensic DNA typing technologies: A review In: Bogusz MJ, editor. The forensic DNA implications of genetic differentiation between endogamous communities. Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal, 4 Alternative methods to PCR include technologies such as nucleic acid sequence-based amplification (NASBA) and loop-mediated isothermal amplification (LAMP) [17, 18]. The .gov means its official. These pathogens are often associated with consumption of raw (e.g., fruits and vegetables) or undercooked foods (e.g., seafood, meat, and poultry) [240]. The analysis of this materialincluding other animal species, plants, or microorganismsis now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. The MiSeq FGx Forensic Genomics Solution (MFGS; Verogen Inc.) is a massively parallel sequencing workflow using Illumina sequencing technology. These genetic markers have been applied to perform identification in a variety of food products such as olive oil [e.g., 209, 210], grapevine cultivars [e.g., 211, 212, 213], composition of honey [e.g., 214, 215, 216], mushrooms [e.g., 217, 218, 219], dairy products [e.g., 220, 221, 222], seafood products [20], or meat species adulteration [223]. Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences, Case report of a fatal bear attack documented by forensic wildlife genetics. National Library of Medicine Nevertheless, several difficulties can arise in practice, especially when dealing with small sized and/or poorly studied populations, as in endangered species. CODIS and PCR-based short tandem repeat loci: law enforcement tools. The application of Bar-HRM (Barcode DNA-High Resolution Melting) analysis for authenticity testing and quantitative detection of bean crops (Leguminosae) without prior DNA purification. Care must be taken when extracting and storing the genetic material to maintain integrity. Baillie GJ, Galiano M, Agapow PM, Myers R, Chiam R, Gall A, et al. Validation of two canine STR multiplex-assays following the ISFG recommendations for non-human DNA analysis. For example, dinucleotide repeats are still used in nonhuman DNA testing [e.g., 37, 88, 91, 94], making it difficult to interpret sample mixtures and heterozygotes due to stutter product formation [102]. We next describe 2 analytic facets of crucial importance for NHFG: the quantitative evaluation of DNA evidence in the context of identification kinship and population/species assignment (i.e., in shallow evolutionary timescales) and the evolutionary analysis of genetic data (e.g., in transmission of fast evolving pathogens). Several DNA-based methods have become remarkably valuable for protecting and certifying the quality and source of food [202, 203]. The methodology used in food forensics is similar to that used in classical crime investigations, facing the same demands of dealing with potentially degraded DNA samples [201]. Jager AC, Alvarez ML, Davis CP, Guzman E, Han Y, Way L, et al. Besides the existing variety of applications, new developments are already at sight such as the genetic profiling of microbiomes and microbial metagenomics [e.g., 27, 2830], or in a not too distant future, the identification of transmitted strains of pathogens or commensals even many years after the crime (as it has been already done for viral transmissions [e.g., 31, 3236]). FOIA Easy to read, but dated. Importantly, these approaches are only possible due to the existence and maintenance of reliable and public databases such as GenBank, EMBL, and Bold. Racing pigeon identification using STR and chromo-helicase DNA binding gene markers. Ceuppens S, Li D, Uyttendaele M, Renault P, Ross P, Ranst MV, et al. Dayton M, Koskinen MT, Tom BK, Mattila AM, Johnston E, Halverson J, et al. Galimberti A, De Mattia F, Losa A, Bruni I, Federici S, Casiraghi M, et al. Establishing a minimum postmortem interval of human remains in an advanced state of skeletonization using the growth rate of bryophytes and plant roots. NHFG, nonhuman forensic genetics. Goncalves J, Pereira F, Amorim A, van Asch B. Identification of virgin olive oil from different cultivars by analysis of DNA microsatellites. A duplex polymerase chain reaction for the quantitative detection of cows milk in goats milk cheese. MPS presents additional advantages for NHFG such as the detection of rare polymorphisms, high resolution of genetic analysis, and informative power. Difficulties in developing a new genotyping system for animals are various, including the collection of representative samples (especially problematic in wild species), the access to high-quality genomic sequences (not available for several species) and obtaining funding for the experiments (often focused on human research). An alternative approach relies on comparing lengths of insertion and deletion polymorphisms without requiring DNA sequencing [46, 47].
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