Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome

Advancements in estimating post-mortem interval in medico-legal practice: A comprehensive review

Estimating the Post-Mortem Interval (PMI) is a crucial aspect of forensic investigations, aiding in the resolution of criminal cases, identifying missing persons, and understanding decomposition processes. This review provides an exhaustive analysis of recent advancements in PMI estimation techniques, encompassing both traditional and emerging methodologies. Included in the study is an exhaustive examination of well-established methodologies, including algor mortis, livor mortis, and rigor mortis, as well as their shortcomings and improvements. It also delves into innovative approaches, including forensic entomology, chemical and molecular biology, microbiology, artificial intelligence, etc. Furthermore, this article discusses the integration of multiple disciplines and the potential of interdisciplinary collaboration to enhance PMI accuracy and reliability. By synthesizing the latest research findings and technological innovations, this review aims to provide forensic practitioners, law enforcement agencies, and medico-legal professionals with a comprehensive understanding of the current state-of-the-art in PMI estimation, facilitating more effective crime scene investigations and judicial proceedings.

A multi-level overview of the hair decomposition process

The process of hair fibre degradation is still not well studied. The first group of decompositional alterations are those caused by an external factor - the action of other organisms or environment. The main groups degrading this biological material include microorganisms such as bacteria, Micromycetes and invertebrates. The mechanism of post-mortem root banding is not well known. It is presumed to be caused by external factors (microorganisms, staining by decaying body), but also internal factors (decomposition of the hair matrix). Other degradative changes described in the literature include the breakdown of proteins (mainly keratin - the main building block of hair), photodegradation, which occurs due to the excitation of melanin radicals and elemental composition during hair decomposition. The aim of this research is to extend and systematise the knowledge of hair decomposition, in particular regarding these degradative changes, and to identify gaps and new directions for research in this field. The publications cited in this study, along with the analyses performed, indicate that hair is a promising biological material with potential applications in various fields, including forensics, archaeology, industry, and ecology. In particular, hair can be valuable for estimating post-mortem interval (PMI), as well as for genetic studies, toxicology, and life history analysis. However, key research gaps remain, notably the lack of comprehensive studies on hair decomposition and the absence of standardized, validated methods that could be widely implemented in forensic laboratories and industry.

Insights into structural and proteomic alterations related to pH-induced changes and protein deamidation in hair

OBJECTIVES

The hair shaft is often exposed to shampoo and haircare products that have unknown or varying pH levels. These products contain a combination of surfactants and other active ingredients to treat the hair or the scalp. As amphoteric proteins, hair keratins have limited buffering capacity, so variations in pH can have multifaceted impacts on them. However, there is limited knowledge about how pH affects keratins and keratin-associated proteins (KAPs). Therefore, this study aims to examine the effects of varying pH levels (pH 3-pH 12) on hair structure and analyse consequent alterations in the hair proteome using mass spectrometry-based proteomics.

METHODS

A scanning electron microscope was used to examine changes in hair-shaft morphology due to exposure to various pH levels, while mass spectrometry was employed to analyse protein alterations.

RESULTS

We found that exposing the hair shaft to varying pH levels led to specific effects on the cuticle, including cuticle lifting at certain pH levels, while proteomics analysis identified alterations in the hair proteome along with significant deamidation of keratins types I and II and KAPs. More pronounced effects were observed at extreme acidic conditions (pH 3) and alkaline conditions (above pH 8) on both hair morphology and hair proteins. pH levels between pH 5 and pH 7 had minimal impact on hair structure and proteins, suggesting that haircare products with pH in this range are ideal for hair-shaft health. In contrast, alkaline pH levels were found to negatively affect hair.

CONCLUSIONS

The structure evaluation and proteomics data emphasize the critical role of pH in hair health. The extreme acidic or alkaline pH impacts the hair structure and hair proteins. The study highlights the optimal pH range for maintaining healthy hair.

Detecting Human Contaminant Genetically Variant Peptides in Nonhuman Samples

During proteomics data analysis, experimental spectra are searched against a user-defined protein database consisting of proteins that are reasonably expected to be present in the sample. Typically, this database contains the proteome of the organism under study concatenated with expected contaminants, such as trypsin and human keratins. However, there are additional contaminants that are not commonly added to the database. In this study, we describe a new set of protein contaminants and provide evidence that they can be detected in mass spectrometry-based proteomics data. Specifically, we provide evidence that human genetically variant peptides (GVPs) can be detected in nonhuman samples. GVPs are peptides that contain single amino acid polymorphisms that result from nonsynonymous single nucleotide polymorphisms in protein-coding regions of DNA. We reanalyzed previously collected nonhuman data-dependent acquisition (DDA) and data-independent acquisition (DIA) data sets and detected between 0 and 135 GVPs per data set. In addition, we show that GVPs are unlikely to originate from nonhuman sources and that a subset of eight GVPs are commonly detected across data sets.

Proteomics of the Dark-Ventral-Patch Sexual Signal in Male Red Deer

Sexual signals in animals encompass a variety of forms including visual, acoustic, and chemical signals that are fundamental for intra- and interspecific communication, including sexual selection processes. Among these, odor signals play a critical role. Chemical compounds involved in sexual signaling vary in nature, with lipids and proteins being particularly important. In the male Iberian red deer (Cervus elaphus hispanicus), the dark ventral patch has been identified as a key sexual signal during mating competition, associated with specific chemical compounds deposited during urination. Hair plays a significant role in this signaling due to its ability to retain compounds on the scales of the hair cuticle. In this study, we used a shotgun proteomic approach to investigate whether the ventral patch hair retains proteins on its surface that could reveal metabolic and cell-signaling adaptations potentially related to reproductive activity. Characterization of the origin and functionality of the proteins found in the hair of the dark ventral patch of male red deer, and their relationship to distinct metabolic pathways, provides an initial understanding of the potential role of these compounds in chemical communication in red deer intrasexual competition for mates.

Proteomic Analysis of Single Hairs

Hair is a ubiquitous and robust mammalian tissue with biological, clinical, forensic, social, and economic significance. The hair shaft proteome reflects both structural proteins, dominated by cuticular intermediate filament keratins and associated proteins, and proteins involved in the final cellular processes of terminally differentiating corneocytes prior to cornification. These distinct biological processes involve cell maintenance, biosynthesis, senescence, and xenobiotic response. Because growth occurs rapidly and predictably, there is also temporal organization. The hair shaft proteome also contains genetic and phylogenetic information in the amino acid sequence. Chemically the shaft is highly robust, the result of a highly structured protein matrix with abundant isopeptide and disulfide intermolecular bonds. Sample processing is therefore a challenge that requires robust chemistries but also minimizes the introduction of additional chemical modifications. This protocol depends on the combination of sodium dodecanoate and high levels of reductant to denature the matrix. The result is a proteome that is both readily accessible and can provide biological information to geneticists, developmental biologists, toxicologists, human and wildlife forensic scientists, scientists in the cosmetics industry, and wildlife ecologists.

Tissue proteomics repositories for data reanalysis

We are approaching the third decade since the establishment of the very first proteomics repositories back in the mid-'00s. New experimental approaches and technologies continuously enrich the field while producing vast amounts of mass spectrometry data. Together with initiatives to establish standard terminology and file formats, proteomics is rapidly transforming into a mature component of systems biology. Here we describe the ProteomeXchange consortium repositories. We specifically search, collect and evaluate public human tissue datasets (categorized as "complete" by the repository) submitted in 2015-2022, to both map the existing information and assess the data set reusability. Human tissue data are variably represented in the repositories reviewed, ranging between 10% and 25% of the total data submitted, with cancers being the most represented, followed by neuronal and cardiovascular diseases. About half of the retrieved data sets were found to lack annotations or metadata necessary to directly replicate the analysis. This poses a rough challenge to data reusability and highlights the need to increase awareness of the mage-tab file format for metadata in the community. Overall, proteomics repositories have evolved greatly over the past 7 years, as they have grown in size and become equipped with various powerful applications and tools that enable data searching and analytical tasks. However, to make the most of this potential, priority must be given to finding ways to secure detailed metadata for each submission, which is likely the next major milestone for proteomics repositories.

From flesh to bones: Multi-omics approaches in forensic science

Recent advancements in omics techniques have revolutionised the study of biological systems, enabling the generation of high-throughput biomolecular data. These innovations have found diverse applications, ranging from personalised medicine to forensic sciences. While the investigation of multiple aspects of cells, tissues or entire organisms through the integration of various omics approaches (such as genomics, epigenomics, metagenomics, transcriptomics, proteomics and metabolomics) has already been established in fields like biomedicine and cancer biology, its full potential in forensic sciences remains only partially explored. In this review, we have presented a comprehensive overview of state-of-the-art analytical platforms employed in omics research, with specific emphasis on their application in the forensic field for the identification of the cadaver and the cause of death. Moreover, we have conducted a critical analysis of the computational integration of omics approaches, and highlighted the latest advancements in employing multi-omics techniques for forensic investigations.

A controlled method for the identification of forensic traces from clandestine grave fill

Deceased human remains are often buried as a forensic countermeasure or method of disposal by homicide perpetrators. Owing to this, the excavation of clandestine grave sites is a task that forensic crime scene teams may only encounter a few times a year. Not all crime scene units have specialised teams for this task, and even those that do, may not have specific protocols for the optimal recovery of forensic traces retained within grave fill as procedures such as sieving require optimisation for the specific soil conditions of the jurisdiction. This study aimed to define the optimal sieving conditions for a sandy environment when searching for minute traces of paint, glass, hair and fibres. Furthermore, this study justifies the practice of retaining grave fill and examining it under controlled laboratory conditions, rather than in-situ adjacent to the grave site. The results demonstrate that using sieve mesh sizes as fine as 0.1 mm can recover up to 82% of the deposited traces and almost all paint, hair and glass traces. The processing of grave fill in the laboratory lead to increased yield of forensic evidence, which on a case-basis may warrant the increased time needed. These findings merit consideration for clandestine grave crime scenes where evidence is scarce or the case is likely to become cold.

Starch treatment improves the salivary proteome for subject identification purposes

Identification of subjects, including perpetrators, is one of the most crucial goals of forensic science. Saliva is among the most common biological fluids found at crime scenes, containing identifiable components. DNA has been the most prominent identifier to date, but its analysis can be complex due to low DNA yields and issues preserving its integrity at the crime scene. Proteins are emerging as viable candidates for subject identification. Previous work has shown that the salivary proteome of the least-abundant proteins may be helpful for subject identification, but more optimized techniques are needed. Among them is removing the most abundant proteins, such as salivary α-amylase. Starch treatment of saliva samples elicited the removal of this enzyme and that of glycosylated, low-molecular-weight proteins, proteases, and immunoglobulins, resulting in a saliva proteome profile enriched with a subset of proteins, allowing a more reliable and nuanced subject identification.

The Importance, Challenges, and Possible Solutions for Sharing Proteomics Data While Safeguarding Individuals' Privacy

Proteomics data sharing has profound benefits at the individual level as well as at the community level. While data sharing has increased over the years, mostly due to journal and funding agency requirements, the reluctance of researchers with regard to data sharing is evident as many shares only the bare minimum dataset required to publish an article. In many cases, proper metadata is missing, essentially making the dataset useless. This behavior can be explained by a lack of incentives, insufficient awareness, or a lack of clarity surrounding ethical issues. Through adequate training at research institutes, researchers can realize the benefits associated with data sharing and can accelerate the norm of data sharing for the field of proteomics, as has been the standard in genomics for decades. In this article, we have put together various repository options available for proteomics data. We have also added pros and cons of those repositories to facilitate researchers in selecting the repository most suitable for their data submission. It is also important to note that a few types of proteomics data have the potential to re-identify an individual in certain scenarios. In such cases, extra caution should be taken to remove any personal identifiers before sharing on public repositories. Data sets that will be useless without personal identifiers need to be shared in a controlled access repository so that only authorized researchers can access the data and personal identifiers are kept safe.

Proteins in scalp hair of preschool children

Background

(1)Early childhood experiences have long-lasting effects on subsequent mental and physical health, education, and employment. Measurement of these effects relies on insensitive behavioral signs, subjective assessments by adult observers, neuroimaging or neurophysiological studies, or retrospective epidemiologic outcomes. Despite intensive search, the underlying mechanisms for these long-term changes in development and health status remain unknown.

Methods

(2)We analyzed scalp hair from healthy children and their mothers using an unbiased proteomics platform using tandem mass spectrometry, ultra-performance liquid chromatography, and collision induced dissociation to reveal commonly observed hair proteins with spectral count of 3 or higher.

Results

(3)We observed 1368 non-structural hair proteins in children, 1438 non-structural hair proteins in mothers, with 1288 proteins showing individual variability. Mothers showed higher numbers of peptide spectral matches and hair proteins compared to children, with important age-related differences between mothers and children. Age-related differences were also observed in children, with differential protein expression patterns between younger (2 years and below) and older children (3-5 years). We observed greater similarity in hair protein patterns between mothers and their biological children as compared to mothers and unrelated children. The top 5% proteins driving population variability represent biological pathways associated with brain development, immune signaling, and stress response regulation.

Conclusion

(4)Non-structural proteins observed in scalp hair include promising biomarkers to investigate the long-term developmental changes and health status associated with early childhood experiences.

Improved Sample Preparation Method for Protein and Peptide Identification from Human Hair

A fast and sensitive direct extraction (DE) method developed in our group can efficiently extract proteins in 30 min from a 5 cm-long hair strand. Previously, we coupled DE to downstream analysis using gel electrophoresis followed by in-gel digestion, which can be time-consuming. In searching for a better alternative, we found that a combination of DE with a bead-based method (SP3) can lead to significant improvements in protein discovery in human hair. Since SP3 is designed for general applications, we optimized it to process hair proteins following DE and compared it to several other in-solution digestion methods. Of particular concern are genetically variant peptides (GVPs), which can be used for human identification in forensic analysis. Here, we demonstrated improved GVP discovery with the DE and SP3 workflow, which was 3 times faster than the previous in-gel digestion method and required significantly less instrument time depending on the number of gel slices processed. Additionally, it led to an increased number of identified proteins and GVPs. Among the tested in-solution digestion methods, DE combined with SP3 showed the highest sequence coverage, with higher abundances of the identified peptides. This provides a significantly enhanced means for identifying proteins and GVPs in human hair.

Genetic landscape of forensic DNA phenotyping markers among Mediterranean populations

Forensic DNA Phenotyping can reveal the appearance of an unknown individual by predicting the External Visible Characteristics (EVC) from DNA obtained at the crime scene. Our aim is to characterize the genetic landscape of Human identification markers responsible for EVC among Mediterranean populations compared to other worldwide groups. We conducted an exhaustive search for genes involved in EVC variation. Then, variants located on these genes were extracted from public genotypic data of Mediterranean, American, African and East Asiatic populations. The genetic landscape of these Human identification markers, their allelic distribution and admixture analyses, were determined using plink, R and ADMIXTURE softwares. Our results showed that the Mediterranean populations appear close to the Mexican populations and distinguished from sub Saharan African populations living in the USA and from East Asiatic populations. We highlighted a total of 103454 common variants shared between the studied populations and among them, 25 common variants associated with EVC. Interestingly, genotype frequencies results showed that the rs17646946, rs13016869, rs977588, rs1805008 and rs2240751 variants located respectively in the TCHH, PRKCE, OCA2, MC1R and MFSD12 genes are significantly different between the Mediterranean and Asiatic populations. The genotype frequencies of the variants rs977589 and rs7179994 located in the OCA2 gene, and of rs12913832 and rs2240751 located respectively in HERC2 and MFSD12 genes are significantly different between the Mediterranean and American populations. Our work generates a large number of EVC variants that could be a valuable resource for future studies in the forensic field.

Recent omics advances in hair aging biology and hair biomarkers analysis

Aging is a complex natural process that leads to a decline in physiological functions, which is visible in signs such as hair graying, thinning, and loss. Although hair graying is characterized by a loss of pigment in the hair shaft, the underlying mechanism of age-associated hair graying is not fully understood. Hair graying and loss can have a significant impact on an individual's self-esteem and self-confidence, potentially leading to mental health problems such as depression and anxiety. Omics technologies, which have applications beyond clinical medicine, have led to the discovery of candidate hair biomarkers and may provide insight into the complex biology of hair aging and identify targets for effective therapies. This review provides an up-to-date overview of recent omics discoveries, including age-associated alterations of proteins and metabolites in the hair shaft and follicle, and highlights the significance of hair aging and graying biomarker discoveries. The decline in hair follicle stem cell activity with aging decreased the regeneration capacity of hair follicles. Cellular senescence, oxidative damage and altered extracellular matrix of hair follicle constituents characterized hair follicle and hair shaft aging and graying. The review attempts to correlate the impact of endogenous and exogenous factors on hair aging. We close by discussing the main challenges and limitations of the field, defining major open questions and offering an outlook for future research.

A human identification system for hair shaft using RNA polymorphism

Hair is one of the common pieces of evidence at crime scenes, with abundant mitochondrial DNA but limited nuclear DNA in its shaft. It also helps to narrow the investigation scope to maternal lineage but fails to provide unique individual information. We assumed that RNA in hair shafts would be an alternative resource used to perform human identification based on the facts that (1) RNA retains the polymorphic information; (2) the multi-copy of RNA in a cell resists degradation as compared to the one-copy of nuclear DNA. In this study, we explored the potential of RNA polymorphism in hair shafts for forensic individual identification. A SNaPshot typing system was constructed using 18 SNPs located on 11 genes (ABCA13, AHNAK, EXPH5, KMT2D, KRT35, PPP1R15A, RBM33, S100A5, TBC1D4, TMC5, TRPV2). The RNA typing system was evaluated for sensitivity, species specificity, and feasibility for aged hair samples. Hair samples from a Shanxi population in China were used for the population study of the system. The detection limit of the assay was 2 ng RNA. The CDP of these 11 genes was 0.999969 in the Shanxi population. We also identified the concordance of the RNA and DNA typing results. In summary, we developed an RNA typing method to perform human identification from hair shafts, which performed as accurately as nuclear DNA typing. Our method provides a potential basis for solving the human identification problem from hair shafts, as well as other biological materials that lack nuclear DNA.

Profiling of hair proteome revealed individual demographics

Human hair is often found at crime scenes, persists for a long time, and is a valuable biological specimen in forensic investigations. Hair contains minimal intact nuclear DNA for the discrimination of individual identity. In such cases, proteomics evaluation of hair proteins could provide an attractive alternative for protein-based human identification. Therefore, this study adopted a proteomic approach to profile hair shafts from both males and females across different ethnic populations including Chinese, Indians, Malays, and Filipinos in their 20-80 s. First, hair proteins were extracted by different methods to adopt the most suitable protocol that produced the highest extraction efficiency based on most significant enrichment of keratins and keratin-associated proteins. Abundance of hair keratins including both types I and II, and keratin-associated proteins, estimated using label-free quantification, showed distinguishable profiles, and the possibilities of distinguishing individuals within each ethnic origin. Similarly, several protein candidates and their abundances could be used to distinguish sex and age of individuals. This study explored the possibility of utilizing hair proteomics phenotyping in forensic science to differentiate individuals across various ethnic groups, sex and age.

Age-Related Changes in Post-Translational Modifications of Proteins from Whole Male and Female Skeletal Elements

One of the key questions in forensic cases relates to some form of age inference, whether this is how old a crime scene is, when in time a particular crime was committed, or how old the victim was at the time of the crime. These age-related estimations are currently achieved through morphological methods with varying degrees of accuracy. As a result, biomolecular approaches are considered of great interest, with the relative abundances of several protein markers already recognized for their potential forensic significance; however, one of the greatest advantages of proteomic investigations over genomics ones is the wide range of post-translational modifications (PTMs) that make for a complex but highly dynamic resource of information. Here, we explore the abundance of several PTMs including the glycosylation, deamidation, and oxidation of several key proteins (collagen, fetuin A, biglycan, serum albumin, fibronectin and osteopontin) as being of potential value to the development of an age estimation tool worthy of further evaluation in forensic contexts. We find that glycosylations lowered into adulthood but deamidation and oxidation increased in the same age range.

Evaluating the discriminating power of amino acid ratios on distinguishing dark colored hair samples

Human hairs are one of the most commonly encountered items of trace evidence. Currently, conventional methods for hair analysis include microscopic comparison and DNA analysis (nuclear and mitochondrial). Each approach has its own drawbacks. Hair proteins are stable and offer an alternative to DNA testing, as demonstrated with proteomics for distinguishing humans. However, proteomics is complicated and requires identifying peptides to remain intact following harsh sample preparation methods. Alternatively, the actual amino acid content of a hair sample may also offer important identifying information and actually requires proteins and peptides to be broken down completely rather than remaining intact. This study evaluated the discriminating power of using hair amino acid ratios to differentiate hair samples from 10 unrelated individuals with dark colored hair. Hair proteins were digested, derivatized, and analyzed using gas chromatography-mass spectrometry. Amino acid ratios were calculated for each individual and comparisons using ANOVA and post-hoc pairwise t-test with Bonferroni correction were made with amino acid ratios for individuals. Overall, out of the 45 possible pairwise comparisons between all hair samples, 38 (84%) were differentiable. Out of the 36 possible pairwise comparisons between brown haired individuals, 32 (89%) were considered differentiable using univariate statistics. Multivariate statistics were also attempted but, overall, univariate models were sufficient for exclusionary purposes. These results indicate that amino acid ratio analysis can potentially be used as an exclusionary method using hair if DNA analysis cannot be performed, or to corroborate conclusions made following microscopic analysis.

DNA and protein analyses of hair in forensic genetics

Hair is one of the most common pieces of biological evidence found at a crime scene and plays an essential role in forensic investigation. Hairs, especially non-follicular hairs, are usually found at various crime scenes, either by natural shedding or by forcible shedding. However, the genetic material in hairs is usually highly degraded, which makes forensic analysis difficult. As a result, the value of hair has not been fully exploited in forensic investigations and trials. In recent years, with advances in molecular biology, forensic analysis of hair has achieved remarkable strides and provided crucial clues in numerous cases. This article reviews recent developments in DNA and protein analysis of hair and attempts to provide a comprehensive solution to improve forensic hair analysis.

Identifying individuals using proteomics: are we there yet?

Multi-omics approaches including proteomics analyses are becoming an integral component of precision medicine. As clinical proteomics studies gain momentum and their sensitivity increases, research on identifying individuals based on their proteomics data is here examined for risks and ethics-related issues. A great deal of work has already been done on this topic for DNA/RNA sequencing data, but it has yet to be widely studied in other omics fields. The current state-of-the-art for the identification of individuals based solely on proteomics data is explained. Protein sequence variation analysis approaches are covered in more detail, including the available analysis workflows and their limitations. We also outline some previous forensic and omics proteomics studies that are relevant for the identification of individuals. Following that, we discuss the risks of patient reidentification using other proteomics data types such as protein expression abundance and post-translational modification (PTM) profiles. In light of the potential identification of individuals through proteomics data, possible legal and ethical implications are becoming increasingly important in the field.

Peptide ancestry informative markers in uterine neoplasms from women of European, African, and Asian ancestry

Characterization of ancestry-linked peptide variants in disease-relevant patient tissues represents a foundational step to connect patient ancestry with disease pathogenesis. Nonsynonymous single-nucleotide polymorphisms encoding missense substitutions within tryptic peptides exhibiting high allele frequencies in European, African, and East Asian populations, termed peptide ancestry informative markers (pAIMs), were prioritized from 1000 genomes. In silico analysis identified that as few as 20 pAIMs can determine ancestry proportions similarly to >260K SNPs (R² = 0.99). Multiplexed proteomic analysis of >100 human endometrial cancer cell lines and uterine leiomyoma tissues combined resulted in the quantitation of 62 pAIMs that correlate with patient race and genotype-confirmed ancestry. Candidates include a D451E substitution in GC vitamin D-binding protein previously associated with altered vitamin D levels in African and European populations. pAIMs will support generalized proteoancestry assessment as well as efforts investigating the impact of ancestry on the human proteome and how this relates to the pathogenesis of uterine neoplasms.

On the Identification of Body Fluids and Tissues: A Crucial Link in the Investigation and Solution of Crime

Body fluid and body tissue identification are important in forensic science as they can provide key evidence in a criminal investigation and may assist the court in reaching conclusions. Establishing a link between identifying the fluid or tissue and the DNA profile adds further weight to this evidence. Many forensic laboratories retain techniques for the identification of biological fluids that have been widely used for some time. More recently, many different biomarkers and technologies have been proposed for identification of body fluids and tissues of forensic relevance some of which are now used in forensic casework. Here, we summarize the role of body fluid/ tissue identification in the evaluation of forensic evidence, describe how such evidence is detected at the crime scene and in the laboratory, elaborate different technologies available to do this, and reflect real life experiences. We explain how, by including this information, crucial links can be made to aid in the investigation and solution of crime.

Alternative LC-MS/MS Platforms and Data Acquisition Strategies for Proteomic Genotyping of Human Hair Shafts

Protein is a major component of all biological evidence. Proteomic genotyping is the use of genetically variant peptides (GVPs) that contain single-amino-acid polymorphisms to infer the genotype of matching nonsynonymous single-nucleotide polymorphisms for the individual from whom the protein sample originated. This can be used to statistically associate an individual to evidence found at a crime scene. The utility of the inferred genotype increases as the detection of GVPs increases, which is the direct result of technology transfer to mass spectrometry platforms typically available. Digests of single (2 cm) human hair shafts from three European and two African subjects were analyzed using data-dependent acquisition on a Q-Exactive Plus Hybrid Quadrupole-Orbitrap system, data-independent acquisition and a variant of parallel reaction monitoring (PRM) on an Orbitrap Fusion Lumos Tribrid system, and multiple reaction monitoring (MRM) on an Agilent 6495 triple quadrupole system. In our hands, average GVP detection from a selected panel of 24 GVPs increased from 6.5 ± 1.1 and 3.1 ± 0.8 using data-dependent and -independent acquisition to 9.5 ± 0.7 and 11.7 ± 1.7 using PRM and MRM (p < 0.05), respectively. PRM resulted in a 1.3-fold increase in detection sensitivity, and MRM resulted in a 1.6-fold increase in detection sensitivity. This increase in biomarker detection has a functional impact on the statistical association of a protein sample and an individual. Increased biomarker sensitivity, using Markov Chain Monte Carlo modeling, produced a median-estimated random match probability of over 1 in 10 trillion from a single hair using targeted proteomics. For PRM and MRM, detected GVPs were validated by the inclusion of stable isotope-labeled peptides in each sample, which served also as a detection trigger. This research accomplishes two aims: the demonstration of utility for alternative analytical platforms in proteomic genotyping and the establishment of validation methods for the evaluation of inferred genotypes.

Elucidation of familial relationships using hair shaft proteomics

This study examines the potential of hair shaft proteomic analysis to delineate genetic relatedness. Proteomic profiling and amino acid sequence analysis provide information for quantitative and statistically-based analysis of individualization and sample similarity. Protein expression levels are a function of cell-specific transcriptional and translational programs. These programs are greatly influenced by an individual's genetic background, and are therefore influenced by familial relatedness as well as ancestry and genetic disease. Proteomic profiles should therefore be more similar among related individuals than unrelated individuals. Likewise, profiles of genetically variant peptides that contain single amino acid polymorphisms, the result of non-synonymous SNP alleles, should behave similarly. The proteomically-inferred SNP alleles should also provide a basis for calculation of combined paternity and sibship indices. We test these hypotheses using matching proteomic and genetic datasets from a family of two adults and four siblings, one of which has a genetic condition that perturbs hair structure and properties. We demonstrate that related individuals, compared to those who are unrelated, have more similar proteomic profiles, profiles of genetically variant peptides and higher combined paternity indices and combined sibship indices. This study builds on previous analyses of hair shaft protein profiling and genetically variant peptide profiles in different real-world scenarios including different human hair shaft body locations and pigmentation status. It also validates the inclusion of proteomic information with other biomolecular substrates in forensic hair shaft analysis, including mitochondrial and nuclear DNA.

Developmental validation of a multiplex proteomic assay for the identification of forensically relevant biological fluids

The aim of this study was to validate a multiplex proteomic assay for the identification of high-specificity protein biomarkers by multiple reaction monitoring mass spectrometry on a triple quadrupole mass spectrometer for the accurate, reliable, and confirmatory identification of bodily fluids commonly encountered in a forensic context. This includes the identification of peripheral blood, semen, saliva, urine, and vaginal/menstrual fluid. The assay is able to efficiently identify pure or mixed stains through the identification of target peptide fragments originating from tissue-specific proteins including: uromodulin from urine; prostatic acid phosphatase, prostate specific antigen and semenogelin-II for semen; statherin, submaxillary gland androgen-regulated protein 3B and amylase for saliva; cornulin, martrigel-induced gene C4 protein, suprabasin and neutrophil gelatinase-associated lipocalin for vaginal/menstrual fluid; and alpha-1 antitrypsin, hemopexin, and hemoglobin subunit beta for peripheral blood. Based on the results of the developmental validation studies which included an assessment of reproducibility and repeatability, sensitivity, species specificity, carryover, mixtures, as well as a series of casework type samples. Only a small selection of case samples was unable to unambiguously identify the target fluid including urine recovered from substrates as well as semen when mixed with personal lubricants. Overall, the mass spectrometry-based workflow offers significant advantages compared to existing serological methods.

Forensic proteomics

Protein is a major component of all biological evidence, often the matrix that embeds other biomolecules such as polynucleotides, lipids, carbohydrates, and small molecules. The proteins in a sample reflect the transcriptional and translational program of the originating cell types. Because of this, proteins can be used to identify body fluids and tissues, as well as convey genetic information in the form of single amino acid polymorphisms, the result of non-synonymous SNPs. This review explores the application and potential of forensic proteomics. The historical role that protein analysis played in the development of forensic science is examined. This review details how innovations in proteomic mass spectrometry have addressed many of the historical limitations of forensic protein science, and how the application of forensic proteomics differs from proteomics in the life sciences. Two more developed applications of forensic proteomics are examined in detail: body fluid and tissue identification, and proteomic genotyping. The review then highlights developing areas of proteomics that have the potential to impact forensic science in the near future: fingermark analysis, species identification, peptide toxicology, proteomic sex estimation, and estimation of post-mortem intervals. Finally, the review highlights some of the newer innovations in proteomics that may drive further development of the field. In addition to potential impact, this review also attempts to evaluate the stage of each application in the development, validation and implementation process. This review is targeted at investigators who are interested in learning about proteomics in a forensic context and expanding the amount of information they can extract from biological evidence.

Proteomics in Forensic Analysis: Applications for Human Samples

Proteomics, the large-scale study of all proteins of an organism or system, is a powerful tool for studying biological systems. It can provide a holistic view of the physiological and biochemical states of given samples through identification and quantification of large numbers of peptides and proteins. In forensic science, proteomics can be used as a confirmatory and orthogonal technique for well-built genomic analyses. Proteomics is highly valuable in cases where nucleic acids are absent or degraded, such as hair and bone samples. It can be used to identify body fluids, ethnic group, gender, individual, and estimate post-mortem interval using bone, muscle, and decomposition fluid samples. Compared to genomic analysis, proteomics can provide a better global picture of a sample. It has been used in forensic science for a wide range of sample types and applications. In this review, we briefly introduce proteomic methods, including sample preparation techniques, data acquisition using liquid chromatography-tandem mass spectrometry, and data analysis using database search, spectral library search, and de novo sequencing. We also summarize recent applications in the past decade of proteomics in forensic science with a special focus on human samples, including hair, bone, body fluids, fingernail, muscle, brain, and fingermark, and address the challenges, considerations, and future developments of forensic proteomics.

Visualizing shed skin cells in fingerprint residue using dark-field microscopy

This proof-of-concept study shows that dark-field microscopy provides sufficient contrast for cell visualization in fingerprints with high sebum content. Although the application is limited to smooth surfaces that do not scatter light, such as polyethylene terephthalate (PET), it was able to measure the number of cells deposited within a fingerprint residue and the reduction in cell transfer with repeated skin contact. On a PET surface, at roughly 5 N of contact force, a typical finger transfers several hundred cells onto the surface. Over subsequent finger contacts onto a clean PET surface, this number decreased exponentially until a steady state was reached, which is characterized by the transfer of (78 ± 36) cells or (0.46 ± 0.21) cells/mm² when normalized for fingerprint area. High uncertainty in cell transfer was due to: the highly variable nature of a human finger (where the number of loose cells varies from person to person and from day to day depending on what they touch) and difficulties in controlling the contact force and finger movement such as twisting during deposition (where twisting of the finger can expose a new patch of skin to the substrate, increasing the number of cell transfer). Plasma etching was also explored as an effective way to validate dark-field microscopy for cell counting. Although limited to inorganic substrates due to etching effects, exposing the fingerprint for less than 10 min can remove a majority of the sebum while keeping the cells intact for a before-and-after comparison using light microscopy.

Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future

Today it is the norm that all relevant proteomics data that support the conclusions in scientific publications are made available in public proteomics data repositories. However, given the increase in the number of clinical proteomics studies, an important emerging topic is the management and dissemination of clinical, and thus potentially sensitive, human proteomics data. Both in the United States and in the European Union, there are legal frameworks protecting the privacy of individuals. Implementing privacy standards for publicly released research data in genomics and transcriptomics has led to processes to control who may access the data, so-called "controlled access" data. In parallel with the technological developments in the field, it is clear that the privacy risks of sharing proteomics data need to be properly assessed and managed. In our view, the proteomics community must be proactive in addressing these issues. Yet a careful balance must be kept. On the one hand, neglecting to address the potential of identifiability in human proteomics data could lead to reputational damage of the field, while on the other hand, erecting barriers to open access to clinical proteomics data will inevitably reduce reuse of proteomics data and could substantially delay critical discoveries in biomedical research. In order to balance these apparently conflicting requirements for data privacy and efficient use and reuse of research efforts through the sharing of clinical proteomics data, development efforts will be needed at different levels including bioinformatics infrastructure, policymaking, and mechanisms of oversight.

Creation of a peptide database of corneous beta-proteins of marine turtles for the identification of tortoiseshell: archaeological combs as case study

Tortoiseshell is a proteinaceous material derived from the scutes of marine turtles, and was shaped into an abundance of objects, especially luxurious items, at its peak in the seventeenth and eighteenth century. It has continued to be used even after the advent of plastics and remains one of the main causes of illegal poaching of marine turtles, in particular the hawksbill turtle Eretmochelys imbricata. Tortoiseshell is made of structural proteins, of which the most abundant are known as β-keratins, or 'corneous beta-proteins' (CBPs), a family of short proteins containing a central structure in β-sheets. There are, however, few CBP sequences of marine turtles in protein databases. The scutes of the five main species of marine turtles (Chelonia mydas, Caretta caretta, Eretmochelys imbricata, Lepidochelys olivacea and Lepidochelys kempii) were analysed by proteomics, using nano-liquid chromatography-Orbitrap-mass spectrometry to generate peptidic markers for species identification. A total of 187 marker sequences were identified, the large majority of them obtained from automated de novo sequencing. The sequences were classified into peptides A to F: A to D at the N-terminus and central region that forms the β-pleated sheets, E1-4 for a variable region of glycine-repeats region and F at the C-terminus. The markers were tested against a set of combs discovered in various archaeological sites of modern period in France, successfully identifying hawksbill turtle and highlighting patterns of degradation in archaeological tortoiseshell.

Ethical Principles, Constraints and Opportunities in Clinical Proteomics

Recent advances in mass spectrometry (MS)-based proteomics have vastly increased the quality and scope of biological information that can be derived from human samples. These advances have rendered current workflows increasingly applicable in biomedical and clinical contexts. As proteomics is poised to take an important role in the clinic, associated ethical responsibilities increase in tandem with impacts on the health, privacy, and wellbeing of individuals. We conducted and here report a systematic literature review of ethical issues in clinical proteomics. We add our perspectives from a background of bioethics, the results of our accompanying paper extracting individual-sensitive results from patient samples, and the literature addressing similar issues in genomics. The spectrum of potential issues ranges from patient re-identification to incidental findings of clinical significance. The latter can be divided into actionable and unactionable findings. Some of these have the potential to be employed in discriminatory or privacy-infringing ways. However, incidental findings may also have great positive potential. A plasma proteome profile, for instance, could inform on the general health or disease status of an individual regardless of the narrow diagnostic question that prompted it. We suggest that early discussion of ethical issues in clinical proteomics can ensure that eventual healthcare practices and regulations reflect the considered judgment of the community and anticipate opportunities and problems that may arise as the technology matures.

Direct seminal fluid identification by protease-free high-resolution mass spectrometry

Serological screening of sexual assault evidence has traditionally focused on enzyme activity and immunochromatographic assays that provide only a presumptive indication of seminal fluid and have limited sensitivity relative to DNA testing. Seminal fluid detection based on protein mass spectrometry represents a "Next Gen" serological technology that overcomes the specificity and sensitivity limitations of traditional serological screening but requires time-consuming sample preparation protocols. This paper describes a novel "peptidomics" approach to seminal fluid detection that eliminates the need for lengthy trypsin digestion. This streamlines sample preparation to a one-step process followed by high-resolution mass spectrometry to identify naturally occurring seminal fluid peptides and low-molecular weight proteins. Multiple protein biomarkers of seminal fluid were consistently and confidently identified based on the multiplexed detection of numerous endogenous peptides. These included Semenogelin I and II (90% and 86% sequence coverage, respectively); Prostate Specific Antigen/p30 (29% sequence coverage); and Prostatic Acid Phosphatase (24% sequence coverage). The performance of this streamlined peptidomics approach to seminal fluid identification in a forensic context was also assessed using simulated casework samples of the type typically collected as part of a sexual assault examination (e.g., oral and vaginal swabs stained with semen). The resulting data demonstrate that sub-microliter quantities of seminal fluid on cotton swabs can be recovered and reliably detected. This supports the forensic applicability of a peptidomic assay for seminal fluid identification with same-day sample preparation and analysis. Future development and streamlined multiplex peptidomic assays for additional biological stains can easily be envisaged.

Untangling the fibre ball: Proteomic characterization of South American camelid hair fibres by untargeted multivariate analysis and molecular networking

The proteomic analysis of hairs, yarns or textiles has emerged as a powerful method to determine species of origin, mainly used in archaeozoological research and fraud control. Differentiation between the South American camelid (SAC) species (the wild guanaco and vicuña and their respective domesticates the llama and alpaca) is particularly challenging due to poor database information and significant hybridization between species. In this study, we analysed 41 modern and 4 archaeological samples from the four SACs species. Despite strong similarities with Old World Camelidae, we identified 7 peptides specific to SACs assigned to keratin K86 and the keratin-associated proteins KAP13-1 and KAP11-1. Untargeted multivariate analysis of the LC-MS data permitted to distinguish SAC species and propose discriminant features. MS/MS-based molecular networking combined with database-assisted de novo sequencing permitted to identify 5 new taxonomic peptides assigned to K33a, K81 and/or K83 keratins and KAP19-1. These peptides differentiate the two wild species, guanaco and vicuña. These results show the value of combining database search and untargeted metabolomic approaches for paleoproteomics, and reveal for the first time the potential of molecular networks to highlight deamidation related to diagenesis and cluster highly similar peptides related to interchain homologies or intra- or inter-specific polymorphism. SIGNIFICANCE: This study used an innovative approach combining multivariate analysis of LC-MS data together with molecular networking and database-assisted de novo sequencing to identify taxonomic peptides in palaeoproteomics. It constitutes the first attempt to differentiate between hair fibres from the four South American camelids (SACs) based on proteomic analysis of modern and archaeological samples. It provides different proteomic signatures for each of the four SAC species and proposes new SAC taxonomic peptides of interest in archaeozoology and fraud control. SACs have been extensively exploited since human colonization of South America but have not been studied to the extent of their economic, cultural and heritage importance. Applied to the analysis of ancient Andean textiles, our results should permit a better understanding of cultural and pastoral practices in South America. The wild SACs are endangered by poaching and black-market sale of their fibre. For the first time, our results provide discriminant features for the determination of species of origin of contraband fibre.

Differentiation of Morphologically Similar Human Head Hairs from Two Demographically Similar Individuals Using Amino Acid Ratios

Human hair is frequently encountered as forensic evidence and can contribute valuable information to investigators. Conventional forensic hair analyses include microscopic hair comparison (MHC) and DNA analysis. However, MHC is not supported by statistics and DNA analysis cannot always be performed. Recent studies have demonstrated that evaluation of differences in the hair proteins may offer an alternate method to these analyses. In this study, an evaluation of the amino acids present in hair was investigated as an approach to differentiate morphologically indistinguishable hair samples from two demographically similar individuals. Proteins in the hair were digested using hydrochloric acid, and the resulting amino acids were derivatized with N,O-Bis(trimethylsilyl)trifluoroacetamide (BSTFA) for analysis using gas chromatography-mass spectrometry (GC-MS). Eight derivatized amino acids were detected and quantified relative to an internal standard, L-norvaline, and used to construct twenty-eight amino acid ratios. Hair samples were collected from four areas of the head on various days over the course of one month, and no significant differences in amino acid ratios (p-value > 0.05) were observed among the areas of the head, and the ratios were consistent over the time period of this study. Additionally, fifteen of these amino acid ratios were found to be significantly different between the two individuals when compared using a two-sample t-test (p-value ≤ 0.05). These data indicate that amino acid analysis was able to differentiate two morphologically similar hair samples from different individuals and demonstrates the applicability of this method to distinguish similar hair samples when DNA analysis cannot be performed.

Fractionation of DNA and protein from individual latent fingerprints for forensic analysis

Human touch samples represent a significant portion of forensic DNA casework. Yet, the generally low abundance of genetic material combined with the predominantly extracellular nature of DNA in these samples makes DNA-based forensic analysis exceptionally challenging. Human proteins present in these same touch samples offer an abundant and environmentally-robust alternative. Proteogenomic methods, using protein sequence variants arising from nonsynonymous DNA mutations, have recently been applied to forensic analysis and may represent a viable option looking forward. However, DNA analysis remains the gold standard and any proteomics-based methods would need to consider how DNA could be co-extracted from samples without significant loss. Herein, we describe a simple workflow for the collection, enrichment and fractionation of DNA and protein in latent fingerprint samples. This approach ensures that DNA collected from a latent fingerprint can be analyzed by traditional DNA casework methods, while protein can be proteolytically digested and analyzed via standard liquid chromatography-tandem mass spectrometry-based proteomics methods from the same touch sample. Sample collection from non-porous surfaces (i.e., glass) is performed through the application of an anionic surfactant over the fingermark. The sample is then split into separate DNA and protein fractions following centrifugation to enrich the protein fraction by pelleting skin cells. The results indicate that this workflow permits analysis of DNA within the sample, yet highlights the challenge posed by the trace nature of DNA in touch samples and the potential for DNA to degrade over time. Protein deposited in touch samples does not appear to share this limitation, with robust protein quantities collected across multiple human donors. The quantity and quality of protein remains robust regardless of fingerprint age. The proteomic content of these samples is consistent across individual donors and fingerprint age, supporting the future application of genetically variable peptide (GVP) analysis of touch samples for forensic identification.

Assessing Single-Source Reproducibility of Human Head Hair Peptide Profiling from Different Regions of the Scalp

Neither microscopical hair comparisons nor mitochondrial DNA sequencing alone, or together, constitutes a basis for personal identification. Due to these limitations, a complementary technique to compare questioned and known hair shafts was investigated. Recently, scientists from Lawrence Livermore National Laboratory's Forensic Science Center and other collaborators developed a peptide profiling technique, which can infer non-synonymous single nucleotide polymorphisms (SNPs) preserved in hair shaft proteins as single amino acid polymorphisms (SAPs). In this study, peptide profiling was evaluated to determine if it can meet forensic expectations when samples are in limited quantities with the possibility that hair samples collected from different areas of a single donor's scalp (i.e., single source) might not exhibit the same SAP profile. The average dissimilarity, percent differences in SAP profiles within each source, ranged from 0% difference to 29%. This pilot study suggests that more work is needed before peptide profiling of hair can be considered for forensic comparisons.

Microscopical discrimination of human head hairs sharing a mitochondrial haplogroup

In forensic analyses, determining the level of consensus among examiners for hair comparison conclusions and ancestry identifications is important for assessing the scientific validity of microscopical hair examinations. Here, we present data from an interlaboratory study on the accuracy of microscopical hair comparisons among a subset of experienced hair examiners currently analyzing hair in forensic laboratories across the United States. We examined how well microscopical analysis of hair can reliably be used to differentiate hair samples, many of which were macroscopically similar. Using cut hair samples, many sharing similar macroscopic and microscopic features, collected from individuals who share the same mitochondrial haplogroup as an indication of genetic relatedness, we tested multiple aspects that could impact hair comparisons. This research tested the extent to which morphological features related to ancestry and hair length influence conclusions. Microscopical hair examinations yielded accurate assessments of inclusion/exclusion relative to the reference samples among 85% of the pairwise comparisons. We found shorter hairs had reduced levels of accuracy and hairs from populations examiners were not familiar with may have impacted their ability to resolve features. The reliability of ancestry determinations is not yet clear, but we found indications that the existing categories are only somewhat related to current ethnic and genetic variation. Our results provide support for the continued utility of microscopical comparison of hairs within forensic laboratories and to advocate for a combined analytical approach using both microscopical analysis and mtDNA data on all forensic analyses of hair.

Mass Spectrometric (MS) Analysis of Proteins and Peptides

The human genome is sequenced and comprised of ~30,000 genes, making humans just a little bit more complicated than worms or flies. However, complexity of humans is given by proteins that these genes code for because one gene can produce many proteins mostly through alternative splicing and tissue-dependent expression of particular proteins. In addition, post-translational modifications (PTMs) in proteins greatly increase the number of gene products or protein isoforms. Furthermore, stable and transient interactions between proteins, protein isoforms/proteoforms and PTM-ed proteins (protein-protein interactions, PPI) add yet another level of complexity in humans and other organisms. In the past, all of these proteins were analyzed one at the time. Currently, they are analyzed by a less tedious method: mass spectrometry (MS) for two reasons: 1) because of the complexity of proteins, protein PTMs and PPIs and 2) because MS is the only method that can keep up with such a complex array of features. Here, we discuss the applications of mass spectrometry in protein analysis.

MinProtMaxVP: Generating a minimized number of protein variant sequences containing all possible variant peptides for proteogenomic analysis

Identifying single-amino-acid variants (SAVs) from mass spectrometry-based experiments is critical for validating single-nucleotide variants (SNVs) at the protein level to facilitate biomedical research. Currently, two approaches are usually applied to convert SNV annotations into SAV-harboring protein sequences. One approach generates one sequence containing exactly one SAV, and the other all SAVs. However, they may neglect the possibility of SAV combinations, e.g., haplotypes, existing in bio-samples. Therefore, it is necessary to consider all SAV combinations of a protein when generating SAV-harboring protein sequences. In this paper, we propose MinProtMaxVP, a novel approach which selects a minimized number of SAV-harboring protein sequences generated from the exhaustive approach, while still accommodating all possible variant peptides, by solving a classic set covering problem. Our study on known haplotype variations of TAS2R38 justifies the necessity for MinProtMaxVP to consider all combinations of SAVs. The performance of MinProtMaxVP is demonstrated by an in silico study on OR2T27 with five SAVs and real experimental data of the HEK293 cell line. Furthermore, assuming simulated somatic and germline variants of OR2T27 in tumor and normal tissues demonstrates that when adopting the appropriate somatic and germline SAV integration strategy, MinProtMaxVP is adaptable to labeling and label-free mass spectrometry-based experiments. SIGNIFICANCE: We present MinProtMaxVP, a novel approach to generate SAV-harboring protein sequences for constructing a customized protein sequence database, which is used in database searching for variant peptide identification. This approach outperforms the existing approaches in generating all possible variant peptides to be included in protein sequences and possibly leading to identification of more variant peptides in proteogenomic analysis.

Age-Related Changes in Hair Shaft Protein Profiling and Genetically Variant Peptides

Recent reports highlight possible improvements in individual identification using proteomic information from human hair evidence. These reports have stimulated investigation of parameters that affect the utility of proteomic information. In addition to variables already studied relating to processing technique and anatomic origin of hair shafts, an important variable is hair ageing. Present work focuses on the effect of age on protein profiling and analysis of genetically variant peptides (GVPs). Hair protein profiles may be affected by developmental and physiological changes with age of the donor, exposure to different environmental conditions and intrinsic processes, including during storage. First, to explore whether general trends were evident in the population at different ages, hair samples were analyzed from groups of different subjects in their 20's, 40's and 60's. No significant differences were seen as a function of age, but consistent differences were evident between European American and African American hair profiles. Second, samples collected from single individuals at different ages were analyzed. Mostly, these showed few protein expression level differences over periods of 10 years or less, but samples from subjects at 44 and 65 year intervals were distinctly different in profile. The results indicate that use of protein profiling for personal identification, if practical, would be limited to decadal time intervals. Moreover, batch effects were clearly evident in samples processed by different staff. To investigate the contribution of storage (at room temperature) in affecting the outcomes, the same proteomic digests were analyzed for GVPs. In samples stored over 10 years, GVPs were reduced in number in parallel with the yield of identified proteins and unique peptides. However, a very different picture emerged with respect to personal identification. Numbers of GVPs sufficed to distinguish individuals despite the age differences of the samples. As a practical matter, three hair samples per person provided nearly the maximal number obtained from 5 or 6 samples. The random match probability (where the log increased in proportion to the number of GVPs) reached as high as 1 in 10⁸. The data indicate that GVP results are dependent on the single nucleotide polymorphism profile of the donor genome, where environmental/processing factors affect only the yield, and thus are consistent despite the ages of the donors and samples and batchwise effects in processing. This conclusion is critical for application to casework where the samples may be in storage for long periods and used to match samples recently collected.