Enzymatic removal of Numts from Panthera tigris DNA samples

Forensic DNA analysis has revolutionized criminal investigations by providing valuable insights into identifying perpetrators, exonerating the innocent and unravelling mysteries of the past. Various molecular biology techniques, such as Short Tandem Repeat (STR) analysis, Single Nucleotide Polymorphism (SNP) profiling, mitochondrial DNA (mtDNA) sequencing, epigenetics and DNA methylation analysis, have played crucial roles in forensic investigations. While these techniques offer exceptional sensitivity and specificity, they also come with unique challenges. This review explores the current approaches of forensic DNA analysis, highlighting each technique. STR analysis, regarded as the gold standard in forensic DNA profiling, provides high discrimination power. However, it is limited in its ability to analyze degraded or mixed samples. On the other hand, SNP profiling offers advantages in analyzing highly degraded DNA samples but lacks the discriminatory power of STRs. Meanwhile, mtDNA analysis, particularly useful in cases involving compromised nuclear DNA, presents challenges due to its maternal inheritance pattern and lower discriminatory power. Furthermore, explore the exciting realm of epigenetics and the analysis of DNA methylation in forensic investigations. Epigenetic markers offer insights into gene expression patterns influenced by environmental factors, potentially aiding in the determination of tissue origin and chronological age estimation. DNA methylation analysis holds promise in forensic applications, providing additional layers of information for identity verification and tissue differentiation. Despite these advancements, several challenges persist in forensic DNA analysis, including the interpretation of complex DNA mixtures, standardization of methodologies, ethical considerations, and privacy concerns associated with the use of genetic information. Moreover, the integration of multi-omics data and machine learning approaches presents both opportunities and challenges in enhancing the accuracy and reliability of forensic DNA analysis. Looking ahead, future directions in molecular biology research for forensic DNA analysis involve the development of novel techniques with increased sensitivity, scalability, and robustness. By addressing these challenges and embracing emerging technologies, the field of forensic DNA analysis is poised for further advancements, offering enhanced capabilities in criminal justice and humanitarian efforts.

Objective To apply multiple displacement amplification (MDA)to improve primer extension preamplification (IPEP) for whole genome amplification (WGA) and to compare their effects on forensic DNA analysis. Methods DNA samples of varying amounts were for WGA based on MDA and IPEP.WGA products yield was evaluated by real-time quantitative PCR and STR genotyping performance was determined with AmpFLSTR? Identifiler(R) Kit. Results The DNA quantity was increased about 103～106 folds by MDA and 25～310 folds by IPEP. The least genome DNA amount is 1ng for MDA and 0.05ng for IPEP to obtain accurate genotypes of all loci. IPEP products and MDA products of 0.01 ng～0.1 ng DNA exhibited more loci observed than original DNA that was not for WGA,and IPEP products exhibited more loci observed than MDA products. Conclusion Both MDA and IPEP can improve STR genotyping of forensic minute DNA. The yield of MDA is higher than IPEP but the sensitivity of IPEP is higher than MDA and the STR genotyping effect of IPEP products is better than MDA products so IPEP is better for forensic trace DNA analysis. Key words: Multiple displacement amplification; Improved primer extension preamplification; Whole genome amplification; STR genotyping

The male-specific part of the human Y chromosome is widely used in forensic DNA analysis, particularly in cases where standard autosomal DNA profiling is not informative. A Y-chromosomal gene fragment is applied for inferring the biological sex of a crime scene trace donor. Haplotypes composed of Y-chromosomal short tandem repeat polymorphisms (Y-STRs) are used to characterise paternal lineages of unknown male trace donors, especially suitable when males and females have contributed to the same trace, such as in sexual assault cases. Y-STR haplotyping applied in crime scene investigation can (i) exclude male suspects from involvement in crime, (ii) identify the paternal lineage of male perpetrators, (iii) highlight multiple male contributors to a trace, and (iv) provide investigative leads for finding unknown male perpetrators. Y-STR haplotype analysis is employed in paternity disputes of male offspring and other types of paternal kinship testing, including historical cases, as well as in special cases of missing person and disaster victim identification involving men. Y-chromosome polymorphisms are applied for inferring the paternal bio-geographic ancestry of unknown trace donors or missing persons, in cases where autosomal DNA profiling is uninformative. In this overview, all different forensic applications of Y-chromosome DNA are described. To illustrate the necessity of forensic Y-chromosome analysis, the investigation of a prominent murder case is described, which initiated two changes in national forensic DNA legislation both covering Y-chromosome use, and was finally solved via an innovative Y-STR dragnet involving thousands of volunteers after 14 years. Finally, expectations for the future of forensic Y-chromosome DNA analysis are discussed.

Forensic DNA typing in China

Assessing non-LUS stutter in DNA sequence data

Forensic Y-SNP analysis beyond SNaPshot: High-resolution Y-chromosomal haplogrouping from low quality and quantity DNA using Ion AmpliSeq and targeted massively parallel sequencing

In forensic science, DNA and fingerprint analysis are crucial methods that are frequently used to identify people and solve criminal cases. DNA analysis matches biological samples from crime scenes with suspects or identifies victims by using the distinct genetic code present in each person's cells. Forensic scientists can examine even minute amounts of DNA using methods like mitochondrial DNA analysis, short tandem repeat (STR) profiling, and polymerase chain reaction (PCR) amplification, which yields highly accurate human identification. Analyzing fingerprints also depends on the distinct patterns of ridges, whorls, and loops seen on human fingertips. Automated fingerprint identification systems (AFIS) have advanced in recent years and enhanced the speed and accuracy of matching fingerprints across large databases. In forensic investigations, DNA and fingerprint analysis work well together as complementary methods. Fingerprints are direct proof of physical touch, whereas DNA provides a genetic blueprint.

Rapid advances in DNA sequencing technologies have made it increasingly cost-effective to obtain accurate and timely large-scale genomic sequence data on individuals (short read massively parallel or next generation [next-gen]). A next-gen molecular diagnostic approach that has seen rapid deployment in the clinic over the last year is exome sequencing. Whole exome sequencing covers all protein-coding genes in the genome (≈1.1% of genome), and an exome test for a single patient generates ≈6 gigabases (109 bp) of DNA sequence data. A key challenge facing routine use of next-gen data in patient diagnosis and management is data interpretation. What sequence variant findings are relevant to diagnosis (pathogenic mutations)? What sequence variant findings are relevant to clinical care but not necessarily to patient diagnosis (clinically actionable incidental data)? What sequence information should be stored, and where can it be stored? This review provides a tutorial on current approaches to answering these questions. A recent landmark study showed that application of next-gen sequencing to a large cohort of idiopathic dilated cardiomyopathy patients found ≈27% of patients to show mutations of the titin gene, the most complex gene in the genome (363 exons). We use titin in cardiomyopathy as an exemplar for explaining next-gen sequencing approaches and data interpretation. Decreasing sequencing costs and broad dissemination of next-generation (next-gen) equipment and expertise are increasing availability of massively parallel sequencing of patient DNA samples (short read massively parallel or next-gen sequencing).1,2 Most rapidly expanding is exome sequencing, where all protein-coding sequences (exons) are selected from total genomic DNA and selectively sequenced.3 Alternative approaches to next-gen sequencing include targeted sequencing (TS) and whole genome (complete genome) sequencing. Currently, marketed targeted Sanger sequencing panels using traditional individual exon-by-exon sequencing remain expensive and time consuming, and massively parallel next-gen approaches are beginning to supplant …

Advances in forensic DNA analysis have led to tremendous improvements in identifying and confirming perpetrators and victims. This has added credibility to DNA evidence, resulting in cases where criminals are more likely to be forced to own up to their criminality and culpability. This paper addresses scientific and technical theories the DNA analytical technologies are founded on as well as the suitability of individual analytical procedures. Beyond these issues, it went on to discuss the requirements that need to be met in order for DNA evidence, collected through forensic DNA testing, to be admissible in court in Korea. DNA testing results are presented in court in the form of certified expert testimony. And according to Article 313, “Statement, etc.” of the Criminal Procedure Act, as long as the DNA evidence offered is free from errors in laboratory procedures and concluding interpretations of the person responsible for producing the expert opinion recording, such procedures and outcomes will be admissible as legitimate evidence in court. In other words, the aforementioned expert testimony is nothing short of legislative intent at acknowledging the testimony as admissible in court, thus should not be understood as standards with which the scientific evidence concerned is admissible and tried at court. For this reason, admissibility in court of DNA evidence from DNA forensic analysis should not only be based on whether it meets the requirements as expert testimony, but also whether its theories of reasoning and analyses are founded on acceptable scientific principles. Furthermore, the tools and methods used in DNAprofiling need to be validated, allowing the analyzed result in question to be assessed for admissibility in criminal court. Trends of precedents regarding DNA evidence seem to require that the relevancy of DNA analytical theories, suitability of DNA analytical methods that have implemented these theories, and maintenance of the chain of custody of evidence by applying scientific procedures to the targets concerned, be met for the evidence to be admissible in court. Furthermore, it may be fair to say that within the structure of Korea’s criminal prosecution, the processes involved in determining whether or not DNA evidence is credible may be part of what is needed to assess its probative value. At the moment, theoretical foundations of DNA analysis are deemed reliable with the overall approval of scientific circles, however there are improvements made all the time in standard analytical methodologies and procedures regarding their implementation and analytical techniques. This has created an unbridgeable gap between common knowledge and the outcomes of scientific research activities that legal experts, particularly trial judges, are left with no choice but to be more and more dependent on expert testimony when they assess the credibility of DNA evidence. Still, the more weight DNA analysis carries, the more likely serious errors in laboratory testing occur; thus, there is increased emphasis on how to keep the chain of custody in determining the admissibility of DNA evidence, for example, the qualification of those involved in testing, sample collection and preservation, stability of the testing methods that have been utilized, and conformance to analytical procedures. Therefore, if there is evidence that is crucial in determining guilt in crime, and the continuity of its preservation is closely related to the presence and integrity of the evidence concerned, namely DNA evidence, the defendant should be afforded the opportunity for the credibility of evidence to be tried in court during the entire processes of such evidence being collected, stored and analyzed to: prevent wrongful accusations; to make court proceedings more impartial; and to comply with appropriate procedures. To this end, cross examination of witnesses, disclosure of extensive evidence of the parties involved, and cross examinat

A proof-of-principle study on implementing polymerase chain displacement reaction (PCDR) to improve forensic low-template DNA analysis

DNA evidence has now become an essential part of forensic investigations since it offers vital information for person identification and crime resolution. However, the biological material is affected by some environmental factors which may impact the DNA in biological samples. This may affect the correctness and reliability of forensic DNA analysis. This review is related to the influence of various environmental conditions on the stability and degradation of DNA in biological stains including blood and saliva stains. The common factors that affect DNA are temperature, humidity, exposure to sunlight, and type of substrate. The information is crucial to improve forensic DNA analysis and forensic protocol optimization. The DNA stability and integrity in biological materials, such as blood and saliva stains, are indispensable for forensic DNA analysis. Environmental influences, however, significantly affect DNA concentration and may jeopardize forensic analysis. The present review explores various environmental factors for their effect on DNA stability in blood and saliva stains. While DNA degradation is slowed but not completely prevented by low temperatures, it is accelerated by high temperatures. Risks of contamination arise from the promotion of microbial growth and DNA breakdown by humidity. DNA photodamage brought on by sunlight exposure results in strand breakage and cross-linking. DNA stability is also influenced by the type of substrate used; porous surfaces, such as cloth, are better at keeping fluids than non-porous ones, such as glass. Maintaining the integrity of DNA evidence requires an understanding of these variables. The present studies will help to create sophisticated DNA preservation methods for use in forensic DNA examination. The study emphasizes the requirement of improvement in forensic DNA analysis skills, related to the preservation of DNA pieces of evidence and the possible effect of environmental factors.

A confession offered in a trial is considered as the most persuasive evidence of the suspect's guilt and crime and is heavily weighted by jurors in the suspect's verdict. This fact leads to a wrongful conviction in case of a false confession. In this case, forensic DNA analysis led to the exoneration of a suspect who gave a false confession during initial police investigation. A 6-year-old male juvenile was missing and reported to the police station in Greentown of the District of Lahore on January 2, 2015. His body was found hanging in the nearby mosque with a rope around his neck. Autopsy outcomes bared that the child was brutally murdered after sexual assault. Standard reference samples of three possible suspects were collected for comparison in DNA analysis, in which one of the suspects (S1) accepted the offense during initial investigation by police. Seminal material was identified on anal swabs as well as from the swabs taken from one of the suspected stains on the floor of the crime scene using serological techniques: acid phosphatase and sperm microscopy. These samples were subjected to differential DNA extraction to separate sperm DNA of the perpetrator from the epithelial cell DNA of the victim. DNA profiles from the evidenced samples and of suspect's samples were developed using forensic DNA analysis techniques. The DNA profile of an unknown male individual was obtained from anal swabs and from a suspected stain found on the floor. It did not match initially but nominated three suspects. S1 was eliminated in this case and was exonerated due to DNA fingerprinting technology. Later on, six more suspects were submitted and their DNA profiles were generated. DNA profiles from a 12-year-old boy and S6 were matched with the DNA profile obtained as evidence of one who confessed to the crime after a polygraph.

Renement of methods for forensic mitochondrial DNA (mtDNA) analysis that were introduced in the early 1990s has led to the present “golden age” of mtDNA testing in public or government laboratories such as the Federal Bureau of Investigation (FBI) and the Armed Forces DNA Identication Laboratory (AFDIL), as well as in private-sector laboratories such as Mitotyping Technologies, the Bode Technology Group, and Orchid Cellmark. e success of mtDNA in forensic DNA analysis can be gauged from the fact that a laboratory such as Mitotyping has completed over 1,000 mtDNA cases since its inception in 1998; hundreds have resulted in resolution of criminal cases, contributory and relevant trial testimonies, and postconviction exonerations. Although it is not possible to retroactively review the history or present the workings of the entire forensic mtDNA community of test providers, a retrospective analysis of the operation at Mitotyping provides a comprehensive overview of the testing process. In this review we will describe how the “state of the art” has evolved since 1996 when mtDNA testing was introduced to the criminal justice system in the case of Tennessee v. Ware (Davis 1998), review alternative methods for mtDNA analysis, and describe forthcoming new methods with the potential to change the ways in which casework is carried out.

Introducing the New Editorial Team

The development of forensic DNA analysis: New debates on the issue of fundamental human rights