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1.
Forensic Sci Rev ; 32(1): 23-54, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-32007927

RESUMO

Advancements in DNA sequencing technologies are occurring at a rapid rate. Various platforms have proven useful in all aspects of health and science research, from molecular diagnostics in cancer research to spore identification in bioterrorism. In the field of forensics, one particular single-molecule sequencing platform shows promise for becoming a viable solution for small to midsize forensic laboratories. Oxford Nanopore Technologies (ONT) has developed a portable, nanopore-based sequencing instrument that has already been utilized for on-site identification of Zika and Ebola viruses, full genome sequencing, evaluation of DNA and RNA base modifications, and enrichment-free mitochondrial DNA analysis. The rapid development of this technology creates possibilities relevant to standard DNA sequencing, direct analysis of forensic samples, including blood, semen, and buccal swabs, mitochondrial DNA analysis, SNP and STR analysis, familial identification, and microbial identification for bioterrorism and geolocation. The small size of the platform, its low cost, and its requirement of only basic laboratory equipment makes this platform well suited for small laboratories wishing to begin developing expertise in sequence-based forensic analyses. Herein, we outline recent developments and applications of nanopore sequencing technologies and their potential application in forensic analysis. We address current and potential techniques in mitochondrial DNA analysis, SNP and STR typing, and microbial identification. Additionally, we discuss recent developments in library preparation and data analysis tool further streamlining the sequencing process that integrate workflows in laboratories or in remote field scenarios.


Assuntos
Genética Forense/métodos , Sequenciamento por Nanoporos , Humanos
2.
J Forensic Sci ; 65(1): 295-303, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30859587

RESUMO

A set of historic murders, known as the "Jack the Ripper murders," started in London in August 1888. The killer's identity has remained a mystery to date. Here, we describe the investigation of, to our knowledge, the only remaining physical evidence linked to these murders, recovered from one of the victims at the scene of the crime. We applied novel, minimally destructive techniques for sample recovery from forensically relevant stains on the evidence and separated single cells linked to the suspect, followed by phenotypic analysis. The mtDNA profiles of both the victim and the suspect matched the corresponding reference samples, fortifying the link of the evidence to the crime scene. Genomic DNA from single cells recovered from the evidence was amplified, and the phenotypic information acquired matched the only witness statement regarded as reliable. To our knowledge, this is the most advanced study to date regarding this case.


Assuntos
Vestuário , Impressões Digitais de DNA/métodos , Genética Forense/métodos , Homicídio/história , Manchas de Sangue , Vestuário/história , Vítimas de Crime , Criminosos , DNA Mitocondrial/genética , DNA Mitocondrial/isolamento & purificação , Fluorescência , História do Século XIX , Humanos , Raios Infravermelhos , Microdissecção e Captura a Laser , Reação em Cadeia da Polimerase , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA , Análise de Célula Única , Reino Unido , Sequenciamento Completo do Genoma
3.
Fa Yi Xue Za Zhi ; 35(5): 512-518, 2019 Oct.
Artigo em Inglês, Chinês | MEDLINE | ID: mdl-31833282

RESUMO

Abstract: Molecular identification of human externally visible characteristic (EVC), which is also called forensic DNA phenotyping (FDP), can serve as a "molecular witness" when the routine investigations can not determine the identity of a criminal and the DNA database find no match after comparison. FDP could assist in investigation of cases by inferring the externally visible phenotypic characteristics from DNA obtained from the biological materials left at crime scenes, or unknown corpses. In the last few years, studies on the selection of EVC related molecular markers have been reported frequently and some of the EVCs could already be inferred with a certain accuracy, such as hair color and iris color. Further fundamental research on molecular genetics of human external phenotypic characteristics, as well as the continuous innovation on molecular biological technology would promote the rapid development of DNA molecular identification of human phenotypic characteristics.


Assuntos
DNA/genética , Genética Forense/métodos , Aparência Física/genética , DNA/análise , Bases de Dados de Ácidos Nucleicos , Cor de Olho/genética , Antropologia Forense/tendências , Genética Forense/tendências , Cor de Cabelo/genética , Humanos , Fenótipo , Pigmentação da Pele/genética
4.
Fa Yi Xue Za Zhi ; 35(5): 519-524, 2019 Oct.
Artigo em Inglês, Chinês | MEDLINE | ID: mdl-31833283

RESUMO

Abstract: Genetic markers, such as single nucleotide polymorphism (SNP), insertion/deletion (InDel), were discovered and widely used with the development of whole genome sequencing and bioinformatics technology. The origin and genetic structure of the modern population had been gradually revealed from the perspective of genetics. The study on biogeographic ancestry inference in the field of forensic genetics emerged and developed rapidly, providing clues and scientific basis for the determination of investigation direction and for the narrow of the scope of investigation in the process of case investigation. This paper briefly reviews the research progress, inference methods and development trends of DNA ancestry inference technology.


Assuntos
Criminosos , Genética Forense/métodos , África , DNA/genética , Impressões Digitais de DNA/métodos , Genética Populacional , Humanos , Filogeografia , Polimorfismo de Nucleotídeo Único
5.
Fa Yi Xue Za Zhi ; 35(5): 531-536, 2019 Oct.
Artigo em Inglês, Chinês | MEDLINE | ID: mdl-31833285

RESUMO

Abstract: Forensic DNA phenotyping (FDP) analysis uses DNA from biological samples left in crime scenes to predict individual phenotypic traits, such as geographical origin of ethnic group, height, weight, skin color, hair color and shape, iris color, male baldness, facial morphology, age, etc., thereby providing clues for case investigations. Among these traits, features of facial morphology are relatively more complicated. This paper makes an overall analysis of the measurement and collection of facial morphology, research on facial morphology related genes, forensic application and establishment of facial morphology depiction model, ethical issues, etc., then summarizes the latest research progress on features of facial morphology.


Assuntos
DNA/genética , Face , Genética Forense/métodos , Aparência Física/genética , Humanos , Masculino , Fenótipo
6.
Fa Yi Xue Za Zhi ; 35(5): 537-544, 2019 Oct.
Artigo em Inglês, Chinês | MEDLINE | ID: mdl-31833286

RESUMO

Abstract: Age estimation is of great significance in the fields of criminal investigation and forensic identification. It can provide the age information of individuals to judicial departments to facilitate the development of judicial work. In recent years, age estimation methods expanded from the morphological level to the molecular biology level. With the rapid development of epigenetics represented by DNA methylation, and the advancement of DNA methylation detection technology together with the detection platform, many age estimation methods based on DNA methylation biomarkers, or using several biological fluids, such as blood, blood stains, saliva, semen stains, etc. are developed. Currently, researches related to age estimation based on DNA methylation are relatively widely carried out. This paper summarizes the researches on age estimation based on DNA methylation, in order to provide references for related studies and forensic applications.


Assuntos
Envelhecimento/genética , Metilação de DNA , Genética Forense/métodos , Epigênese Genética , Epigenômica , Humanos , Sêmen
7.
Fa Yi Xue Za Zhi ; 35(5): 553-559, 2019 Oct.
Artigo em Inglês, Chinês | MEDLINE | ID: mdl-31833288

RESUMO

Abstract: Objective To predict the pigmentation phenotypes of Chinese populations from different language families, analyze the differences and provide reference data for forensic anthropology and genetics. Methods The HIrisPlex-S multiplex amplification system with 41 loci related to pigmentation phenotypes was constructed in the laboratory, and 2 666 DNA samples of adult males of 17 populations from six language families, including Indo-European, Sino-Tibetan, Altaic, Hmong-Mien, Tai-Kadai and Austro-Asiatic language families distributed in different regions of China were genotyped. The pigmentation phenotype category of each individual was predicted using the online prediction system (https://HIrisPlex.erasmusmc.nl/), and then the output data were statistically analyzed. Results About 1.92% of the individuals of Asian-European admixed populations from Indo-European and Altaic language families had blue eyes and 34.29% had brown or gold hair. The phenotypes of the color of eyes and hair of other populations had no significant difference, all individuals had brown eyes and black hair. There were differences in skin color of populations of different language families and geographical areas. The Indo-European language family had the lightest skin color, and the Austro-Asiatic language family had the darkest skin color; the southwestern minority populations had a darker skin color than populations in the plain areas. Conclusion The prediction results of pigmentation phenotype of Chinese populations are consistent with the perception of the appearance of each population, proving the reliability of the system. The color of eyes and hair are mainly related to ancestral components, while the skin color shows the differences between language families, and is closely related to geographical distribution of populations.


Assuntos
Grupo com Ancestrais do Continente Asiático/genética , Cor de Olho/genética , Antropologia Forense , Genética Forense/métodos , Idioma , Pigmentação da Pele/genética , Adulto , China , Humanos , Masculino , Fenótipo , Polimorfismo de Nucleotídeo Único , Reprodutibilidade dos Testes
8.
Fa Yi Xue Za Zhi ; 35(5): 560-566, 2019 Oct.
Artigo em Inglês, Chinês | MEDLINE | ID: mdl-31833289

RESUMO

Abstract: Objective To evaluate the effect of 56 ancestry informative single nucleotide polymorphism (aiSNP) genetic markers in the ForenSeqTM DNA Signature Prep Kit on ancestry inference. Methods A total of 85 samples from five populations including Hebei Han population, Inner Mongolia autonomous region Mongolian population, Tibet autonomous region Tibetan population, Xinjiang Uygur autonomous region Uygur population and Nigerian population were collected. The library was constructed with the ForenSeqTM DNA Signature Prep Kit and sequencing was performed based on the MiSeq FGx Forensic Genomics System. Using universal analysis software (UAS) of ForenSeqTM, principal component analysis (PCA), Structure and likelihood ratio method was used on the genotyping data of 56 aiSNP markers, respectively, and the genetic relationships between populations and inference of the origin of ancestors were analyzed. Results Among the five populations tested, the four ethnic populations in China (Hebei Han population, Inner Mongolia autonomous region Mongolian population, Tibet autonomous region Tibetan population and Xinjiang Uygur autonomous region Uygur population) could be significantly distinguished from Nigerian population. Xinjiang Uygur autonomous region Uygur individuals were shown as having mixed origins of ancestors and could be distinguished from the other three Chinese populations. However, the other three populations in China (Hebei Han population, Inner Mongolia autonomous region Mongolian population and Tibet autonomous region Tibetan population) could not be effectively distinguished by the system. Conclusion The 56 aiSNP markers in the ForenSeqTM DNA Signature Prep Kit can make accurate ancestry inference from the intercontinental level, but it is not yet able to distinguish between Chinese subpopulations.


Assuntos
Grupo com Ancestrais do Continente Asiático/genética , Grupos Étnicos , Genética Forense/métodos , Genética Populacional , China , DNA , Impressões Digitais de DNA , Grupos Étnicos/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Polimorfismo de Nucleotídeo Único
9.
Clin Lab ; 65(9)2019 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-31532110

RESUMO

BACKGROUND: Genetic markers are routinely used in human identification of paternity, maternity, and kinship cases. We describe a DNA paternity case with one mismatch on SE33 locus between the alleged father (AF) and the child (daughter). Because there was a father-daughter relationship to solve this case we used chromosome X-STRs markers too. METHODS: As reference samples we used saliva collected from inside the cheek of each person using buccal swabs (Copan, Italy). The DNA samples were quantified on a 7500 ABI real-time PCR using the Investigator Quantiplex Pro Kit (Qiagen, Germany). Salivary DNA samples were amplified on a ProFlex PCR System (ThermoFischer, USA) using the multiplex STR markers from the AmpF/STR® NGM Select PCR Amplification Kit (Thermo-Fischer, USA) and Investigator® Argus X-12 QS kit markers (Qiagen, Germany). PCR products were run on capillary electrophoresis on an ABI 3500 Genetic Analyzer (ThermoFischer, USA). RESULTS: The AF was excluded from paternity on STRs markers due to one mismatch on SE33 locus. To confirm or exclude the paternity, we used the chromosome X-STRs markers, obtaining a perfect match between the AF and his daughter. CONCLUSIONS: In paternity testing, where one or two mismatches are present between the child (daughter) and the AF on different loci on STR markers, the use of chromosome X-STRs is needed for the confirmation or exclusion of paternity.


Assuntos
Cromossomos Humanos X/genética , Pai , Loci Gênicos/genética , Repetições de Microssatélites/genética , Núcleo Familiar , Paternidade , Criança , DNA/genética , Feminino , Genética Forense/métodos , Humanos , Masculino , Mutação , Saliva/metabolismo
10.
Forensic Sci Int Genet ; 43: 102153, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31505370

RESUMO

Data from all sexual assault cases analysed at the Section of Forensic Biology at Oslo University Hospital in the period 2013-2015 were reviewed to study transfer and persistence of cells deposited on the body. Data were recorded on detection of both sperm and epithelial cells. The final dataset consist of 2141 samples from 765 cases. In this study "positive findings" refer to evidence to support the proposition that the DNA profile was contributed by the POI and do not only correspond to detection of cell type, e.g. sperm cells. Positive findings from analysis of sperm cells could be detected in samples collected up to 72 h after deposition, and was less frequently detected in oral swabs were the longest observed persistence time was 12 h. Positive findings from analysis of epithelial cells were observed up to 43 h after deposition. A high success rate was observed from penile swabs collected within 24 h of the incidence demonstrating the importance of collecting and analysing such samples in cases where no semen is detected.


Assuntos
Impressões Digitais de DNA , DNA/isolamento & purificação , Células Epiteliais/citologia , Delitos Sexuais , Espermatozoides/citologia , Células Epiteliais/química , Feminino , Genética Forense/métodos , Humanos , Masculino , Boca/citologia , Reação em Cadeia da Polimerase , Reto/citologia , Estudos Retrospectivos , Pele/citologia , Manejo de Espécimes , Espermatozoides/química , Fatores de Tempo , Vagina/citologia , Vulva/citologia
11.
Forensic Sci Int ; 303: 109944, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31546163

RESUMO

The past decade has seen rapid development in DNA methylation (DNAm) microarrays, including the Illumina HumanMethylation27 and HumanMethylation450 (450K) chips, which have played an essential role in identifying and evaluating age-related (AR) DNAm markers in different tissues. Recently, a new array, the Illumina MethylationEPIC (EPIC) was introduced, with nearly double the number of probes as the 450K (∼850,000 probes). In this study, we test these newly added probes for age association using a large cohort of 754 DNAm profiles from blood samples assayed on the EPIC BeadChip, for individuals aged 0-88 years old. 52 AR CpG sites (Spearman's abs(rho) >0.6 and P-value <10-83) were identified, 21 of which were novel sites and mapped to 18 genes, nine of which (LHFPL4, SLC12A8, EGFEM1P, GPR158, TAL1, KIAA1755, LOC730668, DUSP16, and FAM65C) have never previously been reported to be associated with age. The data were subsequently split into a 527-sample training set and a 227-sample testing set to build and validate two age prediction models using elastic net regression and multivariate regression. Elastic net regression selected 425 CpG markers with a mean absolute deviation (MAD) of 2.6 years based on the testing set. To build a multivariate linear regression model, AR CpG sites with R2 > 0.5 at FDR < 0.05 were input into stepwise regression to select the best subset for age prediction. The resulting six CpG markers were linearly modelled with age and explained 81% of age-correlated variation in DNAm levels. Age estimation accuracy using bootstrap analysis was 4.5 years, with 95% confidence intervals of 4.56 to 4.57 years based on the testing set. These results suggest that EPIC BeadChip probes for age estimation fall within the range of probes found on the previous Illumina HumanMethylation platforms in terms of their age-prediction ability.


Assuntos
Envelhecimento/genética , Ilhas de CpG/genética , Metilação de DNA , Marcadores Genéticos , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Criança , Pré-Escolar , Estudos de Coortes , Genética Forense/métodos , Humanos , Lactente , Recém-Nascido , Modelos Lineares , Pessoa de Meia-Idade , Análise de Sequência com Séries de Oligonucleotídeos , Adulto Jovem
12.
Forensic Sci Int Genet ; 42: 244-251, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31382159

RESUMO

The emergence of Massively Parallel Sequencing technologies enabled the analysis of full mitochondrial (mt)DNA sequences from forensically relevant samples that have, so far, only been typed in the control region or its hypervariable segments. In this study, we evaluated the performance of a commercially available multiplex-PCR-based assay, the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific), for the amplification and sequencing of the entire mitochondrial genome (mitogenome) from even degraded forensic specimens. For this purpose, more than 500 samples from 24 different populations were selected to cover the vast majority of established superhaplogroups. These are known to harbor different signature sequence motifs corresponding to their phylogenetic background that could have an effect on primer binding and, thus, could limit a broad application of this molecular genetic tool. The selected samples derived from various forensically relevant tissue sources and were DNA extracted using different methods. We evaluated sequence concordance and heteroplasmy detection and compared the findings to conventional Sanger sequencing as well as an orthogonal MPS platform. We discuss advantages and limitations of this approach with respect to forensic genetic workflow and analytical requirements.


Assuntos
DNA Mitocondrial/genética , Genoma Mitocondrial , Sequenciamento de Nucleotídeos em Larga Escala , Reação em Cadeia da Polimerase Multiplex , Genética Forense/métodos , Haplótipos , Humanos , Filogenia , Análise de Sequência de DNA
13.
Forensic Sci Int Genet ; 42: 260-267, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31404905

RESUMO

Inference of biogeographic origin is an important factor in clinical, population and forensic genetics. The information provided by AIMs (Ancestry Informative Markers) can allow the differentiation of major continental population groups, and several AIM panels have been developed for this purpose. However, from these major population groups, Eurasia covers a wide area between two continents that is difficult to differentiate genetically. These populations display a gradual genetic cline from West Europe to South Asia in terms of allele frequency distribution. Although differences have been reported between Europe and South Asia, Middle East populations continue to be a target of further investigations due to the lack of genetic variability, therefore hampering their genetic differentiation from neighboring populations. In the present study, a custom-built ancestry panel was developed to analyze North African and Middle Eastern populations, designated the 'NAME' panel. The NAME panel contains 111 SNPs that have patterns of allele frequency differentiation that can distinguish individuals originating in North Africa and the Middle East when combined with a previous set of 126 Global AIM-SNPs.


Assuntos
Grupo com Ancestrais do Continente Africano/genética , Genética Forense/métodos , Genética Populacional , África do Norte , Impressões Digitais de DNA , Frequência do Gene , Marcadores Genéticos , Técnicas de Genotipagem , Humanos , Oriente Médio , Reação em Cadeia da Polimerase , Polimorfismo de Nucleotídeo Único , Análise de Componente Principal
14.
Forensic Sci Int Genet ; 42: 171-180, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31369993

RESUMO

During the last decade, RNA profiling has emerged as one of the fastest developed methods for discriminating forensically relevant biological samples. As a category of small non-coding RNA, piwi-interacting RNA (piRNA) has recently been proposed to be differentially expressed in different types of body fluids, which indicates that its potential in forensic science is worth exploring. In this study, small RNA from 6 types of biological samples (venous blood, menstrual blood, saliva, semen, vaginal secretions and skin) was prepared and sequenced in order to characterize the expression pattern of piRNA using Ion S5 XL platform. Multiple bioinformatic methods were applied to make interpretation of the massively parallel sequencing data and identify representative biomarkers. A total of 376 piRNAs were initially identified after normalization and filtering. Hierarchical clustering and partial least squares-discriminant analysis (PLS-DA) revealed that their expression profiles exhibited an acceptable discriminating ability for most biological samples. Besides, a panel consists of 37 piRNA candidates was subsequently established for further analysis. The results suggested that with the optimal number of PLS components, the marker-reduced panel was sufficient to construct a PLS-DA model with the same performance as that can be achieved by the entire 376 piRNAs (classification error rate = 0.04). In addition, 5 targeted candidates were further selected for validation. TaqMan RT-qPCR assay results verified the potential of 3 piRNAs (piR-hsa-27622, piR-hsa-1207 and piR-hsa-27493) in distinguishing venous blood and menstrual blood, as well as 2 piRNA (piR-hsa-27493 and piR-hsa-26591) for the discrimination of saliva and vaginal secretions, which emphasized the feasibility of our biomarker selection approach. In brief, our study expanded the amount of potential piRNA biomarkers and demonstrated that the expression features of piRNA could provide valuable information for discriminating forensically relevant biological samples.


Assuntos
Genética Forense/métodos , RNA Interferente Pequeno/genética , Análise Química do Sangue , Muco do Colo Uterino/química , Análise Discriminante , Feminino , Marcadores Genéticos , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Menstruação , Reação em Cadeia da Polimerase em Tempo Real/métodos , Saliva/química , Sêmen/química , Análise de Sequência de RNA , Pele/química
15.
Forensic Sci Int ; 302: 109876, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31419595

RESUMO

Gene expression has become an interesting research area in forensic pathology to investigate the process of death at the molecular level. The aims of this study were to analyze changes in gene expression patterns in relation to the cause of death, and to propose new molecular markers of myocardial ischemia of potential use for the postmortem diagnosis of early ischemic heart damage in cases of sudden cardiac death (SCD). We determined mRNA levels of five proteins related with ischemic myocardial damage and repair - TNNI3, MYL3, TGFB1, MMP9 and VEGFA - in specific sites of the myocardium, blood and pericardial fluid in samples from 30 cadavers with different causes of death (SCD, multiple trauma, mechanical asphyxia, and other natural deaths). TNNI3 expression in blood, and MMP9 expression in pericardial fluid, were significantly higher when the cause of death was mechanical asphyxia, probably because of the more sensitive response of these proteins to acute systemic hypoxia/ischemia. Specifically, among SCD cases, increased MYL3, VEGFA and MMP9 values in the anterior wall of the right ventricle were found when the confirmed cause of death was acute myocardial infarction (AMI). Higher TGFB1 expression was found in the interventricular septum when AMI was not the cause of death, most likely as a reflection of the short duration of ischemia. Molecular biology techniques can provide complementary tools for the forensic diagnosis of early ischemic myocardial damage and AMI, and may make it possible to determine the duration and severity of myocardial ischemia.


Assuntos
Asfixia/diagnóstico , Isquemia Miocárdica/diagnóstico , Miocárdio/metabolismo , Líquido Pericárdico/metabolismo , RNA Mensageiro/metabolismo , Ferimentos e Lesões/diagnóstico , Adulto , Idoso , Idoso de 80 Anos ou mais , Asfixia/mortalidade , Biomarcadores/metabolismo , Morte Súbita Cardíaca/etiologia , Feminino , Genética Forense/métodos , Expressão Gênica , Humanos , MAP Quinase Quinase Quinases/genética , MAP Quinase Quinase Quinases/metabolismo , Masculino , Metaloproteinase 9 da Matriz/genética , Metaloproteinase 9 da Matriz/metabolismo , Pessoa de Meia-Idade , Isquemia Miocárdica/mortalidade , Cadeias Leves de Miosina/genética , Cadeias Leves de Miosina/metabolismo , Fator de Crescimento Transformador beta1/genética , Fator de Crescimento Transformador beta1/metabolismo , Fator A de Crescimento do Endotélio Vascular/genética , Fator A de Crescimento do Endotélio Vascular/metabolismo , Ferimentos e Lesões/mortalidade
16.
Forensic Sci Int Genet ; 42: 181-189, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31374457

RESUMO

Forensic and population genetics often rely on Y-chromosomal studies. Whether it is a human identification case, trace evidence examination or phylogenetic analysis, a Y-STR haplotype is an important tool in the hands of law enforcement agencies. A common obstacle in achieving satisfactory results in all of the above mentioned circumstances, is low DNA quantity and quality within samples obtained. In this study we have examined Y-STR haplotypes in 75 bone material samples, coming from different time periods. For this purpose we have chosen YFiler Plus PCR Amplification Kit (ThermoFisher Scientific) and ForenSeq Signature DNA Prep Kit (Verogen Inc.), which use two different allele calling technologies - capillary electrophoresis and Massively Parallel Sequencing respectively. Full profiles were obtained from DNA extracts with as little as 0.1896 ng (Degradation Index 1.3) (ForenSeq) and 0.0591 ng (Degradation Index 26.8) (YFiler Plus) DNA input. The results that we present in this paper show differences in amplification rates between common markers in both kits. The differences strictly reflect mean amplicon length of markers. This, however, does not seem to influence Y-haplogroup estimation results noticeably. In one sample a discordance occurred between haplotypes obtained with both methods, where a 24 allele was called in DYS390 marker by capillary electrophoresis, while for the same sample in this locus a 23 allele was shown with MPS. A reason for this is yet to be investigated. The sequence analysis revealed a significant variation between isometric alleles, especially within repetitive regions of studied Y-STR markers.


Assuntos
Cromossomos Humanos Y , Degradação Necrótica do DNA , Impressões Digitais de DNA , Haplótipos , Reação em Cadeia da Polimerase/métodos , Osso e Ossos/química , Eletroforese Capilar , Genética Forense/métodos , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Repetições de Microssatélites , Análise de Sequência de DNA , Dente/química
17.
Forensic Sci Int Genet ; 43: 102141, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31442930

RESUMO

The use of microhaplotypes (MHs) for ancestry inference has added to an increasing number of ancestry-informative markers (AIMs) for forensic application that includes autosomal single nucleotide polymorphisms (SNPs) and insertions/deletions (indels). This study compares bi-allelic and tri-allelic SNPs as well as MH markers for their ability to differentiate African, European, South Asian, East Asian, and American population groups from the 1000 Genomes Phase 3 database. A range of well-established metrics were applied to rank each marker according to the population differentiation potential they measured. These comprised: absolute allele frequency differences (δ); Rosenberg's informativeness for (ancestry) assignment (In); the fixation index (FST); and the effective number of alleles (Ae). A panel consisting of all three marker types resulted in the lowest mean divergence per population per individual (MDPI = 2.16%) when selected by In. However, when marker types were not mixed, MHs were the highest performing markers by most metrics (MDPI < 4%) for differentiation between the five continental populations.


Assuntos
Grupos de Populações Continentais/genética , Marcadores Genéticos , Haplótipos , Polimorfismo de Nucleotídeo Único , Bases de Dados de Ácidos Nucleicos , Genética Forense/métodos , Frequência do Gene , Humanos
18.
Genes (Basel) ; 10(9)2019 08 22.
Artigo em Inglês | MEDLINE | ID: mdl-31443502

RESUMO

In 1990 in Griswold, Connecticut, archaeologists excavated a burial found in a "skull and crossbones" orientation. The lid of the 19th century coffin had brass tacks that spelled "JB55", the initials of the person lying there and age at death. JB55 had evidence of chronic pulmonary infection, perhaps tuberculosis. It is possible that JB55 was deemed a vampire due to his disease, and therefore had to be "killed" by mutilating his corpse. In an attempt to reveal the identity of JB55, DNA testing was performed. Ancestry informative single nucleotide polymorphism (SNP) analysis using the Precision ID Ancestry Panel indicated European ancestry. A full Y-chromosomal short tandem repeat (Y-STR) profile was obtained, belonging to haplogroup R1b. When the Y-STR profile was searched in the publicly accessible FamilyTreeDNA R1b Project website, the two closest matches had the surname "Barber". A search of historical records led to a death notice mentioning John Barber, whose son Nathan Barber was buried in Griswold in 1826. The description of Nathan Barber closely fits the burial of "NB13," found near JB55. By applying modern forensic DNA tools to a historical mystery, the identity of JB55 as John Barber, the 19th century Connecticut vampire, has been revealed.


Assuntos
Genética Forense/métodos , Criaturas Lendárias , Linhagem , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA/métodos , Cemitérios , Cromossomos Humanos Y/genética , Connecticut , Haplótipos , Humanos , Masculino , Repetições de Microssatélites
19.
Forensic Sci Int Genet ; 43: 102146, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31446343

RESUMO

Current approaches for parsing true variation (i.e. signal) from noise, broadly involve estimating a baseline value of the latter, below which all sequence data are ignored. In an effort to deliver a more objective criterion for setting such thresholds, a novel approach based on phylogenetic principles is presented here., Our method deconstructs a special category of noise from true mitochondrial genome data, namely nuclear insertions of mitochondrial DNA (Numts). This bioinformatic approach leverages the relationship of massively parallel sequence reads and is capable of discovering putative Numts (pNumts) in absence of a reference genome. The new method was tested on a whole mitochondrial genome dataset (n = 41 individuals from an admixed population sample from Rio de Janeiro) and led to the discovery of 451 pNumt variants. Comparison of these pNumts haplotypes against an existing Numt database revealed 147 exact matches to previously discovered Numts, while 122 haplotypes differed only by a single base pair and none matched exclusively to the mitochondrial genome. In general, these sequences were considerably more divergent from the mitochondrial genome than from those of the Numt database, supporting that the novel pNumts were probably hitherto uncatalogued variants. Unlike previous techniques, our method appears to be able to detect both polymorphic and fixed Numt sequences. It was also found that the region containing the D-Loop and associated Promoters (DLP) in the human mitochondrial genome, which harbors markers of forensic genetics importance, is the origin of several Numts. Though currently designed for the mitochondrial genome, our novel approach has the potential to be expanded to other scenarios that might require construing signal from noise, including the deconvolution of mixtures, thus significantly improving how analytical thresholds may be established.


Assuntos
Genoma Mitocondrial , Haplótipos , Filogenia , DNA Mitocondrial/genética , Genética Forense/métodos , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Modelos Teóricos , Reação em Cadeia da Polimerase , Análise de Sequência de DNA
20.
Forensic Sci Int Genet ; 42: 227-234, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31377480

RESUMO

Next generation sequencing (NGS) technologies have enabled the possibility of analyzing a large number of SNPs simultaneously from multiple samples in a single experiment, for complementing the shortcomings of STR based methods. To efficiently genotype the desired SNPs, it is critical to optimize the library construction procedures. In this study, we formulated a strategy combining the molecular inversion probe (MIP) based target region capture method and NGS for genotyping 1245 SNPs. All the SNPs we selected exhibited high heterozygosity (minor allele frequency (MAF) > 0.3) according to 1000 genomes data. We applied the method to genotype a population of 210 unrelated individuals from the Hubei province of China and assessed the allele frequencies, Hardy-Weinberg equilibrium and linkage disequilibrium. The MAFs of more than 95% of the SNPs were ≥0.2, and no significant deviation or strong linkage was observed for 98% of the SNPs. The data indicated that, even within a relatively confined region, our SNP panel is suitable for individual identifications. Furthermore, we performed paternity test for 7 trio families using low quality DNA samples. The conclusions are in total agreement with these of STR-based analyses, with higher confidence indexes. Finally, we evaluated the performance of the MIP-NGS method with mock degraded DNA samples. We were able to genotype most of the SNPs even when the genomic DNA was sonicated to ˜100 bp range. In summary, we established a highly accurate and cost-effective method of SNP genotyping, which is potentially capable of solving complex issues encountered in forensic practices.


Assuntos
Genética Populacional , Técnicas de Genotipagem/métodos , Sequenciamento de Nucleotídeos em Larga Escala , Técnicas de Sonda Molecular , Polimorfismo de Nucleotídeo Único , China , Impressões Digitais de DNA , Grupos Étnicos/genética , Genética Forense/métodos , Frequência do Gene , Genótipo , Humanos
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