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1.
Anal Bioanal Chem ; 415(22): 5487-5498, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37423904

RESUMO

Accurate estimation of the postmortem interval (PMI) is crucial in forensic medico-legal investigations to understand case circumstances (e.g. narrowing down list of missing persons or include/exclude suspects). Due to the complex decomposition chemistry, estimation of PMI remains challenging and currently often relies on the subjective visual assessment of gross morphological/taphonomic changes of a body during decomposition or entomological data. The aim of the current study was to investigate the human decomposition process up to 3 months after death and propose novel time-dependent biomarkers (peptide ratios) for the estimation of decomposition time. An untargeted liquid chromatography tandem mass spectrometry-based bottom-up proteomics workflow (ion mobility separated) was utilized to analyse skeletal muscle, collected repeatedly from nine body donors decomposing in an open eucalypt woodland environment in Australia. Additionally, general analytical considerations for large-scale proteomics studies for PMI determination are raised and discussed. Multiple peptide ratios (human origin) were successfully proposed (subgroups < 200 accumulated degree days (ADD), < 655 ADD and < 1535 ADD) as a first step towards generalised, objective biochemical estimation of decomposition time. Furthermore, peptide ratios for donor-specific intrinsic factors (sex and body mass) were found. Search of peptide data against a bacterial database did not yield any results most likely due to the low abundance of bacterial proteins within the collected human biopsy samples. For comprehensive time-dependent modelling, increased donor number would be necessary along with targeted confirmation of proposed peptides. Overall, the presented results provide valuable information that aid in the understanding and estimation of the human decomposition processes.


Assuntos
Proteômica , Espectrometria de Massas em Tandem , Humanos , Cromatografia Líquida , Mudanças Depois da Morte , Biópsia
2.
Twin Res Hum Genet ; 23(5): 271-277, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-33190678

RESUMO

Previous genetic studies on hair morphology focused on the overall morphology of the hair using data collected by self-report or researcher observation. Here, we present the first genome-wide association study (GWAS) of a micro-level quantitative measure of hair curvature. We compare these results to GWAS results obtained using a macro-level classification of observable hair curvature performed in the same sample of twins and siblings of European descent. Observational data were collected by trained observers, while quantitative data were acquired using an Optical Fibre Diameter Analyser (OFDA). The GWAS for both the observational and quantitative measures of hair curvature resulted in genome-wide significant signals at chromosome 1q21.3 close to the trichohyalin (TCHH) gene, previously shown to harbor variants associated with straight hair morphology in Europeans. All genetic variants reaching genome-wide significance for both GWAS (quantitative measure lead single-nucleotide polymorphism [SNP] rs12130862, p = 9.5 × 10-09; observational measure lead SNP rs11803731, p = 2.1 × 10-17) were in moderate to very high linkage disequilibrium (LD) with each other (minimum r2 = .45), indicating they represent the same genetic locus. Conditional analyses confirmed the presence of only one signal associated with each measure at this locus. Results from the quantitative measures reconfirmed the accuracy of observational measures.


Assuntos
Estudo de Associação Genômica Ampla , Cabelo , Polimorfismo de Nucleotídeo Único , Loci Gênicos , Humanos , Desequilíbrio de Ligação , População Branca/genética
3.
Forensic Sci Med Pathol ; 16(3): 395-405, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32656643

RESUMO

Forensic genotyping can be impeded by γ-irradiation of biological evidence in the event of radiological crime; that is, criminal activity involving radioactive material. Oxidative effects within the mitochondria of living cells elicits greater damage to mitochondrial DNA (mtDNA) than nuclear DNA (nuDNA) at low doses. This study presents a novel approach for the assessment of nuDNA versus mtDNA damage from a comparison of genotype and quantity data, while exploring likely mechanisms for differential damage after high doses of γ-irradiation. Liquid (hydrated) and dried (dehydrated) whole blood samples were exposed to high doses of γ-radiation (1-50 kilogray, kGy). The GlobalFiler PCR Amplification Kit was used to evaluate short tandem repeat (STR) genotyping efficacy and nuDNA degradation; a comparison was made to mtDNA degradation measured using real-time PCR assays. Each assay was normalized before comparison by calculation of integrity indices relative to unirradiated controls. Full STR profiles were attainable up to the highest dose, although DNA degradation was noticeable after 10 and 25 kGy for hydrated and dehydrated blood, respectively. This was manifested by heterozygote imbalance more than allele dropout. Degradation was greater for mtDNA than nuDNA, as well as for hydrated than dehydrated cells, after equivalent doses. Oxidative effects due to water radiolysis and mitochondrial function are dominant mechanisms of differential damage to nuDNA versus mtDNA after high-dose γ-irradiation. While differential DNA damage was reduced by cell desiccation, its persistence after drying indicates innate differences between nuDNA and mtDNA radioresistance and/or continued oxidative effects within the mitochondria.


Assuntos
Degradação Necrótica do DNA/efeitos da radiação , DNA Mitocondrial/efeitos da radiação , Raios gama , Genótipo , Impressões Digitais de DNA , Relação Dose-Resposta à Radiação , Humanos , Repetições de Microssatélites , Reação em Cadeia da Polimerase em Tempo Real
4.
Int J Legal Med ; 133(6): 1711-1719, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31388795

RESUMO

Inference of ancestry from biological evidence can provide investigative information, especially for unknown DNA donors. Although tools for predicting ancestry have been developing, ancestry research focusing on populations relevant for South Korea is not common and markers are seldom chosen specifically to differentiate Koreans from other East Asian and South East Asian populations. Here, we report ancestry informative markers (AIMs) for distinguishing six East/South East Asian regional populations: China, Japan, Indonesia, Philippines, South Korea and Thailand. Individual genotypes from these six populations were available in PanSNPdb: The HUGO Pan-Asian SNP Database. To select AIMs, we calculated four population divergence metrics for each SNP: Nei's FST, Rosenberg's Informativeness (In), the average absolute allele frequency difference between populations (δFmean) and the maximum allele frequency difference between populations (δFmax). Based on these values, we selected 100 single nucleotide polymorphisms (SNPs) for distinguishing the six populations, 13 of which exhibited large allele frequency differences between Koreans and non-Koreans. To assess the performance of the AIMs, we performed principal coordinates analysis (PCoA) on the individuals from all six populations and inferred ancestral population clusters using the STRUCTURE program. In conclusion, we found that the selected AIMs can be applied to distinguish the six East/South East Asian groups and we suggest the markers in this study will be helpful to establish ancestry panels for Korea and neighbouring populations.


Assuntos
Povo Asiático/genética , Marcadores Genéticos , Genética Populacional , Polimorfismo de Nucleotídeo Único , Ásia , Impressões Digitais de DNA , Bases de Dados Genéticas , Frequência do Gene , Genótipo , Humanos , Análise de Componente Principal
5.
Int J Legal Med ; 132(6): 1581-1594, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-29556719

RESUMO

AbstractThe ability to provide accurate DNA-based forensic intelligence requires analysis of multiple DNA markers to predict the biogeographical ancestry (BGA) and externally visible characteristics (EVCs) of the donor of biological evidence. Massively parallel sequencing (MPS) enables the analysis of hundreds of DNA markers in multiple samples simultaneously, increasing the value of the intelligence provided to forensic investigators while reducing the depletion of evidential material resulting from multiple analyses. The Precision ID Ancestry Panel (formerly the HID Ion AmpliSeq™ Ancestry Panel) (Thermo Fisher Scientific) (TFS)) consists of 165 autosomal SNPs selected to infer BGA. Forensic validation criteria were applied to 95 samples using this panel to assess sensitivity (1 ng-15 pg), reproducibility (inter- and intra-run variability) and effects of compromised and forensic casework type samples (artificially degraded and inhibited, mixed source and aged blood and bone samples). BGA prediction accuracy was assessed using samples from individuals who self-declared their ancestry as being from single populations of origin (n = 36) or from multiple populations of origin (n = 14). Sequencing was conducted on Ion 318™ chips (TFS) on the Ion PGM™ System (TFS). HID SNP Genotyper v4.3.1 software (TFS) was used to perform BGA predictions based on admixture proportions (continental level) and likelihood estimates (sub-population level). BGA prediction was accurate at DNA template amounts of 125pg and 30pg using 21 and 25 PCR cycles respectively. HID SNP Genotyper continental level BGA assignments were concordant with BGAs for self-declared East Asian, African, European and South Asian individuals. Compromised, mixed source and admixed samples, in addition to sub-population level prediction, requires more extensive analysis.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/instrumentação , Polimorfismo de Nucleotídeo Único , Grupos Raciais/genética , Análise de Sequência de DNA , Impressões Digitais de DNA , Feminino , Marcadores Genéticos , Genótipo , Humanos , Masculino , Reação em Cadeia da Polimerase , Reprodutibilidade dos Testes
6.
Sci Justice ; 58(2): 153-158, 2018 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-29526267

RESUMO

Use of DNA in forensic science will be significantly influenced by new technology in coming years. Massively parallel sequencing and forensic genomics will hasten the broadening of forensic DNA analysis beyond short tandem repeats for identity towards a wider array of genetic markers, in applications as diverse as predictive phenotyping, ancestry assignment, and full mitochondrial genome analysis. With these new applications come a range of legal and policy implications, as forensic science touches on areas as diverse as 'big data', privacy and protected health information. Although these applications have the potential to make a more immediate and decisive forensic intelligence contribution to criminal investigations, they raise policy issues that will require detailed consideration if this potential is to be realised. The purpose of this paper is to identify the scope of the issues that will confront forensic and user communities.


Assuntos
Impressões Digitais de DNA/legislação & jurisprudência , Genética Forense/legislação & jurisprudência , Genômica/legislação & jurisprudência , Sequenciamento de Nucleotídeos em Larga Escala , Privacidade Genética/legislação & jurisprudência , Humanos , Formulação de Políticas
7.
Forensic Sci Med Pathol ; 14(1): 70-75, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29353346

RESUMO

Mitochondrial DNA (mtDNA) can provide a means for forensic identity testing when genotyping of nuclear DNA (nuDNA) targets is not possible due to degradation or lack of template. For degraded samples, an indication of the quantity and quality of mtDNA is essential to allow selection of appropriately sized targets for hypervariable region (HVR) analysis, which may conserve sample and resources. Three human-specific mtDNA targets of increasing length (86, 190 and 452 base pairs) were amplified by singleplex quantitative real-time PCR (qPCR), capable of providing an index of mtDNA degradation from fragment length information. Quantification was achieved by preparation of a standard curve for each target, using a purified mtDNA standard containing all three targets of interest, which produced a linear, accurate and precise result from 1×108 to 10 copies. These novel assays demonstrated excellent sensitivity, specificity and reproducibility in line with the minimum information for qPCR experiments (MIQE) guidelines. Further, a separate inhibition control reaction was included to guide sample clean-up and ensure the validity of degradation assays. This protocol assists the selection and analysis of appropriately sized targets to maximize the chance of obtaining an informative result in downstream assays like sequencing.


Assuntos
DNA Mitocondrial/genética , Reação em Cadeia da Polimerase em Tempo Real/métodos , Degradação Necrótica do DNA , Primers do DNA , Eletroforese em Gel de Ágar , Humanos , RNA Ribossômico , RNA Ribossômico 16S
8.
Int J Legal Med ; 131(4): 901-912, 2017 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-27995319

RESUMO

DNA can provide forensic intelligence regarding a donor's biogeographical ancestry (BGA) and other externally visible characteristics (EVCs). A number of algorithms have been proposed to assign individual human genotypes to a BGA using ancestry informative marker (AIM) panels. This study compares the BGA assignment accuracy of the population clustering program STRUCTURE and three generic classification approaches including a Bayesian algorithm, genetic distance, and multinomial logistic regression (MLR). A selection of 142 ancestry informative single nucleotide polymorphisms (SNPs) were chosen from existing marker panels (SNPforID 34-plex, Eurasiaplex, Seldin, and Kidd's AIM panels) to assess BGA classification at the continental level for Africans, Europeans, East Asians, and Amerindians. A training set of 1093 individuals with self-declared BGA from the 1000 Genomes phase 1 database was used by each classifier to predict BGA in a test set of 516 individuals from the HGDP-CEPH (Stanford) cell line panel. Tests were repeated with 0, 10, 50, 70, and 90% of the genotypes missing. Comparison of the area under the receiver operating characteristic curves (AUROCs) showed high accuracy in STRUCTURE and the generic Bayesian approach. The latter algorithm offers a computationally simpler alternative to STRUCTURE with little loss in accuracy and is suitable for phenotype prediction while STRUCTURE is not.


Assuntos
Genótipo , Grupos Raciais/genética , Algoritmos , Frequência do Gene , Genealogia e Heráldica , Marcadores Genéticos , Humanos , Funções Verossimilhança , Modelos Logísticos , Polimorfismo de Nucleotídeo Único
9.
Int J Legal Med ; 131(1): 21-37, 2017 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-27841004

RESUMO

Short tandem repeats are the gold standard for human identification but are not informative for forensic DNA phenotyping (FDP). Single-nucleotide polymorphisms (SNPs) as genetic markers can be applied to both identification and FDP. The concept of DNA intelligence emerged with the potential for SNPs to infer biogeographical ancestry (BGA) and externally visible characteristics (EVCs), which together enable the FDP process. For more than a decade, the SNaPshot® technique has been utilised to analyse identity and FDP-associated SNPs in forensic DNA analysis. SNaPshot is a single-base extension (SBE) assay with capillary electrophoresis as its detection system. This multiplexing technique offers the advantage of easy integration into operational forensic laboratories without the requirement for any additional equipment. Further, the SNP panels from SNaPshot® assays can be incorporated into customised panels for massively parallel sequencing (MPS). Many SNaPshot® assays are available for identity, BGA and EVC profiling with examples including the well-known SNPforID 52-plex identity assay, the SNPforID 34-plex BGA assay and the HIrisPlex EVC assay. This review lists the major forensically relevant SNaPshot® assays for human DNA SNP analysis and can be used as a guide for selecting the appropriate assay for specific identity and FDP applications.


Assuntos
DNA/genética , Eletroforese Capilar , Genética Forense/métodos , Polimorfismo de Nucleotídeo Único , Animais , Bactérias/genética , Tipagem e Reações Cruzadas Sanguíneas/métodos , Cromossomos Humanos Y , Conservação dos Recursos Naturais , Espécies em Perigo de Extinção , Cor de Olho/genética , Genética Populacional , Genótipo , Técnicas de Genotipagem , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Insetos/genética , Reação em Cadeia da Polimerase Multiplex , Grupos Raciais/genética , Pigmentação da Pele/genética
10.
Am J Forensic Med Pathol ; 38(2): 162-166, 2017 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-28398911

RESUMO

BACKGROUND: Sudden death from stable coronary artery atherosclerosis (SCAA) is well recognized. However, individuals can have ischemic heart disease or coronary artery atherosclerosis but die of noncardiac causes. Recently, it has been recognized that increased epicardial fat is detrimental to normal heart function. We hypothesize that individuals who die of SCAA have increased epicardial fat. AIM: The aim of this study was to investigate whether there is an increase in epicardial fat in individuals who suddenly died of SCAA. METHODS: This was a 1-year retrospective study comparing the average epicardial fat thickness using postmortem computed tomography scan between individuals who suddenly died of SCAA (SCAA group) with individuals who primarily died of natural noncardiac causes but had established ischemic heart disease or significant coronary artery atherosclerosis (NCC group). RESULTS: Average epicardial fat thickness was significantly higher in the SCAA group (8 ± 2 mm) than in the NCC group (6 ± 2 mm, P = 0.008). CONCLUSIONS: Individuals who die of SCAA appear to have higher epicardial fat thickness. The increase in epicardial fat may have an additional detrimental effect to the heart predisposing sudden death in individuals with coronary artery atherosclerosis.


Assuntos
Tecido Adiposo/diagnóstico por imagem , Doença da Artéria Coronariana/mortalidade , Morte Súbita Cardíaca/etiologia , Pericárdio/diagnóstico por imagem , Adulto , Idoso , Idoso de 80 Anos ou mais , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos , Tomografia Computadorizada por Raios X
11.
Forensic Sci Med Pathol ; 13(3): 293-301, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28523436

RESUMO

Single nucleotide polymorphisms (SNPs) have been widely used in forensics for prediction of identity, biogeographical ancestry (BGA) and externally visible characteristics (EVCs). Single base extension (SBE) assays, most notably SNaPshot® (Thermo Fisher Scientific), are commonly used for forensic SNP genotyping as they can be employed on standard instrumentation in forensic laboratories (e.g. capillary electrophoresis). High resolution melt (HRM) analysis is an alternative method and is a simple, fast, single tube assay for low throughput SNP typing. This study compares HRM and SNaPshot®. HRM produced reproducible and concordant genotypes at 500 pg, however, difficulties were encountered when genotyping SNPs with high GC content in flanking regions and differentiating variants of symmetrical SNPs. SNaPshot® was reproducible at 100 pg and is less dependent on SNP choice. HRM has a shorter processing time in comparison to SNaPshot®, avoids post PCR contamination risk and has potential as a screening tool for many forensic applications.


Assuntos
Genética Forense/métodos , Técnicas de Genotipagem/métodos , Desnaturação de Ácido Nucleico , Polimorfismo de Nucleotídeo Único , Eletroforese Capilar , Cor de Olho/genética , Técnicas de Genotipagem/instrumentação , Humanos , Fenótipo , Reação em Cadeia da Polimerase/instrumentação , Reação em Cadeia da Polimerase em Tempo Real/métodos , Reprodutibilidade dos Testes
12.
Forensic Sci Med Pathol ; 13(1): 10-19, 2017 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-28019002

RESUMO

Yersinia pestis is a biological agent of high risk to national security due to its ability to be easily disseminated and transmitted among humans. If Y. pestis was to be utilized in a deliberate disease outbreak it would be essential to rapidly and accurately identify the agent. Current identification methods for Yersinia species are limited by their reliance on cultivation, the time taken to achieve results and/or the use of protocols that are not amenable for field use. Faster identification methods are urgently required. Microfluidic capillary electrophoresis was used to identify seven Yersinia species based on their protein profiles. Further objectives included determining if Yersinia species could be detected in mixtures of milk products and Escherichia coli, determining if Yersinia could be detected in a blinded identification and reproducibility across two platforms. Two characteristic protein bands were detected at 50 kilodaltons (kDa) and between 50 and 75 kDa for the Yersinia species. Individual Yersinia species could be differentiated from one another and distinguished from E. coli, Bacillus anthracis Sterne strain and Dipel (containing Bacillus thuringiensis). Due to the high protein content of milk products Yersinia could not be detected when mixed with these but was detected when mixed with E. coli. Species were correctly identified with 96% success in blinded procedures using 12 individuals. Whilst protein profile patterns were reproducible across platforms there was some discrepancy in protein sizing. This study demonstrates that protein profiling using microfluidic capillary electrophoresis is able to rapidly and reproducibly identify and characterize Yersinia species. Results show this technique is a powerful front-line, rapid and broad range screening method capable of identifying and differentiating biological agents, hoax agents and environmental bacterial species.


Assuntos
Proteínas de Bactérias/isolamento & purificação , Eletroforese Capilar/métodos , Yersinia/isolamento & purificação , Animais , Bacillus/isolamento & purificação , Armas Biológicas , Escherichia coli/isolamento & purificação , Humanos , Microfluídica , Leite/microbiologia , Reprodutibilidade dos Testes
13.
Electrophoresis ; 37(21): 2832-2840, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27605155

RESUMO

Forensic DNA-based intelligence, or forensic DNA phenotyping, utilises SNPs to infer the biogeographical ancestry and externally visible characteristics of the donor of evidential material. SNaPshot® is a commonly employed forensic SNP genotyping technique, which is limited to multiplexes of 30-40 SNPs in a single reaction and prone to PCR contamination. Massively parallel sequencing has the ability to genotype hundreds of SNPs in multiple samples simultaneously by employing an oligonucleotide sample barcoding strategy. This study of the Illumina MiSeq massively parallel sequencing platform analysed 136 unique SNPs in 48 samples from SNaPshot PCR amplicons generated by five established forensic DNA phenotyping assays comprising the SNPforID 52-plex, SNPforID 34-plex, Eurasiaplex, Pacifiplex and IrisPlex. Approximately 3 GB of sequence data were generated from two MiSeq flow cells and profiles were obtained from just 0.25 ng of DNA. Compared with SNaPshot, an average 98% genotyping concordance was achieved. Our customised approach was successful in attaining SNP profiles from extremely degraded, inhibited, and compromised casework samples. Heterozygote imbalance and sequence coverage in negative controls highlight the need to establish baseline sequence coverage thresholds and refine allele frequency thresholds. This study demonstrates the potential of the MiSeq for forensic SNP analysis.


Assuntos
DNA/análise , Genética Forense/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Polimorfismo de Nucleotídeo Único/genética , Análise de Sequência de DNA/métodos , DNA/genética , Feminino , Humanos , Substâncias Húmicas , Masculino , Reação em Cadeia da Polimerase , Reprodutibilidade dos Testes
14.
Int J Legal Med ; 130(3): 607-13, 2016 May.
Artigo em Inglês | MEDLINE | ID: mdl-26530406

RESUMO

Disaster victim identification (DVI) often occurs in remote locations with extremes of temperatures and humidities. Access to mortuary facilities and refrigeration are not always available. An effective and robust DNA sampling and preservation procedure would increase the probability of successful DNA profiling and allow faster repatriation of bodies and body parts. If the act of tissue preservation also released DNA into solution, ready for polymerase chain reaction (PCR), the DVI process could be further streamlined. In this study, we explored the possibility of obtaining DNA profiles without DNA extraction, by adding aliquots of preservative solutions surrounding fresh human muscle and decomposing human muscle and skin tissue samples directly to PCR. The preservatives consisted of two custom preparations and two proprietary solutions. The custom preparations were a salt-saturated solution of dimethyl sulfoxide (DMSO) with ethylenediaminetetraacetic (EDTA) and TENT buffer (Tris, EDTA, NaCl, Tween 20). The proprietary preservatives were DNAgard (Biomatrica(®)) and Tissue Stabilising Kit (DNA Genotek). We obtained full PowerPlex(®) 21 (Promega) and GlobalFiler(®) (Life Technologies) DNA profiles from fresh and decomposed tissue preserved at 35 °C for up to 28 days for all four preservatives. The preservative aliquots removed from the fresh muscle tissue samples had been stored at -80 °C for 4 years, indicating that long-term archival does not diminish the probability of successful DNA typing. Rather, storage at -80 °C seems to reduce PCR inhibition.


Assuntos
Impressões Digitais de DNA/métodos , DNA/análise , Reação em Cadeia da Polimerase , Preservação de Tecido , Crioprotetores , Dimetil Sulfóxido , Ácido Edético , Genótipo , Humanos , Repetições de Microssatélites , Músculo Esquelético/química , Pele/química , Manejo de Espécimes/métodos
15.
Twin Res Hum Genet ; 19(4): 351-8, 2016 08.
Artigo em Inglês | MEDLINE | ID: mdl-27291867

RESUMO

Hair diameter and curvature are two characteristics of human scalp hair used in forensic contexts. While previous data show that subjective categorization of hair curvature is highly heritable, the heritability of objectively measured curvature and diameter, and variability of hair characteristics within each individual have not yet been studied. The present study measured hair diameter and curvature using an optical fiber diameter analyzer in a sample of 2,332 twins and siblings. Heritability was estimated using maximum likelihood structural equation modeling. Results show sex differences in the magnitude of genetic influence for mean diameter and curvature, with the vast majority of the variance accounted for by genetic effects in males (diameter = 86%, curvature = 53%) and females (diameter = 77%, curvature = 61%). The consistency of diameter (variance within an individual) was also highly heritable, but did not show sex limitation, with 68% of the variance accounted for by genetic factors. Moderate phenotypic correlations were seen between diameter and consistency (r = 0.3) but there was little correlation between diameter and curvature (r = -0.13). A bivariate Cholesky analysis was used to estimate the genetic and environmental correlations between hair diameter and consistency, yielding genetic correlations of r gF = 0.27 for females and r gM = 0.25 for males.


Assuntos
Cabelo/fisiologia , Gêmeos Dizigóticos/genética , Gêmeos Monozigóticos/genética , Adolescente , Austrália , Criança , Feminino , Cabelo/anatomia & histologia , Humanos , Masculino , Fatores Sexuais , População Branca
16.
Int J Legal Med ; 129(4): 681-91, 2015 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-25104323

RESUMO

Genetic markers included in forensic identity panels must exhibit Hardy-Weinberg and linkage equilibrium (HWE and LE). "Universal" panels designed for global use can fail these tests in regional jurisdictions exhibiting high levels of genetic differentiation such as the Indonesian archipelago. This is especially the case where a single DNA database is required for allele frequency estimates to calculate random match probabilities (RMPs) and associated likelihood ratios (LRs). A panel of 65 single nucleotide polymorphisms (SNPs) and a reduced set of 52 SNPs have been selected from 15 Indonesian subpopulations in the HUGO Pan Asian SNP database using a SNP selection strategy that could be applied to any panel of forensic identity markers. The strategy consists of four screening steps: (1) application of a G test for HWE; (2) ranking for high heterozygosity; (3) selection for LE; and (4) selection for low inbreeding depression. SNPs in our Indonesian panel perform well in comparison to some other universal SNP and short tandem repeat (STR) panels as measured by Fisher's exact test for HWE and LE and Wright's F statistics.


Assuntos
Impressões Digitais de DNA , Polimorfismo de Nucleotídeo Único , Bases de Dados de Ácidos Nucleicos , Frequência do Gene , Marcadores Genéticos , Genética Populacional , Heterozigoto , Homozigoto , Humanos , Indonésia , Funções Verossimilhança
17.
Forensic Sci Med Pathol ; 11(3): 326-38, 2015 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-25999132

RESUMO

PURPOSE: The primary method for analysis of low template DNA (LTDNA) is known as the low copy number (LCN) method involving an increased number of PCR cycles (typically 34). In common with other LTDNA methods, LCN profiles are characterized by allelic imbalance, drop in, and drop out that require complicated interpretation rules. They often require replicate PCR reactions to generate a "consensus" profile in a specialized facility. An ideal method for analysis of LTDNA should enhance profiling outcomes without elevated error rates and be performed using standard facilities, with minimum additional cost. METHODS: In this study, we present a comparison of four method variations for the amplification of STRs from LTDNA with a widely used, commercially available kit (AmpFℓSTR(®) Profiler Plus(®)): the standard method, the standard method with a post-PCR clean up, the LCN method, and a reduced reaction volume with increased Taq DNA polymerase concentration. RESULTS: Using telogen hairs-a common source of LTDNA-and matched reference DNA, the LCN method produced the highest number of concordant and non-concordant (i.e., dropped-in) alleles. In comparison, the reduced reaction volume with increased Taq polymerase yielded more full and concordant DNA profiles (all alleles combined) and less off-ladder alleles from a broad range of input DNA. In addition, this method resulted in less non-concordant alleles than LCN and no more than for standard PCR, which suggests that it may be preferred over increased PCR cycles for LTDNA analysis, either with or without consensus profiling and statistical modelling. CONCLUSIONS: Overall, this study highlights the importance and benefit of optimizing PCR conditions and developing improved laboratory methods to amplify and analyze LTDNA.


Assuntos
Impressões Digitais de DNA/métodos , DNA/análise , Cabelo/química , Repetições de Microssatélites , Taq Polimerase/análise , Alelos , Primers do DNA , Humanos , Reação em Cadeia da Polimerase em Tempo Real
18.
Electrophoresis ; 35(21-22): 3036-43, 2014 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-25142205

RESUMO

High resolution melting (HRM) analysis is a simple, cost effective, closed tube SNP genotyping technique with high throughput potential. The effectiveness of HRM for forensic SNP genotyping was assessed with five commercially available HRM kits evaluated on the ViiA™ 7 Real Time PCR instrument. Four kits performed satisfactorily against forensically relevant criteria. One was further assessed to determine the sensitivity, reproducibility, and accuracy of HRM SNP genotyping. The manufacturer's protocol using 0.5 ng input DNA and 45 PCR cycles produced accurate and reproducible results for 17 of the 19 SNPs examined. Problematic SNPs had GC rich flanking regions which introduced additional melting domains into the melting curve (rs1800407) or included homozygotes that were difficult to distinguish reliably (rs16891982; a G to C SNP). A proof of concept multiplexing experiment revealed that multiplexing a small number of SNPs may be possible after further investigation. HRM enables genotyping of a number of SNPs in a large number of samples without extensive optimization. However, it requires more genomic DNA as template in comparison to SNaPshot®. Furthermore, suitably modifying pre-existing forensic intelligence SNP panels for HRM analysis may pose difficulties due to the properties of some SNPs.


Assuntos
DNA/análise , Genética Forense/métodos , Técnicas de Genotipagem/métodos , Desnaturação de Ácido Nucleico/genética , Polimorfismo de Nucleotídeo Único/genética , DNA/genética , Humanos , Reprodutibilidade dos Testes , Sensibilidade e Especificidade
19.
Forensic Sci Med Pathol ; 10(3): 380-9, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-24943711

RESUMO

PURPOSE: In recent times, but especially since 2001, bioterrorism has been of increasing concern. In addition to the use of biological agents, including Bacillus anthracis (anthrax), there have been numerous hoax white powder "scares." It is imperative to rapidly and accurately identify any suspicious powder as hazardous or hoax. Classical methods for identification typically rely on time-consuming cultivation or highly specific molecular tests which are limited if the agent is unknown. Faster and field portable methods for analysis of suspicious powders are urgently required. METHODS: Potential hoax agents, including Bacillus species and household powders, were analyzed using automated microfluidic capillary electrophoresis to determine if protein profiling can distinguish between, and identify, samples. RESULTS: Distinctive protein profiles were produced for Bacillus species, with the presence and/or absence of certain bands, aiding identification. In particular B. anthracis Sterne strain contained a distinctive doublet band above 100 kDa which was not present in any other Bacillus species or hoax agents examined. The majority of powders produced distinctive banding that could enable the identification of the sample while simultaneously ruling out B. anthracis with a high degree of confidence. CONCLUSIONS: Results show automated microfluidic capillary electrophoresis can rapidly and reproducibly characterize Bacillus species and hoax agents based on protein profiles without the need for culture. Results were reproducible and there was enhanced resolution and rapidity compared to traditional protein profiling methods. Results show this technique is amenable to field use at a bioterrorism incident, thereby providing essential information to investigators regarding containment and treatment strategies.


Assuntos
Bacillus anthracis/química , Proteínas de Bactérias/análise , Bioterrorismo , Eletroforese Capilar , Técnicas Analíticas Microfluídicas , Proteômica/métodos , Automação Laboratorial , Bacillus anthracis/classificação , Biomarcadores/análise , Humanos , Pós , Reprodutibilidade dos Testes , Fatores de Tempo
20.
Forensic Sci Int Genet ; 69: 102994, 2024 03.
Artigo em Inglês | MEDLINE | ID: mdl-38086200

RESUMO

Machine learning (ML) is a range of powerful computational algorithms capable of generating predictive models via intelligent autonomous analysis of relatively large and often unstructured data. ML has become an integral part of our daily lives with a plethora of applications, including web, business, automotive industry, clinical diagnostics, scientific research, and more recently, forensic science. In the field of forensic DNA, the manual analysis of complex data can be challenging, time-consuming, and error-prone. The integration of novel ML-based methods may aid in streamlining this process while maintaining the high accuracy and reproducibility required for forensic tools. Due to the relative novelty of such applications, the forensic community is largely unaware of ML capabilities and limitations. Furthermore, computer science and ML professionals are often unfamiliar with the forensic science field and its specific requirements. This manuscript offers a brief introduction to the capabilities of machine learning methods and their applications in the context of forensic DNA analysis and offers a critical review of the current literature in this rapidly developing field.


Assuntos
Impressões Digitais de DNA , Ciências Forenses , Humanos , Reprodutibilidade dos Testes , Aprendizado de Máquina , DNA/genética
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