Mitochondrial DNA and STR analyses of maggot crop contents: effect of specimen preservation technique

DNA analysis of maggot crop contents can be used to identify a missing body or aid entomologists with interpreting evidence used for PMI estimations. Entomological evidence is often collected and preserved to keep identifiable external features intact. The preservation methods currently in use may not be suitable for preserving DNA in the maggot crop for later analysis. In this study, carrion maggots raised on human tissue were preserved under the following 8 preservation conditions: no fluid at -70 degrees C, no fluid at 4 degrees C, no fluid at 24 degrees C, 70% ethanol at 4 degrees C, 70% ethanol at 24 degrees C, 95% ethanol at 24 degrees C, Kahle's solution at 24 degrees C and formaldehyde at 24 degrees C. Maggots were dissected following 2 weeks, 8 weeks and 6 months of preservation. The maggot crops were extracted, human DNA was quantitated, and an attempt was made at amplifying mitochondrial DNA (mtDNA) and short tandem repeat (STR) loci. Both mtDNA and STRs were successfully amplified from maggots stored in ethanol or without any preservation fluid. Formalin-containing preservation solutions reduced the recovery of DNA. The best results were observed from maggots stored without any preservation fluid at -70 degrees C.     

Successful DNA typing of a urine sample in a doping control case using human mitochondrial DNA analysis

In a doping control case, a urine sample was tested positive for nandrolon. We were asked by the athlete to perform DNA investigations on the questioned urine sample and compare these to a fresh blood sample taken from the athlete in order to detect or rule out manipulation and/or switching of the samples. The urine sample had been collected nine months prior to the investigation and had been stored at 4 degrees C. In a first approach, nuclear DNA systems were investigated that failed with the exception of the Amelogenin system. Due to the high copy number of mitochondrial DNA molecules and the robustness of the mitochondrial genome, we investigated the HVR I and HVR II regions of mitochondrial DNA and obtained reproducible and clear sequencing results for both the blood and the urine samples. Due to the identical sequences, it could not be excluded that the blood sample and the urine sample were from the same individual or an individual having the same maternal lineage.     

Quantification of human mitochondrial DNA using synthesized DNA standards

Successful mitochondrial DNA (mtDNA) forensic analysis depends on sufficient quantity and quality of mtDNA. A real-time quantitative PCR assay was developed to assess such characteristics in a DNA sample, which utilizes a duplex, synthetic DNA to ensure optimal quality assurance and quality control. The assay's 105-base pair target sequence facilitates amplification of degraded DNA and is minimally homologous to nonhuman mtDNA. The primers and probe hybridize to a region that has relatively few sequence polymorphisms. The assay can also identify the presence of PCR inhibitors and thus indicate the need for sample repurification. The results show that the assay provides information down to 10 copies and provides a dynamic range spanning seven orders of magnitude. Additional experiments demonstrated that as few as 300 mtDNA copies resulted in successful hypervariable region amplification, information that permits sample conservation and optimized downstream PCR testing. The assay described is rapid, reliable, and robust.     

STR analysis of degraded DNA using a miniplex

Analysis of short tandem repeat (STR) markers currently represents the most useful instrument in the field of forensic genetics. The problem with forensic material is the degradation of the sample material. In recent years, several papers have demonstrated that short amplicon STR (miniSTR) represents one of the most useful tools for analyzing degraded DNA samples.In the present study, we attempted to develop a short amplicon STR multiplex system (autosomal and y-chromosomal) for analyzing degraded DNA using some newly designed primer sets for a multiplex polymerase chain reaction (PCR) systems for typing.An assay of degraded DNA samples using the designed multiplex systems, including artificially degraded samples and degraded forensic casework samples, proved remarkably effective. Comparing the multiplex with commercial kits, first results show a well success rate.     

Forensic mitochondrial DNA analysis of 691 casework hairs

A five year retrospective review of mitochondrial DNA (mtDNA) analysis on 691 casework hairs was carried out. A full or partial mtDNA profile was obtained for > 92% of hairs. With increasing age of the hair, the likelihood of obtaining a full profile decreased, although "mini-primer sets" could often be used to capture a partial profile. With increasing color and diameter of the hair, the likelihood of obtaining a profile increased. Full or partial profiles were obtained on more than 80% of 114 hairs < or = 1.0 cm. Mixtures were observed in 8.7% of hairs tested; mixtures increased with the age of the hair and were presumed to be due to exterior surface contamination that could not be sufficiently cleaned prior to extraction, since the overall level of laboratory contamination was low. The frequency of sequence heteroplasmy was 11.4%, and both hot-spot and novel sites were observed. In about one-third of these observations, another sample in the case showed either the same heteroplasmic site or a nucleotide substitution at that site.     

线粒体DNA编码区的多态性

目的研究线粒体DNA(mtDNA)编码区单核苷酸多态性,建立mtDNA编码区多态性在法庭科学中应用的理论基础。方法针对mtDNA编码区nt8162-8483以及nt13070-13299两段序列设计引物,应用直接测序技术研究其多态性。结果两对引物扩增片段长分别为322bp和230bp,共检测到21种变异,24种单倍型,基因多样性为0.7511,两个无关个体的偶合概率为0.2564。结论线粒体DNA编码区多态性位点作为线粒体DNA控制区多态性位点的补充,联合应用可以提高线粒体DNA在法医学应用中的个体识别能力。     

DNA analysis of digested tomato seeds in stomach contents

Examination of stomach contents is one of the important steps in medical legal autopsy. Vegetative materials such as stems, roots, and seeds in stomach contents can be valuable evidence for providing investigative leads in death investigation. Currently, the identification of plant materials relies on microscopic and morphologic examination. We have found that many seeds are often protected from acid degradation during stomach digestion by their tough exterior seed coat. Tomato seeds were selected as a model system to assess DNA analysis and plant variety marker identification. The DNA-amplified fragment length polymorphism method was performed to determine if the DNA obtained from single seeds could be used for PCR analysis. From the amplified fragment length polymorphism results, some candidate markers for individualizing seeds from morphologically distinct tomatoes were identified. These data on DNA analysis of tomato seeds indicate amplified fragment length polymorphism is a viable procedure for the individualization of seeds from stomach contents in forensic investigations.     

Forensic mitochondrial DNA analysis of 116 casework skeletal samples

Between February 1999 and May 2005, 116 DNA extractions were completed on skeletal remains from routine casework. Overall, at least a partial mitochondrial DNA (mtDNA) profile was obtained on 83.6% of samples. Skeletal remains fell into two general categories: (1) samples for body identifications submitted by law enforcement and (2) samples submitted to answer historical or family identity questions. Body identification cases were more likely to yield full mtDNA profiles, whereas historical cases were more likely to result in partial profiles. Overall, the ability to obtain a full or partial profile primarily reflects the difference in the average age and condition of the samples in these two categories and thus, difference in the quantity and quality of the DNA. Cremated remains were uniformly unsuccessful, whereas infant/fetal remains were uniformly successful. Heteroplasmy in skeletal remains was observed at a rate similar to that in hair ( approximately 10%). For body identification cases, skeletal remains had the same mtDNA profile as the accompanying reference sample in 50% of cases.     

Optimization and validation of 10 mitochondrial DNA SNPs using SNaPshot Kit

In some forensic cases, nuclear DNA is degraded and cannot be analyzed. In such a case mitochondrial DNA (mtDNA) is usually used in forensic cases for identification because of its special features as high number of copies per cell, maternal inheritance and high mutation rate. Single nucleotide polymorphisms (SNPs) represent the most abundant class of human polymorphisms. The aim of this study was optimization of 10 mtDNA SNPs by using SNaPshot minisequencing technique on ABI310 genetic analyser in forensic molecular genetics laboratory. At the end of this study, the optimization of minisequencing technique was done by changing some assay parameters. Also, during the optimization of 10 mtSNP loci in our laboratory.     

Appearance of chemical burns resulting from the washing of a deceased body with bleach

The authors report on a case of postmortem washing of a body with bleach. An adult female victim was found nude in an alleyway with both hands removed in the City of Westminster, CO. Cause of death was attributed to severe blunt force trauma to the head. The victim had been dumped in the alleyway within 7 h of discovery. Evidence discovered at the crime scene and autopsy indicated that the murder and subsequent washing of the body with bleach occurred at a secondary location(s). The victim was wet to the touch, presenting a strong odor of bleach. Several "ribbon"-like burn patterns were observed on the victim's back and upper thighs. These burn marks were replicated by dowsing a deceased pig with an over-the-counter concentration of bleach.     

Information does not affect the validity of a comparison question test

Purpose . Detailed information about the comparison question test (CQT) and possible countermeasures are now available on the Internet. This study examined whether the provision of such information would affect the validity of the Test for Espionage and Sabotage, a directed lie variant of the CQT. Method . Forty participants were divided into four equal groups: guilty, guilty informed, innocent, and innocent informed. During a first appointment, participants either did or did not commit a mock crime: then some were provided with a book containing detailed information on the CQT, including possible countermeasures. After 1 week with the book, all participants were administered a CQT during their second appointment. Following the polygraph, participants responded to a questionnaire that asked them about their behaviour and perceptions during their examination. Results . There were no significant effects of providing information on the validity of the CQT. However, the reported use of countermeasures was associated with a lower probability of truthfulness. Results of the debriefing questionnaire were found to support predictions made by the theory of the CQT. Conclusions . Concerns that readily available information will enable guilty individuals to produce false‐negative errors seem unfounded. Moreover, the results actually indicate that the use of countermeasures was associated with a lower probability of truthfulness, which was exactly the opposite outcome predicted by the CQT critics.     

人线粒体DNA序列分析在法医学中的应用研究及其进展

综述人线粒体DNA(m tDNA)序列分析在法医学种属鉴别、个体识别,以及个体年龄推断中的应用研究及其进展,展望对m tDNA异质性的研究及建立人m tDNA数据库,并具有重要的法医学实践意义。     

Real-time forensic DNA analysis at a crime scene using a portable microchip analyzer

An integrated lab-on-a-chip system has been developed and successfully utilized for real-time forensic short tandem repeat (STR) analysis. The microdevice comprises a 160-nL polymerase chain reaction reactor with an on-chip heater and a temperature sensor for thermal cycling, microvalves for fluidic manipulation, a co-injector for sizing standard injection, and a 7-cm-long separation channel for capillary electrophoretic analysis. A 9-plex autosomal STR typing system consisting of amelogenin and eight combined DNA index system (CODIS) core STR loci has been constructed and optimized for this real-time human identification study. Reproducible STR profiles of control DNA samples are obtained in 2 h and 30 min with ≤0.8 bp allele typing accuracy. The minimal amount of DNA required for a complete DNA profile is 100 copies. To critically evaluate the capabilities of our portable microsystem as well as its compatibility with crime scene investigation processes, real-time STR analyses were carried out at a mock crime scene prepared by the Palm Beach County Sheriff's Office (PBSO). Blood stain sample collection, DNA extraction, and STR analyses on the portable microsystem were conducted in the field, and a successful “mock” CODIS hit was generated on the suspect's sample within 6 h. This demonstration of on-site STR analysis establishes the feasibility of real-time DNA typing to identify the contributor of probative biological evidence at a crime scene and for real-time human identification.     

Quantification of mitochondrial DNA in human blood cells using an automated detection system

The 4977 bp deletion of mitochondrial DNA (mtDNA) accumulates in postmitotic tissues with advancing age. The purpose of our study was to detect and quantify these deletion even in blood cells with a high turnover activity. Whole venous blood, isolated human platelets and peripheral blood mononuclear cells (PBMCs) were collected from 10 unrelated donors aged 20-71 years and total DNA was extracted. PCR was performed for total and mutated mtDNA using two different primer pairs and two fluorogenic probes labeled with the fluorescent dyes FAM and VIC. Specific PCR products were generated, detected and quantified in a real-time PCR. The amplification products of total and deleted mtDNA could be detected in each sample and did not exhibit any differences in the amount of the deleted mtDNA in whole blood, human platelets or PBMCs. Our data did not show any accumulation of the 4977 bp deletion with increasing age as it was observed for several other tissues.     

Quantification of human mitochondrial DNA in a real time PCR

Recently, a moderately priced machine for real-time quantitative PCR has become available, the Perkin Elmer 5700. The rapid and quantitative assay of mitochondrial DNA (mtDNA) copy number is potentially useful in a variety of molecular, evolutionary and forensic fields. Using this new tool, we have evaluated the precision and reliability of the real time PCR to quantify undeleted mitochondrial genome copy number, and to determine the frequency of an age-associated deletion of 4977 base pairs in length, in 42 human iliopsoas muscle DNA samples from persons of known age. We have evaluated the accuracy with which age can be predicted, knowing only the frequency of this common 4977 bp deletion, and derived a statistical formula which describes the confidence with which the 4977 bp frequency predicts age. The results indicate that the mutation frequency could be used to distinguish between tissue from young and old individuals. However in this data set, while there was considerable agreement of 4977 bp frequency among replicates from the same individual sample, there was substantial diversity of mean mutation frequency between individuals of the same or similar ages. The simplest interpretation of these results is that there are biological modifiers of 4977 bp frequency that are age-independent, which are potentially interesting but may limit the usefulness of this deletion frequency alone as a "molecular forensic clock."     

Evaluation of a multicapillary electrophoresis instrument for mitochondrial DNA typing

Laser-induced detection of fluorescent labeled PCR products and multi-wavelength detection (i.e., multicolor analysis) enables rapid generation of mtDNA sequencing profiles. Traditionally, polyacrylamide slab gels have been used as the electrophoretic medium for mtDNA sequencing in forensic analyses. Replacement of slab gel electrophoresis with capillary electrophoresis (CE) can facilitate automation of the analytical process. Automation and high throughput can be further enhanced by using multicapillary electrophoretic systems. The use of the ABI Prism 3100 Genetic Analyzer (ABI 3100, Applied Biosystems, Foster City, CA) as well as the ABI Prism 310 Genetic Analyzer (ABI 310, Applied Biosystems, Foster City, CA) were evaluated for mtDNA sequencing capabilities and compared with sequencing results obtained on the platform currently in use in the FBI Laboratory (the ABI Prism 377 DNA Sequencer, ABI 377, Applied Biosystems, Foster City, CA). Various studies were performed to assess the utility of the ABI 3100, as well as the ABI 310 for mtDNA sequencing. The tests included: comparisons of results obtained among the ABI 3100, the ABI 310 and the ABI 377 instruments; comparisons of results obtained within and between capillary arrays; evaluation of capillary length; evaluation of sample injection time; evaluation of the resolution of mixtures/heteroplasmic samples; and evaluation of the sensitivity of detection of a minor component with reduced template on the ABI 3100. In addition, other studies were performed to improve sample preparation; these included: comparison of template suppression reagent (TSR, Applied Biosystems, Foster City, CA) versus formamide; the use of Performa DTR Gel Filtration Cartridges (Edge BioSystems Inc., Gaithersburg, MD) versus Centri-Sep Spin Columns (Princeton Separations, Adelphia, NJ) for product purification after cycle sequencing; and sample stability after denaturation. The data support that valid and reliable results can be obtained using either capillary electrophoresis instrument, and the quality of sequencing results are comparable to or better than those obtained from the ABI 377 instrument.     

Alternative light source (polilight) illumination with digital image analysis does not assist in determining the age of bruises

The age of a bruise may be of interest to forensic investigators. Previous research has demonstrated that an alternative light source may assist in the visualisation of faint or non-visible bruises. This project aimed to determine if an alternative light source could be utilised to assist investigators estimate the age of a bruise. Forty braises, sustained from blunt force trauma, were examined from 30 healthy subjects. The age of the bruises ranged from 2 to 231 h (mean = 74.6, median = 69.0). Alternative light source (polilight) illumination at 415 and 450 nm was used. The black and white photographs obtained were assessed using densitometry. A statistical analysis indicated that there was no correlation between time and the mean densitometry values. The alternative light source used in this study was unable to assist in determining the age of a bruise.     

人类线粒体DNA非编码区的序列分析与法医学应用

一、人类线粒体ＤＮＡ(ｍｔＤＮＡ)序列分析和应用的历史沿革1 981年Ａｎｄｅｒｓｏｎ完成了人类线粒体基因组的全部核苷酸序列的测定 ,并提出人类ｍｔＤＮＡ呈闭合环状 ,总长度为 1 6 5 6 9ｂｐ[1 ] 。在此基础上 ,许多学者致力于分析这一环状小分子ＤＮＡ ,以揭示ｍｔＤＮＡ的序列多态性程度。早期主要采用ＲＦＬＰ技术 ,如Ｇｒｅｅｎｂｅｒｇ等[2 ] 、Ｈｏｒａｉ等[3] 用ＲＦＬＰ技术对人类ｍｔＤＮＡ进行了序列分析 ,结果显示 :人类ｍｔＤＮＡ的序列多态性仅局限于长度约为 1 .1ｋｂ的非编码区 ,称之为Ｄ -Ｌｏｏｐ区 ,其中包含两个长度…     

Typing of mitochondrial DNA coding region SNPs of forensic and anthropological interest using SNaPshot minisequencing

The development of new methodologies for high-throughput SNP analysis is one of the most stimulating areas in genetic research. Here, we describe a rapid and robust assay to simultaneously genotype 17 mitochondrial DNA (mtDNA) coding region SNPs by minisequencing using SNaPshot. SNaPshot is a methodology based on a single base extension of an unlabeled oligonucleotide with labeled dideoxy terminators. The set of SNPs implemented in this multiplexed SNaPshot reaction allow us to allocate common mitochondrial West Eurasian haplotypes into their corresponding branch in the mtDNA skeleton, with special focus on those haplogroups lacking unambiguous diagnostic positions in the first and second hypervariable regions (HVS-I/II; by far, the most common segments analyzed by sequencing). Particularly interesting is the set of SNPs that subdivide haplogroup H; the most frequent haplogroup in Europe (40-50%) and one of the most poorly characterized phylogenetically in the HVS-I/II region. In addition, the polymorphic positions selected for this multiplex reaction increase considerably the discrimination power of current mitochondrial analysis in the forensic field and can also be used as a rapid screening tool prior to full sequencing analysis. The method has been validated in a sample of 266 individuals and shows high accuracy and robustness avoiding both the use of alternative time-consuming classical strategies (i.e. RFLP typing) and the need for high quantities of DNA template.