DNA fingerprinting in forensics: past, present, future

Homology Identification and Cross-Contamination Analysis: A Method for Evaluating the Quality of Biological Samples Stored in a Biobank Using the Advanta Sample ID Genotyping Panel

Biological samples are important resources for scientific research. These samples are stored in biobanks over years until needed, and some of them can never be retrieved if they are improperly stored, causing them to be wasted. Thus, they are priceless, and they should be used correctly and effectively. Sample quality substantially affects biomedical research results. However, sample misidentification or mix-up is common. It is necessary to establish quality standards for sample identification. In this study, we used the Advanta Sample ID genotyping panel to detect homology identification and cross-contamination. We compared the single-nucleotide polymorphism (SNP) typing results of two different samples and calculated the similarity score of homologous sample pairs and nonhomologous sample pairs. Through analysis, we obtained a similarity score cutoff point of 0.8620, which was an effective way to distinguish homology and nonhomology. Cross-contamination was detected in two sets of mixtures (STD8:STD6 and jj3:1-P) mixed at a series of special ratios. Sensitivity was dependent on the sample characteristics and mixing ratios. Finally, we assessed the effect of sample degradation degree on SNP genotyping and found that degraded samples with a minimal DNA integrity number of 1.9 had complete genotyping results. On the whole, this study shows that the Sample ID panel is reliable for homology identification and cross-contamination analysis. Moreover, this technology has promising further applications in biological sample quality control.

Bioluminescent Intercalating Dyes for Ratiometric Nucleic Acid Detection

Rapid and sensitive DNA detection methods that can be conducted at the point of need may aid in disease diagnosis and monitoring. However, translation of current assays has proven challenging, as they typically require specialized equipment or probe-specific modifications for every new target DNA. Here, we present Luminescent Multivalent Intercalating Dye (LUMID), off-the-shelf bioluminescent sensors consisting of intercalating dyes conjugated to a NanoLuc luciferase, which allow for nonspecific detection of double-stranded DNA through a blue-to-green color change. Through the incorporation of multiple, tandem-arranged dyes separated by positively charged linkers, DNA-binding affinities were improved by over 2 orders of magnitude, detecting nanomolar DNA concentrations with an 8-fold change in green/blue ratio. We show that LUMID is easily combined with loop-mediated isothermal amplification (LAMP), enabling sequence-specific detection of viral DNA with attomolar sensitivity and a smartphone-based readout. With LUMID, we have thus developed a tool for simple and sensitive DNA detection that is particularly attractive for point-of-need applications.

Microsatellites used in forensics are in regions enriched for trait-associated variants

The 20 short tandem repeat (STR) loci of the combined DNA index system (CODIS) are the basis of the vast majority of forensic genetics in the United States. One argument for permissive rules about the collection of CODIS genotypes is that the CODIS loci are thought to contain little information about ancestry or traits. However, in the past 20 years, a growing field has identified hundreds of thousands of genotype-trait associations. Here, we conduct a survey of the landscape of such associations surrounding the CODIS loci as compared with non-CODIS STRs. Although this study cannot establish or quantify associations between CODIS genotypes and phenotypes, we find that the regions around the CODIS loci are enriched for both known pathogenic variants (> 90th percentile) and for trait-associated SNPs identified in genome-wide association studies (GWAS) (≥ 95th percentile in 10kb and 100kb flanking regions), compared with other random sets of autosomal tetranucleotide-repeat STRs.

Effect of Carcinomas on Autosomal Trait Screening: A Review Article

This review highlights the effect of carcinomas on the results of the examination of autosomal genetic traits for identification and paternity tests when carcinoid tissue is the only source and no other samples are available. In DNA typing or genetic fingerprinting, variable elements are isolated and identified within the base pair sequences that form the DNA. The person's probable identity can be determined by analysing nucleotide sequences in particular regions of DNA unique to everyone. Genetics plays an increasingly important role in the risk stratification and management of carcinoma patients. The available information from previous studies has indicated that in some incidents, including mass disasters and crimes such as terrorist incidents, biological evidence may not be available at the scene of the accident, except for some unknown human remains found in the form of undefined human tissues. If these tissues have cancerous tumours, it may affect the examination of the genetic traits derived from these samples, thereby resulting in a failure to identify the person. Pathology units, more often, verify the identity of the patients who were diagnosed with cancer in reference to their deceased tumorous relatives. Genetic fingerprinting (GF) is also used in paternity testing when the alleged parent disappeared or died and earlier was diagnosed and treated for cancer.

Novel strategy of multiple-locus variable number tandem repeats analysis for genetic fingerprinting of human

BACKGROUND

The variable number of tandem repeat (VNTR) analyses are methods based on the detection of repeated sequences within the human genome. In order to perform DNA typing at the personal laboratory, it is necessary to improve the VNTR analysis.

OBJECTIVE

The VNTR markers were difficult to popularize because PCR amplification was difficult due to its GC-rich and long nucleotide sequence. The aim of this study was to select the multiple VNTR markers that could only be identified by PCR amplification and electrophoresis.

METHODS

We genotyped each of the 15 VNTR markers using genomic DNA from 260 unrelated individuals by PCR amplification. Differences in the fragment length of PCR products are visualized by agarose gel electrophoresis. To confirm their usefulness as a DNA fingerprint these 15 markers were simultaneously analyzed with the DNA of 213 individuals and verified the statistical significance. In addition, to investigate the usefulness of each of the 15 VNTR markers as paternity markers, Mendelian segregation by meiotic division within a family consisting of two or three generations was confirmed.

RESULTS

Fifteen VNTR loci selected in this study could be easily amplified by PCR and analyzed by electrophoresis, and were newly named DTM1 ~ 15. The number of total alleles in each VNTR showed from 4 to 16, and 100 to 1600 bp in length, and their heterozygosity ranged from 0.2341 to 0.7915. In simultaneous analysis of 15 markers from 213 DNAs, the probability of chance appearing the same genotype in different individuals was less than 4.09E-12, indicating its usefulness as a DNA fingerprint. These loci were transmitted through meiosis by Mendelian inheritance in families.

CONCLUSION

Fifteen VNTR markers have been found to be useful as DNA fingerprints for personal identification and kinship analysis that can be used at the personal laboratory level.

Recent advancements in identification and detection of saliva as forensic evidence: a review

Background

Saliva is the most common biological evidence found at any crime scene next to blood. It is a clear liquid which makes it immune to any possible evidence of alteration by the perpetrator. In forensics, saliva is used as biological evidence and is very helpful in determining various aspects of an individual such as sex, individuality, ABO blood groups, microbial signature, biomarkers, or habits like smoking.

Main body

Saliva shares a great resemblance with plasma as it encompasses similar organic or inorganic compound contents. In forensic casework, identifying any evidence is the primary goal to establish the groundwork for further investigation. Saliva may be found in the form of a pool or stained form, but its identification is challenging because of its transparency. It has been widely used as an informative tool in forensic situations like poisoning, hanging, or cases of drug abuse, etc. for more than two decades now. Over the years, many proposed ways or methods have been identified and described, which helped in the detection and identification of saliva as evidence.

Conclusion

This review article represents the significance of saliva as important forensic evidence, along with the different forms it may be encountered at the crime scene. The use of diverse collection and detection methods, over the past few decades, has been discussed. An attempt has been made to collect the available data, highlighting the merit and demerits of different identification techniques. The relevant data has been collected from all the published and reported literature (1987–2021).

Microsatellites used in forensics are located in regions unusually rich in trait-associated variants

The 20 short tandem repeat (STR) markers of the combined DNA index system (CODIS) are the basis of the vast majority of forensic genetics in the United States. One argument for permissive rules about the collection of CODIS genotypes is that the CODIS markers are thought to contain information relevant to identification only (such as a human fingerprint would), with little information about ancestry or traits. However, in the past 20 years, a quickly growing field has identified hundreds of thousands of genotype-trait associations. Here we conduct a survey of the landscape of such associations surrounding the CODIS loci as compared with non-CODIS STRs. We find that the regions around the CODIS markers are enriched for both known pathogenic variants (>90th percentile) and for SNPs identified as trait-associated in genome-wide association studies (GWAS) (≥95th percentile in 10kb and 100kb flanking regions), compared with other random sets of autosomal tetranucleotide-repeat STRs. Although it is not obvious how much phenotypic information CODIS would need to convey to strain the "DNA fingerprint" analogy, the CODIS markers, considered as a set, are in regions unusually dense with variants with known phenotypic associations.

Precise DNA cleavage using CRISPR-SpRYgests

Methods for in vitro DNA cleavage and molecular cloning remain unable to precisely cleave DNA directly adjacent to bases of interest. Restriction enzymes (REs) must bind specific motifs, whereas wild-type CRISPR-Cas9 or CRISPR-Cas12 nucleases require protospacer adjacent motifs (PAMs). Here we explore the utility of our previously reported near-PAMless SpCas9 variant, named SpRY, to serve as a universal DNA cleavage tool for various cloning applications. By performing SpRY DNA digests (SpRYgests) using more than 130 guide RNAs (gRNAs) sampling a wide diversity of PAMs, we discovered that SpRY is PAMless in vitro and can cleave DNA at practically any sequence, including sites refractory to cleavage with wild-type SpCas9. We illustrate the versatility and effectiveness of SpRYgests to improve the precision of several cloning workflows, including those not possible with REs or canonical CRISPR nucleases. We also optimize a rapid and simple one-pot gRNA synthesis protocol to streamline SpRYgest implementation. Together, SpRYgests can improve various DNA engineering applications that benefit from precise DNA breaks.

Science, Values, and the New Demarcation Problem

In recent years, many philosophers of science have rejected the "value-free ideal" for science, arguing that non-epistemic values have a legitimate role to play in scientific inquiry. However, this philosophical position raises the question of how to distinguish between legitimate and illegitimate influences of values in science. In this paper, we argue that those seeking to address this "new" demarcation problem can benefit by drawing lessons from the "old" demarcation problem, in which philosophers tried to find a way of distinguishing between science and non-science. Many of those who worked on this problem ultimately found that efforts to provide necessary and sufficient conditions for defining science failed, and most concluded that the best solution to the problem was to characterize scientific hypotheses, theories, and research programs in terms of some common norms. We suggest that those seeking to distinguish between legitimate and illegitimate value influences on science would do well to adopt a similar approach. Rather than attempting to establish necessary and sufficient conditions for identifying appropriate value influences, it will be more fruitful to evaluate scientific activities based on their adherence to a set of epistemic and ethical norms that can be implemented in scientific practice by means of rules, conventions, policies, and procedures.

Poaching Forensics: Animal Victims in the Courtroom

Poaching and the international trade in wildlife are escalating problems driven by poverty and greed and coordinated by increasingly sophisticated criminal networks. Biodiversity loss, caused by habitat change, is exacerbated by poaching, and species globally are facing extinction. Forensic evidence underpins human and animal criminal investigations and is critical in criminal prosecution and conviction. The application of forensic tools, particularly forensic genetics, to animal case work continues to advance, providing the systems to confront the challenges of wildlife investigations. This article discusses some of these tools, their development, and implementations, as well as recent advances. Examples of cases are provided in which forensic evidence played a key role in obtaining convictions, thus laying the foundation for the future application of techniques to disrupt the criminal networks and safeguard biodiversity through species protection.

Long time stability of 35 small endogenous biomolecules in dried urine spotted on various surfaces and environmental conditions

Analysis of endogenous biomolecules is an important aspect of many forensic investigations especially with focus on DNA analysis for perpetrator/victim identification and protein analysis for body fluid identification. Recently, small endogenous biomolecules have been used for differentiation of synthetic "fake" urine from authentic urine and might be also useful for biofluid identification. Therefore, the aim of this study was to adapt and optimize a method for analysis of small EBs and to investigate long time stability of 35 small endogenous biomolecules (including acylcarnitines with their isomers and metabolites as well as amino acids with their metabolites) in spotted urine samples. Urine samples were spotted on seven different surfaces (Whatman 903 Protein Saver Cards, cotton swabs, cotton glove, denim, underwear, and smooth and rough flagstone) and stored under six environmental conditions (reference condition, sunlight, LED light, 4 °C, 37 °C, humidity of 95%). At certain time points (d0, d7, d28 and d56) samples were analyzed in triplicates by an optimized extraction and LC-HRMS approach. In addition, the urine marker Tamm-Horsfall-Protein was determined on cotton swabs at the same time points using a commercial lateral flow test. Twenty-one of 35 small endogenous biomolecules were stable on most materials/surfaces and under most storage conditions. Significant lower endogenous biomolecule peak areas were found for rough flagstone and underwear as well as for high humidity storage. Kynurenic acid proved to be photo labile. While high long time stabilities were found for 19 of 28 acylcarnitines, nine acylcarnitines showed aberrant stability patterns without evident structural reason. For Tamm-Horsfall-Protein degradation within 28 days was observed even under reference conditions. The presented study demonstrated the value of sensitive LC-HRMS analysis for small endogenous biomolecules / pattern. However, further studies will be indispensable for unambiguous body fluid identification by small endogenous biomolecules.

Tooth as a Source of DNA in Forensic or Investigative Genetics: An Overview

Deoxyribonucleic acid (DNA) is the genetic code of most organisms including humans. In the last few years, DNA analysis methods are applied to forensic cases for human identification which is termed forensic or investigative genetics. It is often challenging to obtain and interpret DNA from routine samples like blood in severely decomposed or disfigured bodies recovered from incineration, immersion, trauma, mutilation, and decomposition as in incidents of fire, explosion, or murder. The tooth can survive any extreme environment with minimum risk of contamination making it a valuable alternative source of DNA in such cases. Tooth structures like the enamel (amelogenin protein), dentin, cementum, pulp, and adherent tissues like bone and periodontal fibers are sources from which DNA can be obtained. Various methods have been described for DNA extraction. There are numerous applications of DNA analysis like identification of the deceased or missing victim or the unknown culprit from a crime scene, solving paternity issues, determining the occurrence of any genetic disease, and determining the ancestry. This article briefly summarizes an overview of the tooth as a valuable DNA source and various methods and challenges related to DNA analysis.

Innovative Approach by Modifying the Fitting Surface of Prosthesis Used for Individual Identification Post Heat Treatment- SEM Analysis

Aims: To visualize the surface irregularities and changes after heat treatment on the prosthesis. This was done by Scanning Electron Microscopy. Material and Methods: Eight prosthesis were prepared with modification on the fitting surfaces. The occlusal surface of the tooth to receive the prosthesis was modified and engraved with the initials in the form of identification features. These were heat treated under furnace at temperatures of 500°C, 1000°C and 1500°C after which the scanning was done under Electron Microscope. Results: After heat treatment it was observed that the inner surface of the prosthesis was merely distorted and the details were intact. Analysis of the surface irregularities shows that there are slit surface changes on the occlusal surface at 1000°C and the fitting surface details are well protected. Conclusion: It was identified that after heat treatment at temperatures 1000°C and above some changes started occurring on the fitting surface and the identification features. At these temperatures the whole human body is charred and even the bones start to get destroyed. SEM images give the detailed pictures of the same and that if this method is incorporated in day today dentistry it will be a boom in the forensic identification.

Not so simple: Understanding the complexities of establishing identity for cases of unidentified human remains in an Australian medico-legal system

Discussions regarding the importance and complexities associated with the identification of deceased persons have typically focused on disaster or humanitarian contexts where there has been large scale loss of life. In contrast, identification efforts for unidentified human remains (UHR) cases in routine domestic casework contexts have received relatively little attention. The aim of this paper was to present the situation regarding the count of UHR cases in the state of Victoria, Australia, dating between 1960 and 2020, and to provide a constructively critical appraisal of the factors that have, and continue to, hinder their identification. Over the six decades a total of 132 coronial cases remained unidentified; an average of 2-3 cases per annum. For each case, the preservation of the remains, geographical location of where they were recovered from, primary (fingerprints, dental, DNA) and secondary identification methods that had been employed, potential for additional identification testing and current curation of the remains, were recorded. The difficulty with providing a "total count" of UHR cases is discussed, as well as the ways in which preservation, availability of identification methods, changes in policies and procedures, record management, changes in practice and advancements in technology, have impacted the identification process. This paper demonstrates the complexity of the investigation of UHR cases, and why individuals continue to remain unidentified in 2021.

Finding Needle in the Haystack: “Kasur’s Bogeyman” Brought to Justice by Geographic Profiling and Mass DNA Screening

This article describes the application of the concept of geographic profiling in hunting a serial child rapist in Kasur, Pakistan. It also discusses, how DNA became the prime witness against the serial rapist in the court of law. In January 2018, the blind rape and murder case of Zainab Amin hit the headlines. Following autopsy and the subsequent forensic examination, the only piece of evidence, the agencies had, was the DNA profile of the perpetrator and the information that the source of DNA profile is a serial child rapist, involved in at least seven more cases. The analysis of all crime sites and the distance between them strongly suggested that the offender most likely was a local resident. Mass DNA screening in the target region was conducted by CSI teams of Punjab forensic science agency. The DNA matched with suspect number 814 who later confessed all his crimes. In Polygraph examination, the offender revealed his modus operandi which was in line with the hypotheses made during the geographic profiling of the crime scenes. Thus, geographic profiling proved to be a very useful investigative tool in predicting the probable location of the criminal involved in a series of crimes.

Optimization of proteomics sample preparation for forensic analysis of skin samples

We present an efficient protein extraction and in-solution enzymatic digestion protocol optimized for mass spectrometry-based proteomics studies of human skin samples. Human skin cells are a proteinaceous matrix that can enable forensic identification of individuals. We performed a systematic optimization of proteomic sample preparation for a protein-based human forensic identification application. Digestion parameters, including incubation duration, temperature, and the type and concentration of surfactant, were systematically varied to maximize digestion completeness. Through replicate digestions, parameter optimization was performed to maximize repeatability and increase the number of identified peptides and proteins. Final digestion conditions were selected based on the parameters that yielded the greatest percent of peptides with zero missed tryptic cleavages, which benefit the analysis of genetically variable peptides (GVPs). We evaluated the final digestion conditions for identification of GVPs by applying MS-based proteomics on a mixed-donor sample. The results were searched against a human proteome database appended with a database of GVPs constructed from known non-synonymous single nucleotide polymorphisms (SNPs) that occur at known population frequencies. The aim of this study was to demonstrate the potential of our proteomics sample preparation for future implementation of GVP analysis by forensic laboratories to facilitate human identification. SIGNIFICANCE: Genetically variable peptides (GVPs) can provide forensic evidence that is complementary to traditional DNA profiling and be potentially used for human identification. An efficient protein extraction and reproducible digestion method of skin proteins is a key contributor for downstream analysis of GVPs and further development of this technology in forensic application. In this study, we optimized the enzymatic digestion conditions, such as incubation time and temperature, for skin samples. Our study is among the first attempts towards optimization of proteomics sample preparation for protein-based skin identification in forensic applications such as touch samples. Our digestion method employs RapiGest (an acid-labile surfactant), trypsin enzymatic digestion, and an incubation time of 16 h at 37 °C.

Developments in forensic DNA analysis

The analysis of DNA from biological evidence recovered in the course of criminal investigations can provide very powerful evidence when a recovered profile matches one found on a DNA database or generated from a suspect. However, when no profile match is found, when the amount of DNA in a sample is too low, or the DNA too degraded to be analysed, traditional STR profiling may be of limited value. The rapidly expanding field of forensic genetics has introduced various novel methodologies that enable the analysis of challenging forensic samples, and that can generate intelligence about the donor of a biological sample. This article reviews some of the most important recent advances in the field, including the application of massively parallel sequencing to the analysis of STRs and other marker types, advancements in DNA mixture interpretation, particularly the use of probabilistic genotyping methods, the profiling of different RNA types for the identification of body fluids, the interrogation of SNP markers for predicting forensically relevant phenotypes, epigenetics and the analysis of DNA methylation to determine tissue type and estimate age, and the emerging field of forensic genetic genealogy. A key challenge will be for researchers to consider carefully how these innovations can be implemented into forensic practice to ensure their potential benefits are maximised.

Effect of postmortem interval and conditions of teeth on STR based DNA profiling from unidentified dead bodies

Teeth are important exhibits to establish the identity of unidentified dead bodies by DNA profiling. Tooth acts as a cage to protect DNA from harsh environmental conditions. Unidentified bodies are sometimes found many years after death causing loss of valuable soft tissues which can be used for DNA extraction. Skeletal remains and dental evidence provide the best alternative when decomposed or burnt bodies are examined to establish the identity. In this study, the powder-free method was used to extract DNA from ninety-five teeth of unidentified dead bodies across seven years (2014-2020). Intact and broken dental remains were analyzed majorly from decomposed remains. The present study reports successful STR profiles obtained from dental evidence using powder free method. Complete DNA profiles were obtained from intact teeth while damaged teeth either gave partial profiles or no results. This data suggest that intact teeth are excellent samples for DNA profiling from decomposed unidentified dead bodies even with greater post mortem interval. Findings from this study can hence be useful in establishing the identity in forensic and archeological casework.

Forensic databases, a perspective from the penitentiary centers of Spain

Scientific and technological progress in the field of forensic genetics is very useful in the resolution of criminal cases, but it entails the need for a deep ethical reflection, as the individual Fundamental Rights may be violated. This project aims to collect and compare the opinion of prisoners and prison officials on what characteristics the country's forensic database should have. In this context, 210 subjects were surveyed, 101 of them prisoners and the rest prison officials, from three different Spanish penitentiary centers. Among the results obtained, most prisoners and officials consider the national DNA database to be useful, and additionally, a 40% of the participants would support the integration of the profiles of the entire population. 64% considered it ethical to use the DNA profiles of the database as a tool for familial searching. Despite this, half of the respondents are concerned about the future uses of the DNA database. Integrating the opinion of these analyzed groups with other relevant judicial, scientific and ethical convictions, ensures the regulation between security and individual's Human Rights.

Capture enrichment and massively parallel sequencing for human identification

In the past decade, hybridization capture has gained attention within the forensic field for its possible use in human identification. One of the primary benefits to capture enrichment is its applicability to degraded DNA fragments that, due to their reduced size, are not amenable to traditional PCR enrichment techniques. Hybridization capture is typically introduced after genomic library preparation of extracted DNA templates for the subsequent enrichment of mitochondrial DNA or single nucleotide polymorphisms within the nuclear genome. The enriched molecules are then subjected to massively parallel sequencing (MPS) for sensitive and high-throughput DNA sequence generation. Bioinformatic analysis of capture product removes PCR duplicates that were introduced during the laboratory workflow in order to characterize the original DNA template molecules. In the case of aged and degraded skeletal remains, the fraction of endogenous human DNA may be very low; therefore low-coverage sequence analysis may be required. This review contains an overview of current capture methodologies and the primary literature on hybridization capture as evaluated for forensic applications.

Systematic microsatellite repeat expansion cloning and validation

Approximately 3% of the human genome is composed of short tandem repeat (STR) DNA sequence known as microsatellites, which can be found in both coding and non-coding regions. When associated with genic regions, expansion of microsatellite repeats beyond a critical threshold causes dozens of neurological repeat expansion disorders. To better understand the molecular pathology of repeat expansion disorders, precise cloning of microsatellite repeat sequence and expansion size is highly valuable. Unfortunately, cloning repeat expansions is often challenging and presents a significant bottleneck to practical investigation. Here, we describe a clear method for seamless and systematic cloning of practically any microsatellite repeat expansion. We use cloning and expansion of GGGGCC repeats, which are the leading genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), as an example. We employ a recursive directional ligation (RDL) technique to build multiple GGGGCC repeat-containing vectors. We describe methods to validate repeat expansion cloning, including diagnostic restriction digestion, PCR across the repeat, and next-generation long-read MinION nanopore sequencing. Validated cloning of microsatellite repeats beyond the critical expansion threshold can facilitate step-by-step characterization of disease mechanisms at the cellular and molecular level.

Development of an automated AmpliSeq™ library building workflow for biological stain samples on the Biomek® 3000

Here, we present the development of an automated AmpliSeq™ (ThermoFischer, MA, USA) workflow for library building using the Biomek^® 3000 Laboratory Automation Workstation (Beckman Coulter Inc., CA, USA), in which the total volume of PCR reagents and reagents for library preparation are reduced by one-half. The automated AmpliSeq workflow was tested using 43 stain samples (blood, bone, muscle tissue, semen, swab, nail scrape and cigarette butts) collected from crime scenes. The sequencing data were evaluated for locus balance, heterozygous allele balance and noise. The performance of libraries built with the automated AmpliSeq workflow using one-half of the recommended reagent volumes were similar to the performance of libraries built with the recommended (full) volumes of the reagents.

Scalable optical annealing of microfluidic droplets via whispering gallery mode geometry and infrared illumination

This work presents a solution to limitations on scalability in traditional on-chip optofluidic polymerase chain reaction (PCR) methods that are based on infrared annealing and droplet-based microfluidics. The scalability in these PCR optofluidic methods is limited by the optical penetration depth of light in a fluid droplet. Traditionally, such an implementation has minimal absorption when the droplet diameter is scaled well below the optical penetration depth due to the small interaction length. In the presented whispering gallery mode (WGM) optofluidic method, a WGM wave is created through total internal reflection, where light is trapped within a droplet. The effect of the trapped light can extend the interaction length beyond the penetration depth, even for small diameter droplets. Thus, this WGM wave permits the use of droplets with diameters scaled below the penetration depth of the light. A theoretical analysis of traditional optical annealing and of the WGM optofluidic method is conducted using finite-difference time-domain analyses. The WGM wave optofluidic method is also demonstrated experimentally, providing higher annealing temperatures than traditional optical annealing. It is envisioned that the presented work will allow for scalable PCR devices implemented on-chip.

Facial recognition from DNA using face-to-DNA classifiers

Facial recognition from DNA refers to the identification or verification of unidentified biological material against facial images with known identity. One approach to establish the identity of unidentified biological material is to predict the face from DNA, and subsequently to match against facial images. However, DNA phenotyping of the human face remains challenging. Here, another proof of concept to biometric authentication is established by using multiple face-to-DNA classifiers, each classifying given faces by a DNA-encoded aspect (sex, genomic background, individual genetic loci), or by a DNA-inferred aspect (BMI, age). Face-to-DNA classifiers on distinct DNA aspects are fused into one matching score for any given face against DNA. In a globally diverse, and subsequently in a homogeneous cohort, we demonstrate preliminary, but substantial true (83%, 80%) over false (17%, 20%) matching in verification mode. Consequences of future efforts include forensic applications, necessitating careful consideration of ethical and legal implications for privacy in genomic databases.

Rapid detection of Salmonella contamination in seafoods using multiplex PCR

Effective monitoring of Salmonella contamination in seafood processing to conform the requirements of HACCP is a great challenge today. Such challenges can be effectively addressed, if the conventional detection methods are replaced with DNA-based molecular methods. Accordingly, it was aimed to develop a robust PCR protocol for specific detection of Salmonella spp. Out of the different primers screened, one pair of primers developed in this study targeting invA gene demonstrated 100% inclusivity for a wide range of Salmonella serotypes and 100% exclusivity for wide range of non-target species. The in silico analysis of the nucleotide sequence obtained from the PCR product suggests its potential as a hybridization probe for genus specific detection of Salmonella spp. contamination. The PCR protocol was sensitive enough to detect 15 cells per reaction using crude DNA prepared within a short time directly from artificially contaminated shrimp tissue. The study demonstrated that the result of PCR reaction can come out on the same day of sample arrival. Incorporation of this pair of primers in a multiplex PCR designed for simultaneous detection of four common seafood-borne human pathogens yielded 147 bp, 302 bp, 403 bp, and 450 bp distinct DNA bands specifically targeting E. coli, toxigenic Vibrio cholerae, Salmonella spp., and V. parahaemolyticus, respectively in a single PCR tube. The PCR methods developed in this study has the potential to be used in the seafood processing plants for effective monitoring of CCPs required for implementation of HACCP-based quality assurance system.

Next-Generation Sequencing for Biodefense: Biothreat Detection, Forensics, and the Clinic

BACKGROUND

Next-generation sequencing (NGS) is revolutionizing a variety of molecular biology fields including bioforensics, biosurveillance, and infectious disease diagnostics. For pathogen detection, the ability to sequence all nucleic acids in a sample allows near limitless multiplexability, free from a priori knowledge regarding an etiologic agent as is typically required for targeted molecular assays such as real-time PCR. Furthermore, sequencing capabilities can generate in depth genomic information, allowing detailed molecular epidemiological studies and bioforensics analysis, which is critical for source agent identification in a biothreat outbreak. However, lack of analytical specificity, inherent to NGS, presents challenges for regulated applications such as clinical diagnostics and molecular attribution.

CONTENT

Here, we discuss NGS applications in the context of preparedness and biothreat readiness. Specifically, we investigate current and future applications of NGS technologies to affect the fields of biosurveillance, bioforensics, and clinical diagnostics with specific focus on biodefense.

SUMMARY

Overall, there are many advantages to the implementation of NGS for preparedness and readiness against biowarfare agents, from forensics to diagnostics. However, appropriate caveats must be associated with any technology. This includes NGS. While NGS is not the panacea replacing all molecular techniques, it will greatly enhance the ability to detect, characterize, and diagnose biowarfare agents, thus providing an excellent addition to the biodefense toolbox of biosurveillance, bioforensics, and biothreat diagnosis.

Microbial Degradation of Forensic Samples of Biological Origin: Potential Threat to Human DNA Typing

Forensic biology is a sub-discipline of biological science with an amalgam of other branches of science used in the criminal justice system. Any nucleated cell/tissue harbouring DNA, either live or dead, can be used as forensic exhibits, a source of investigation through DNA typing. These biological materials of human origin are rich source of proteins, carbohydrates, lipids, trace elements as well as water and, thus, provide a virtuous milieu for the growth of microbes. The obstinate microbial growth augments the degradation process and is amplified with the passage of time and improper storage of the biological materials. Degradation of these biological materials carriages a huge challenge in the downstream processes of forensic DNA typing technique, such as short tandem repeats (STR) DNA typing. Microbial degradation yields improper or no PCR amplification, heterozygous peak imbalance, DNA contamination from non-human sources, degradation of DNA by microbial by-products, etc. Consequently, the most precise STR DNA typing technique is nullified and definite opinion can be hardly given with degraded forensic exhibits. Thus, suitable precautionary measures should be taken for proper storage and processing of the biological exhibits to minimize their decaying process by micro-organisms.

The Danish STR sequence database: duplicate typing of 363 Danes with the ForenSeq™ DNA Signature Prep Kit

Some STR loci have internal sequence variations, which are not revealed by the standard STR typing methods used in forensic genetics (PCR and fragment length analysis by capillary electrophoresis (CE)). Typing of STRs with next-generation sequencing (NGS) uncovers the sequence variation in the repeat region and in the flanking regions. In this study, 363 Danish individuals were typed for 56 STRs (26 autosomal STRs, 24 Y-STRs, and 6 X-STRs) using the ForenSeq™ DNA Signature Prep Kit to establish a Danish STR sequence database. Increased allelic diversity was observed in 34 STRs by the PCR-NGS assay. The largest increases were found in DYS389II and D12S391, where the numbers of sequenced alleles were around four times larger than the numbers of alleles determined by repeat length alone. Thirteen SNPs and one InDel were identified in the flanking regions of 12 STRs. Furthermore, 36 single positions and five longer stretches in the STR flanking regions were found to have dubious genotyping quality. The combined match probability of the 26 autosomal STRs was 10,000 times larger using the PCR-NGS assay than by using PCR-CE. The typical paternity indices for trios and duos were 500 and 100 times larger, respectively, than those obtained with PCR-CE. The assay also amplified 94 SNPs selected for human identification. Eleven of these loci were not in Hardy-Weinberg equilibrium in the Danish population, most likely because the minimum threshold for allele calling (30 reads) in the ForenSeq™ Universal Analysis Software was too low and frequent allele dropouts were not detected.

A call for more science in forensic science

Forensic science is critical to the administration of justice. The discipline of forensic science is remarkably complex and includes methodologies ranging from DNA analysis to chemical composition to pattern recognition. Many forensic practices developed under the auspices of law enforcement and were vetted primarily by the legal system rather than being subjected to scientific scrutiny and empirical testing. Beginning in the 1990s, exonerations based on DNA-related methods revealed problems with some forensic disciplines, leading to calls for major reforms. This process generated a National Academy of Science report in 2009 that was highly critical of many forensic practices and eventually led to the establishment of the National Commission for Forensic Science (NCFS) in 2013. The NCFS was a deliberative body that catalyzed communication between nonforensic scientists, forensic scientists, and other stakeholders in the legal community. In 2017, despite continuing problems with forensic science, the Department of Justice terminated the NCFS. Just when forensic science needs the most support, it is getting the least. We urge the larger scientific community to come to the aid of our forensic colleagues by advocating for urgently needed research, testing, and financial support.

Multiple Reaction Monitoring Tandem Mass Spectrometry Approach for the Identification of Biological Fluids at Crime Scene Investigations

Knowledge of the nature of biofluids at a crime scene is just as important as DNA test to link the nature of the biofluid, the criminal act, and the dynamics of the crime. Identification of methods currently used for each biological fluid (blood, semen, saliva, urine) suffer from several limitations including instability of assayed biomolecules, and low selectivity and specificity; as an example of the latter issue, it is not possible to discriminate between alpha-amylase 1 (present in saliva) and alpha-amylase 2 (present in semen and vaginal secretion. In this context, the aim of the work has been to provide a predictive protein signature characteristic of each biofluid by the recognition of specific peptides unique for each protein in a single analysis. A panel of four protein biomarkers for blood, four for saliva, five for semen, and two for urine has been monitored has been monitored by using a single multiple reaction monitoring (MRM)-based method targeting concomitantly 46 different peptides. Then, The optimized method allows four biological matrices to be identified when present on their own or in 50:50 mixture with another biofluid. Finally, a valid strategy combining both DNA analysis and liquid chromatographic-tandem mass spectrometric multiple reaction monitoring (LC-MS-MRM) identification of biofluids on the same sample has been demonstrated to be particularly effective in forensic investigation of real trace evidence collected at a crime scene.

New literacy challenge for the twenty-first century: genetic knowledge is poor even among well educated

We live in an age of rapidly advancing genetic research. This research is generating new knowledge that has implications for personal health and well-being. The present study assessed the level of genetic knowledge and personal engagement with genetics in a large sample (N = 5404) of participants. Participants received secondary education in 78 countries, with the largest samples from Russia, the UK and the USA. The results showed significant group differences in genetic knowledge between different countries, professions, education levels and religious affiliations. Overall, genetic knowledge was poor. The questions were designed to assess basic genetic literacy. However, only 1.2% of participants answered all 18 questions correctly, and the average score was 65.5%. Genetic knowledge was related to peoples’ attitudes towards genetics. For example, those with greater genetic knowledge were on average more willing to use genetic knowledge for their personal health management. Based on the results, the paper proposes a number of immediate steps that societies can implement to empower the public to benefit from ever-advancing genetic knowledge.

Development and Application of Genomic Resources in an Endangered Palaeoendemic Tree, Parrotia subaequalis (Hamamelidaceae) From Eastern China

Parrotia subaequalis is an endangered palaeoendemic tree from disjunct montane sites in eastern China. Due to the lack of effective genomic resources, the genetic diversity and population structure of this endangered species are not clearly understood. In this study, we conducted paired-end shotgun sequencing (2 × 125 bp) of genomic DNA for two individuals of P. subaequalis on the Illumina HiSeq platform. Based on the resulting sequences, we have successfully assembled the complete chloroplast genome of P. subaequalis, as well as identified the polymorphic chloroplast microsatellites (cpSSRs), nuclear microsatellites (nSSRs) and mutational hotspots of chloroplast. Ten polymorphic cpSSR loci and 12 polymorphic nSSR loci were used to genotype 96 individuals of P. subaequalis from six populations to estimate genetic diversity and population structure. Our results revealed that P. subaequalis exhibited abundant genetic diversity (e.g., cpSSRs: Hcp = 0.862; nSSRs: HT = 0.559) and high genetic differentiation (e.g., cpSSRs: RST = 0.652; nSSRs: RST = 0.331), and characterized by a low pollen-to-seed migration ratio (r ≈ 1.78). These genetic patterns are attributable to its long evolutionary histories and low levels of contemporary inter-population gene flow by pollen and seed. In addition, lack of isolation-by-distance pattern and strong population genetic structuring in both marker systems, suggests that long-term isolation and/or habitat fragmentation as well as genetic drift may have also contributed to the geographic differentiation of P. subaequalis. Therefore, long-term habitat protection is the most important methods to prevent further loss of genetic variation and a decrease in effective population size. Furthermore, both cpSSRs and nSSRs revealed that P. subaequalis populations consisted of three genetic clusters, which should be considered as separated conservation units.

Genetic Fingerprinting Using Microsatellite Markers in a Multiplex PCR Reaction: A Compilation of Methodological Approaches from Primer Design to Detection Systems

Microsatellites are polymorphic DNA loci comprising repeated sequence motifs of two to five base pairs which are dispersed throughout the genome. Genotyping of microsatellites is a widely accepted tool for diagnostic and research purposes such as forensic investigations and parentage testing, but also in clinics (e.g. monitoring of bone marrow transplantation), as well as for the agriculture and food industries. The co-amplification of several short tandem repeat (STR) systems in a multiplex reaction with simultaneous detection helps to obtain more information from a DNA sample where its availability may be limited. Here, we introduce and describe this commonly used genotyping technique, providing an overview on available resources on STRs, multiplex design, and analysis.

Origin of the U87MG glioma cell line: Good news and bad news

Human tumor-derived cell lines are indispensable tools for basic and translational oncology. They have an infinite life span and are easy to handle and scalable, and results can be obtained with high reproducibility. However, a tumor-derived cell line may not be authentic to the tumor of origin. Two major questions emerge: Have the identity of the donor and the actual tumor origin of the cell line been accurately determined? To what extent does the cell line reflect the phenotype of the tumor type of origin? The importance of these questions is greatest in translational research. We have examined these questions using genetic profiling and transcriptome analysis in human glioma cell lines. We find that the DNA profile of the widely used glioma cell line U87MG is different from that of the original cells and that it is likely to be a bona fide human glioblastoma cell line of unknown origin.

The future of forensic DNA analysis

The author's thoughts and opinions on where the field of forensic DNA testing is headed for the next decade are provided in the context of where the field has come over the past 30 years. Similar to the Olympic motto of 'faster, higher, stronger', forensic DNA protocols can be expected to become more rapid and sensitive and provide stronger investigative potential. New short tandem repeat (STR) loci have expanded the core set of genetic markers used for human identification in Europe and the USA. Rapid DNA testing is on the verge of enabling new applications. Next-generation sequencing has the potential to provide greater depth of coverage for information on STR alleles. Familial DNA searching has expanded capabilities of DNA databases in parts of the world where it is allowed. Challenges and opportunities that will impact the future of forensic DNA are explored including the need for education and training to improve interpretation of complex DNA profiles.