Application of mtDNA sequence analysis in forensic casework for the identification of human remains

Mitochondrial Replacement Therapy: An Islamic Perspective

Mitochondrial replacement technology (MRT) is an emerging and complex bioethical issue. This treatment aims to eliminate maternal inherited mitochondrial DNA (mtDNA) disorders. For Muslims, its introduction affects every aspect of human life, especially the five essential interests of human beings-namely, religion, life, lineage, intellect, and property. Thus, this technology must be assessed using a comprehensive and holistic approach addressing these human essential interests. Consequently, this article analyses and assesses tri-parent baby technology from the perspective of Maqasidic bioethics-that is, Islamic bioethics based on the framework of Maqasid al-Shariah. Using this analysis, this article suggests that tri-parent baby technology should not be permitted for Muslims due to the existence of third-party cell gametes which lead to lineage mixing and due to the uncertain safety of the therapy itself and because the major aim of the technology is to fulfil the affected couples interest to conceive their own genetically healthy child, not to treat and cure mtDNA disorders sufferers.

Diagnostic models to predict nuclear DNA and mitochondrial DNA recovery from incinerated teeth

Teeth are frequently used for human identification from burnt remains, as the structure of a tooth is resilient against heat exposure. The intricate composition of hydroxyapatite (HA) mineral and collagen in teeth favours DNA preservation compared to soft tissues. Regardless of the durability, the integrity of the DNA structure in teeth can still be disrupted when exposed to heat. Poor DNA quality can negatively affect the success of DNA analysis towards human identification. The process of isolating DNA from biological samples is arduous and costly. Thus, an informative pre-screening method that could aid in selecting samples that can potentially yield amplifiable DNA would be of excellent value. A multiple linear regression model to predict the DNA content in incinerated pig teeth was developed based on the colourimetry, HA crystallite size and quantified nuclear and mitochondrial DNA. The chromaticity a* was found to be a significant predictor of the regression model. This study outlines a method to predict the viability of extracting nuclear and mitochondrial DNA from pig teeth that were exposed to a wide range of temperatures (27 to 1000 °C) with high accuracy (99.5-99.7%).

Nucleic Acids Persistence-Benefits and Limitations in Forensic Genetics

The analysis of genetic material may be the only way to identify an unknown person or solve a criminal case. Often, the conditions in which the genetic material was found determine the choice of the analytical method. Hence, it is extremely important to understand the influence of various factors, both external and internal, on genetic material. The review presents information on DNA and RNA persistence, depending on the chemical and physical factors affecting the genetic material integrity. One of the factors taken into account is the time elapsing to genetic material recovery. Temperature can both preserve the genetic material or lead to its rapid degradation. Radiation, aquatic environments, and various types of chemical and physical factors also affect the genetic material quality. The substances used during the forensic process, i.e., for biological trace visualization or maceration, are also discussed. Proper analysis of genetic material degradation can help determine the post-mortem interval (PMI) or time since deposition (TsD), which may play a key role in criminal cases.

Genealogical obscurement: mitochondrial replacement techniques and genealogical research

Mitochondrial replacement techniques (MRTs) are a new group of biotechnologies that aim to aid women whose eggs have disease-causing deleteriously mutated mitochondria to have genetically related healthy children. These techniques have also been used to aid women with poor oocyte quality and poor embryonic development, to have genetically related children. Remarkably, MRTs create humans with DNA from three sources: nuclear DNA from the intending mother and father, and mitochondrial DNA from the egg donor. In a recent publication Françoise Baylis argued that MRTs are detrimental for genealogical research via mitochondrial DNA because they would obscure the lines of individual descent. In this paper, I argue that MRTs do not obscure genealogical research, but rather that MRT-conceived children can have two mitochondrial lineages. I argue for this position by showing that MRTs are reproductive in nature and, thus, they create genealogy.

Assessment of Multiple Annealing and Looping-Based Amplification Cycle-Based Whole-Genome Amplification for Short Tandem Repeat Genotyping of Low Copy Number-DNA

Aim: A common problem in forensic practice is the lack of sufficient amounts of good quality genomic DNA. A possible solution is the amplification of the available genomic DNA before locus-specific polymerase chain reaction (PCR) analysis. The aim of this study was to evaluate multiple annealing and looping-based amplification cycle (MALBAC)-based whole-genome amplification (WGA) for short tandem repeat (STR) genotyping of low copy number DNA (LCN-DNA). Materials and Methods: DNA isolated from five blood samples was quantified and diluted to 250, 150, 100, 50, 25, and 5 pg/μL. After preamplification with MALBAC, WGA products were quantified. PCR-STR genotyping was performed in triplicate using dilution or purification-treated WGA products for each level of DNA. STR profiles were analyzed and compared with that from non-WGA DNA. Results: The purification treatment performed better than dilution of the MALBAC-based WGA products. Compared with the non-WGA DNA, both the average number and peak heights of correct alleles were significantly improved after preamplification with the MALBAC-based WGA at DNA inputs of ≤50 pg. Like other WGA methods, allele dropout and allele drop-in were observed in the profiling results for many samples. Conclusions: MALBAC shows great potential in LCN-DNA analysis and could find broader application in the fields of forensics and genetics.

Human Mitochondrial Control Region and mtGenome: Design and Forensic Validation of NGS Multiplexes, Sequencing and Analytical Software

Forensic mitochondrial DNA (mtDNA) analysis conducted using next-generation sequencing (NGS), also known as massively parallel sequencing (MPS), as compared to Sanger-type sequencing brings modern advantages, such as deep coverage per base (herein referred to as read depth per base pair (bp)), simultaneous sequencing of multiple samples (libraries) and increased operational efficiencies. This report describes the design and developmental validation, according to forensic quality assurance standards, of end-to-end workflows for two multiplexes, comprised of ForenSeq mtDNA control region and mtDNA whole-genome kits the MiSeq FGx^TM instrument and ForenSeq universal analysis software (UAS) 2.0/2.1. Polymerase chain reaction (PCR) enrichment and a tiled amplicon approach target small, overlapping amplicons (60–150 bp and 60–209 bp for the control region and mtGenome, respectively). The system provides convenient access to data files that can be used outside of the UAS if desired. Studies assessed a range of environmental and situational variables, including but not limited to buccal samples, rootless hairs, dental and skeletal remains, concordance of control region typing between the two multiplexes and as compared to orthogonal data, assorted sensitivity studies, two-person DNA mixtures and PCR-based performance testing. Limitations of the system and implementation considerations are discussed. Data indicated that the two mtDNA multiplexes, MiSeq FGx and ForenSeq software, meet or exceed forensic DNA quality assurance (QA) guidelines with robust, reproducible performance on samples of various quantities and qualities.

Factors influencing DNA extraction from human skeletal remains: bone characteristic and total demineralization process

Background

The extraction of DNA from skeletal remains with good quality and quantity is often challenging for the ability to generate DNA typing. Previous studies demonstrated the DNA extraction with total demineralization from fresh teeth and bones; however, the application in old skeletal remains has been less performed. To obtain good quality and high yield of DNA amount extracted from skeletal remains, the objective of this study was focused on exploring the factors influencing the total demineralization process to obtain developing effective methods.

Results

The concentration of EDTA was found to significantly enhance calcium chelation from the bone while pH of EDTA solution, incubation temperature, incubation time, and volume of EDTA solution were not significant. The optimal condition of total demineralization obtained from Placket-Burmann results represented good-quality DNA and the highest concentration of extracted DNA yield. Subsequently, the STR typing in some bone specimens processed by total demineralization process prior to DNA extraction was improved.

Conclusions

EDTA concentration was a key influencing factor on the total demineralization process to chelate calcium from human skeletal remains. The total demineralization process in old bone specimens probably improved the STR profiles.

Massively parallel sequencing of mitogenome sequences reveals the forensic features and maternal diversity of tai-kadai-speaking hlai islanders

As a single maternally inherited locus, human mitochondrial DNA (mtDNA) is geographically arranged and plays a key role in forensic applications. Hlai population has been evidenced as the most typical and unmixed representative of the Tai-Kadai-speaking populations via genome-wide analyses. However, forensic features and maternal diversity of the complete mitogenomes in this Tai-Kadai ancestrally related population are scarce. Thus, we sequenced the complete mitogenomes in 127 Hainan Hlais and found 109 distinct haplotypes belonging to 43 terminal haplogroups resulting in the haplotype diversity of 0.9970. Our results of comprehensive population comparisons showed that Hlai islanders had a close genetic affinity with Tai-Kadai-speaking populations from Southeast Asia, which is consistent with the back-migration of Chinese Neolithic farmers into this region via the inland route. Besides, maternally genetic evidence further revealed a close genetic relationship between Tai-Kadai-speaking and Austronesian-speaking populations when only East Asian dataset was considered, which is consistent with the common origin from Yangtze rice farmers and then spread southward along the inland and coastal routes, respectively. In the reconstructed phylogenetic tree and median-joining networks, the vast majority of Hlais were clustered in exclusive clades, which demonstrated that Hlai people probably had undergone founder effect or genetic bottleneck in their history, and remained genetically isolated for a long time. Collectively, Hainan Hlai did not exhibit detectable maternal gene flow from surrounding or incoming populations. Mitogenome information generated in this study is a contribution in mitigating the underrepresentation of Chinese data in forensic mitogenetics and will assist geography-, metapopulation-, as well as phylogeny-based queries.

Mitochondrial DNA screening by melting curve analysis using peptide nucleic acid probes

Analysis of single nucleotide polymorphisms (SNPs) in mitochondrial (mt)DNA hypervariable regions (HV) 1/2 is valuable in forensic investigations. We developed a method for mtDNA screening of the HV1 and HV2 regions by melting curve analysis, using peptide nucleic acid (PNA) probes. This method focuses on melting peak patterns obtained by thermal dissociation of PNA/DNA duplexes in amplified mtDNA products. Five PNA probe sets were designed to detect 25 SNPs in the two HV regions. We also detected non-target SNPs based on unexpected melting temperature (T_m) shifts. In fact, 62 SNPs (42 SNPs in HV1 and 20 in HV2) were identified, including the 25 target SNPs. Using this method, 46 melting peak patterns, including 8 pattern groups, were obtained in 60 unrelated individuals. The peak patterns were compared to 55 haplotypes identified by Sanger sequencing. The results obtained from analysis of target mtDNA SNPs were entirely consistent with those obtained by Sanger sequencing. Screening the HV1 and HV2 regions of mtDNA by this method may help minimize unnecessary recourse to full sequence analysis, allows to rapidly exclude samples that do not match evidence and reference samples, and may reduce turnaround times and analysis costs. Overall, this method may be effective and helpful in forensic investigations.

Tri-parent Baby Technology and Preservation of Lineage: An Analysis from the Perspective of Maqasid al-Shari'ah Based Islamic Bioethics

Tri-parent baby technology is an assisted reproductive treatment which aims to minimize or eliminate maternal inheritance of mutated mitochondrial DNA (mtDNA). The technology became popular following the move by the United Kingdom in granting license to a group of researchers from the Newcastle Fertility Centre, Newcastle University to conduct research on the symptoms of defective mtDNA. This technology differs from other assisted reproductive technology because it involves the use of gamete components retrieved from three different individuals. Indirectly, it affects the preservation of lineage which is important from an Islamic point of view. This paper aims to analyze and discuss the implications of the tri-parent technology on preservation of lineage from the perspective of Maqasid al-Shari'ah based the Islamic bioethics. The analysis shows that there are a few violations of the preservation of lineage, hence the tri-parent baby technology should not be permitted.

An analysis of dental intercanine distance for use in court cases involving bite marks

High levels of crime in South Africa and the resulting court cases requiring bite mark evidence have necessitated continuous research into the prevalence and interrelationship of recognisable dental features present in bite marks. This study represents the largest data set of descriptive statistics related to intercanine distance, in which the means, standard deviations, medians and interquartile ranges across four racial groups were determined. Intercanine distances were also statistically weighted by determining the common, uncommon and very uncommon values for each of the racial groups. The results of this research show that we can consider any maxillary intercanine distance more than 24.1 mm and less than 43.0 mm to represent a human bite mark. Black males had the largest mean (average) intercanine distance of 36.33 mm (standard deviation 2.49 mm) and white females the smallest mean intercanine distance of 33.4 mm (standard deviation 2.13 mm). The analyses showed statistically significant differences between the mean intercanine distances of different race and gender groupings. The authors do not advocate trying to determine the race or gender from intercanine distances determined, but rather the relevance of the intercanine distances in the specific race and gender groupings. This study makes a meaningful scientific contribution to the presentation of bite mark evidence at a time when subjective opinions need to be replaced with scientific data.

Extraction of DNA from Human Skeletal Material

In recent years the recovery and analysis of DNA from skeletal remains has been applied to several contexts ranging from disaster victim identification to the identification of the victims of conflict. Here are described procedures for processing the bone and tooth samples including mechanical and chemical cleaning, cutting and powdering in the presence of liquid nitrogen, complete demineralization of bone and tooth powder, DNA extraction, DNA purification using magnetic beads, and the precautions and strategies implemented to avoid and detect contamination. It has proven highly successful in the analysis of bones and teeth from Second World War victims' skeletal remains that have been excavated from mass graves in Slovenia and is also suitable for genetic identification of relatively fresh human remains.

Genetic identification by using short tandem repeats analysis in a case of suicide by self-incineration: a case report

Suicide by self-incineration is an uncommon method of suicide in the western world in contrast with Asian countries, where this type of suicide is more common. If there is a lack of witnesses, genetic analysis for identification is mandatory, especially when anthropologic or dental identification is barely significant.The authors report a case of self-incineration of a 55-year-old white man, which occurred near Siena, Tuscany, Italy.The recovered bones were classified according to the Crow-Glassman scale and assigned to category 5 (the highest extent of combustion according to this scale). Therefore, because of the extent of the bone damage, analyzing the residual soft tissue around the pelvic bones was the only way to reach a genetic identification.The authors report this case to emphasize that even if the highest level of burn injury to human body is reached, an accurate analysis of the findings may lead to a genetic identification. In these cases, an efficient cooperation among police, fire experts, and forensics is necessary, especially because it is the only way to determine if the modality of death was accidental, suicidal, or homicidal.

Forensic human identification in the United States and Canada: a review of the law, admissible techniques, and the legal implications of their application in forensic cases

Forensic human identification techniques are successful if they lead to positive personal identification. However, the strongest personal identification is of no use in the prosecution--or vindication--of an accused if the associated evidence and testimony is ruled inadmissible in a court of law. This review examines the U.S. and Canadian legal rulings regarding the admissibility of expert evidence and testimony, and subsequently explores four established methods of human identification (i.e., DNA profiling, forensic anthropology, forensic radiography, forensic odontology) and one complementary technique useful in determining identity, and the legal implications of their application in forensic cases.

Whole genome amplification of degraded and nondegraded DNA for forensic purposes

Degraded DNA is often analyzed in forensic genetics laboratories. Reliable analysis of degraded DNA is of great importance, since its results impact the quality and reliability of expert testimonies. Recently, a number of whole genome amplification (WGA) methods have been proposed as preamplification tools. They work on the premise of being able to generate microgram quantities of DNA from as little as the quantity of DNA from a single cell. We chose, investigated, and compared seven WGA methods to evaluate their ability to “recover” degraded and nondegraded DNA: degenerate oligonucleotide-primed PCR, primer extension preamplification PCR, GenomePlex™ WGA commercial kit (Sigma), multiple displacement amplification, GenomiPhi™ Amplification kit (Amersham Biosciences), restriction and circularization-aided rolling circle amplification, and blunt-end ligation-mediated WGA. The efficiency and reliability of those methods were analyzed and compared using SGMPlus, YFiler, mtDNA, and Y-chromosome SNP typing. The best results for nondegraded DNA were obtained with GenomiPhi and PEP methods. In the case of degraded DNA (200 bp), the best results were obtained with GenomePlex which successfully amplified also severely degraded DNA (100 bp), thus enabling correct typing of mtDNA and Y-SNP loci. WGA may be very useful in analysis of low copy number DNA or degraded DNA in forensic genetics, especially after introduction of some improvements (sample pooling and replicate DNA typing).

Reliable genetic identification of burnt human remains

The identification of severely burnt human remains by genetic fingerprinting is a common task in forensic routine work. In cases of extreme fire impact, only hard tissues (bones, teeth) may be left for DNA analysis. DNA extracted from burnt bone fragments may be highly degraded, making an amplification of genetic markers difficult or even impossible. Furthermore, heavily burnt bones are very prone to contamination with external DNA. We investigated whether authentic DNA profiles can be generated from human bones showing different stages of fire induced destruction (well preserved, semi-burnt, black burnt, blue-grey burnt, blue-grey-white burnt). DNA was extracted from 71 bone fragments derived from 13 individuals. Obtained genetic patterns (STRs and mtDNA sequences) were compared to the genetic pattern of the respective bodies. Our results show that the identification via DNA analysis is reliably and reproducibly possible from well preserved and semi-burnt bones. In black burnt bones the DNA was highly degraded and in some cases no nuclear DNA was left, leaving mitochondrial DNA analysis as an option. Blue-grey burnt bones lead only sporadically to authentic profiles. The investigation of blue-grey-white burnt bones barely led to reliable results.

Sequence analysis for HV I region of mitochondrial DNA using WGA (Whole Genome Amplification) method

The hypervariable (HV) region in mitochondrial DNA (mtDNA) has been studied for forensic identification, DNA analysis of mother-child relationship and comparison between ethnic groups. Meanwhile, the WGA (Whole Genome Amplification) method is a technique to amplify genome DNA, and it may be useful for analyzing degraded or limited DNA. However, we need to make a comparative study to confirm whether or not amplified DNAs have the same sequence as the original DNA because the amplification procedure may have some influence on sequencing. We sequenced mtDNA HV I region using amplified human DNAs by WGA method and original human DNAs, and compared the results. DNAs were extracted from four tissue samples from each of 10 healthy volunteers: blood, oral mucosa, nail and hair shaft. WGA was then performed and sequences were analyzed using the amplified samples. After sequencing of the PCR products, the results were compared with the Anderson reference sequence. For each individual, DNA sequences of mtDNA HV I region from the four tissues were the same and WGA amplified samples also showed identical results. Although the WGA procedure may have little influence on the data, we still have to investigate the effectiveness and technical limitation of the method.

Development and validation of the AmpFlSTR MiniFiler PCR Amplification Kit: a MiniSTR multiplex for the analysis of degraded and/or PCR inhibited DNA

DNA typing of degraded DNA samples can be a challenging task when using the current commercially available multiplex short tandem repeat (STR) analysis kits. However, the ability to type degraded DNA specimens improves by redesigning current STR marker amplicons such that smaller sized polymerase chain reaction (PCR) products are generated. In an effort to increase the amount of information derived from these types of DNA samples, the AmpFlSTR MiniFiler PCR Amplification Kit has been developed. The kit contains reagents for the amplification of eight miniSTRs which are the largest sized loci in the AmpFlSTR Identifiler PCR Amplification Kit (D7S820, D13S317, D16S539, D21S11, D2S1338, D18S51, CSF1PO, and FGA). Five of these STR loci (D16S539, D21S11, D2S1338, D18S51, and FGA) also are some of the largest loci in the AmpFlSTR SGM Plus kit. This informative nine-locus multiplex, which includes the gender-identification locus Amelogenin, has been validated according to the FBI/National Standards and SWGDAM guidelines. Our results demonstrate significant performance improvements in models of DNA degradation, PCR inhibition, and nonprobative samples when compared to the AmpFlSTR Identifiler and SGM Plus kits. These data support that the MiniFiler kit will increase the likelihood of obtaining additional STR information from forensic samples in situations in which standard STR chemistries fail to produce complete profiles.

The application of miniplex primer sets in the analysis of degraded DNA from human skeletal remains

A new set of multiplexed PCR primers has been applied to the analysis of human skeletal remains to determine their efficacy in analyzing degraded DNA. These primer sets, known as Miniplexes, produce shorter amplicons (50-280 base pairs (bp)) than standard short tandem repeat (STR) kits, but still utilize the 13 CODIS STR loci, providing results that are searchable on national DNA databases. In this study, a set of 31 different human remains were exposed to a variety of environmental conditions, extracted, and amplified with commercial and Miniplex DNA typing kits. The amplification efficiency of the Miniplex sets was then compared with the Promega PowerPlex 16 system. Sixty-four percent of the samples generated full profiles when amplified with the Miniplexes, while only 16% of the samples generated full profiles with the Powerplex 16 kit. Complete profiles were obtained for 11 of the 12 Miniplex loci with amplicon sizes less than 200 bp. These data suggest smaller PCR amplicons may provide a useful alternative to mitochondrial DNA for anthropological and forensic analysis of degraded DNA from human skeletal remains.

A Technique to Capture, Analyze, and Quantify Anterior Teeth Rotations for Application in Court Cases Involving Tooth Marks

Anterior teeth within the human dentition have a specific numerical rotation value. Bite marks show an array of angled indentations, abrasions, microlacerations, and contusions. These marks generally represent the incisal surfaces of the suspect's dentition reflecting the rotation values of the teeth in the dental arch. This study described a method for capturing and analyzing anterior dental rotations. The rotations of individual anterior teeth within the study population were categorized as common, uncommon, and very uncommon according to Allen's classification. In the absence of a large number of incisal patterns present in a bite mark, a single but heavily weighted tooth rotation could be of equal discriminatory potential to several common rotation values. No prevalence studies quantifying individual tooth rotations are available. The measurement of each individual tooth rotation together with its individual discrimination potential will enhance the evaluation of the concordant features observed in bite marks.

Mitochondrial DNA D-loop hypervariable regions: Czech population data

In order to identify polymorphic sites and to find out their frequencies and the frequency of haplotypes, the complete D-loop of mitochondrial DNA (mtDNA) from 93 unrelated Czech Caucasians was sequenced. Sequence comparison showed that 85 haplotypes were found and of these 78 were unique, 6 were observed twice and 1 was observed three times. Genetic diversity (GD) was estimated at 0.999 and the probability of two randomly selected sequences matching (random match probability, RMP) at 1.2%. Additionally these calculations were carried out for hypervariable regions 1, 2 (HV1, HV2), for the area between HV1 and HV2 and for the area of the hypervariable region HV3. The average number of nucleotide differences (ANND) was established to be 10.2 for the complete D-loop. The majority of sequence variations were substitutions, particularly transitions. Deletions were found only in the region where HV3 is situated and insertions in the same place and in poly-C tracts between positions 303 and 315 in HV2. A high degree of length heteroplasmy was found especially in the regions of poly-C tracts between positions 16184 and 16193 in HV1 and between positions 303 and 315 in HV2. Position heteroplasmies were found in two cases.

Advances ofcapillary electrophoresis in clinical and forensic analysis (1999-2000)

In this paper, capillary electrophoresis in clinical and forensic analysis is reviewed on the basis of the literature of 1999, 2000 and the first papers in 2001. An overview of progress relevant examples for each major field of application, namely (i) analysis of drug seizures, explosives residues, gunshot residues and inks, (ii) monitoring of drugs, endogenous small molecules and ions in biofluids and tissues, (iii) general screening for serum proteins and analysis of specific proteins (carbohydrate deficient transferrin, alpha1-antitrypsin, lipoproteins and hemoglobins) in biological fluids, and (iv) analysis of nucleic acids and oligonucleotides in biological samples, including oligonucleotide therapeutics, are presented.

The reliability of forensic osteology--a case in point. Case study

The medico-legal investigation of skeletons is a trans-disciplinary effort by forensic scientists as well as physical anthropologists. The advent of DNA extraction and amplification from bones and teeth has led to the assumption that morphological assessment of skeletal remains might soon become obsolete. But despite the introduction and success of molecular biology, the analysis of skeletal biology will remain an integral part of the identification process. This is due to the fact, that the skeletal record allows relatively fast and accurate inferences about the identity of the victim. Moreover, a standard biological profile may be established to effectively narrow the police investigator's search parameters. The following study demonstrates how skeletal biology may collaborate in the forensic investigation and support DNA fingerprinting evidence. In this case, the information gained from standard morphological methods about the unknown person's sex, age and heritage immediately led the police to suspect, that the remains were that of a young man from Vietnam, who had been missing for 2.5 years. The investigation then quickly shifted to prove the victim's identity via DNA extraction and mtDNA sequence analysis and biostatistical calculations involving questions of kinship [4].