DNA Phenotyping Research Articles

Developing legal regulation of forensic DNA-phenotyping in Hungary

Traditional DNA forensics uses short tandem repeats (STRs) to match a DNA sample to a suspect or a database. However, when no suspect has been identified and there is a lack of database hits, these markers cannot help the investigators to solve a crime. A considerable amount of literature has been published on DNA phenotyping in the past few years. Not surprisingly, some ethical and legal aspects are needed to be discussed about FDP since this technology provides a greater number of details about the proprietary ownership of samples, their family members, even as about their larger community (ethnical group).

Evaluation of the HIrisPlex-S system in a Brazilian population sample

The main goal of DNA phenotyping is to predict externally visible characteristics (EVCs) of an individual using only its genetic information. Nowadays, the HIrisPlex-S system stands as a reliable model designed for skin color prediction. However, prediction of skin color phenotypes has not been thoroughly tested in recently admixed populations, so it is important to evaluate the applicability of this tool in these populations. This study aims to analyze the HIrisPlex-S system accuracy in an admixed sample of 276 individuals from the region of Ribeirão Preto city in Southeastern Brazil. Predictive markers were directly genotyped by Next-Generation Sequencing (NGS), Infinium Multi-Ethnic Global-8 (MEGA) Kit Array (Illumina), or imputed using the IMPUTE2 software. Skin color predictions were performed using the HIrisPlex-S online tool. Our report shows that, except for dark to black color, the tool consistently fails in determining skin phenotypes. Therefore, results reveal that the HIrisPlex-S System is less reliable when dealing with admixed population samples, not supporting its utility for forensic casework in Brazil.

Perception of blue and brown eye colours for forensic DNA phenotyping

Eye colour is a prominent visible trait in Europeans and is of significance in forensic genetics. Eye colour is most commonly categorised in a three-category system comprising brown, intermediate, and blue eye colours. However, the general perception of eye colour categories has not been explored. Here, we categorised eye colour based on the subjective evaluation of 442 digital close-up photos of eyes assessed by 30 Danish volunteers. The participants were asked to categorise each eye in a three-category (brown, intermediate, blue) and a two-category (brown, blue) system. We found that the two-category system corresponded best with the perception of eye colour. Disagreements in the eye colour categorisation by at least 10% of the participants were observed for 33% of the eye pictures using the three-category system. In comparison, only 10% of the pictures were categorised differently by at least 10% of participants when using the two-category system. The genetic basis for distinction between blue and brown eye colour primarily depends on a single SNP, rs12913832. Likelihood ratios based on the genotype of rs12913832 and the two-category system were: LR = P(rs12913832:GG|brown)/P(rs12913832:GG|blue) = 0.1, LR = P(rs12913832:AA|brown)/P(rs12913832:AA|blue) = 54, and LR = P(rs12913832:GA|brown)/P(rs12913832:GA|blue) = 19. This SNP is included in the Precision ID Ancestry panel used for ancestry inference, which enables genetic ancestry profiles to be accompanied by prediction of blue or brown eye colour.

Development of a forensic DNA phenotyping panel using massive parallel sequencing

The HIrisPlex-S system, targeting a total of 41 SNPs, allows the simultaneous eye, hair and skin color prediction from DNA. In the present study, we developed a massive parallel sequencing (MPS) multiplex assay in order to genotype all the HIrisPlex-S markers in degraded casework samples. PCR amplicons sizes of target regions were kept below 180 bp, in order to allow analysis of degraded DNA samples. Individuals with known phenotype, artificially degraded DNA samples and a set of 2800M control DNA dilutions were sequenced on a Ion PGM System, in order to evaluate the concordance testing results and the forensic suitability of this 41-plex MPS assay. Full and reliable profiles could be obtained with 0.1 ng of input DNA. The increment of the number of PCR cycles results in improvement of sensitivity or in typing results but an increase of artifacts were also observed.

Evaluation of skin-related variants in African ancestry populations and their role in personal identification

Pigment-related genetic variants point out their role in personal identification as they can be considered predictors suitable for Forensic DNA Phenotyping (FDP) and mounting evidence suggest also their bio-geographic inferential power for gaining information about the individual geographical origin. As they could be regarded as AIMs (Ancestry Informative Markers) they are powerful tools for inferring genetic composition of admixed population. Despite the huge range of skin tones across our species, little is known about genetic basis in global population and particularly our knowledge is less precise for those showing a complex historical and genomic background. The current research aims to explore the allelic status in several SNPs mapped in selected genes known to be involved in skin pigmentation: OCA2, HERC2, SLC45A2, SLC24A5 and two intergenic regions between BEND7/PRPF18 and EIF2S2/ASIP. The genetic evaluation has been performed on selected African and African derived populations: Fon, Dendi, Bariba and Berba communities from Benin, and Afroecuadorians. Data integration has been made up merging genotypic results with available information from major biological data warehouse as Phase 3–1000 Genomes Project or International HapMap Project in order to obtain a selected populations panel useful for their use as inferential model training set to test the likelihood of correct assignment to geographically differentiated human groups. The proposed variants panel seems to properly interpret the geographic variation and some new interesting evidence could be pointed out in African mixed populations, that seem to be differentially distributed if the total panel is considered. Understanding human pigmentation architecture can provide fundamental insight into genetic interaction of complex traits and the relationship between environmental adaptation and population history. In addition, the results support the use of phenotypic inference along with bio-geographical ancestry information as valid auxiliary tools in personal identification.

What makes your “eyes” look different?

Facial morphology is the most distinguishable appearance and represents a promising subfield of Forensic DNA phenotyping. Located in the center of the face, eyes are important for facial recognition. In this study, epicanthal fold and palpebral fissure were selected for a preliminary genotype-phenotype analysis. Two SNPs were genotyped with SNaPshot method in 156 Chinese Han adults. A significant increased incidence of high ratio of palpebral fissure width to height was observed in the populations with AG genotype for SNP rs2074612 on gene HBEGF: AG versus GG, OR = 2.36, 95%CI = 1.08–5.18, p <0.05; AG versus GG/AA, OR = 2.07, 95%CI = 1.03–4.16, p < 0.05. No significant genotype difference was detected between epicanthal fold positive/negative populations for both SNPs (p > 0.05). Further study including more samples should be conducted to discover SNPs associated with epicanthal fold and palpebral fissure traits.

Civil society stakeholder views on forensic DNA phenotyping: Balancing risks and benefits

Forensic DNA phenotyping (FDP) is an umbrella term for practices seeking to infer likely phenotypic characteristics based on crime scene DNA. Specifically, it is intended to help criminal investigators find an unknown suspected perpetrator by providing information about what the suspected perpetrator may look like based on the analysis of DNA left at the crime scene. While many purport the usefulness of FDP in this regard, its probabilistic nature, as well as its ability to disclose information about an individual that may be considered private raises a range of ethical and social concerns. This paper reports findings from interviews with thirty civil society stakeholders across nine European countries. Our findings reflect the wide variation of views in Europe regarding if, when and/or how the technology should be used in the criminal justice system, and we illustrate this by presenting the different ways in which our participants strike a balance between the potential usefulness of the technology, and the various ethical and social considerations.

HIrisPlex-S system for eye, hair, and skin color prediction from DNA: Massively parallel sequencing solutions for two common forensically used platforms

Forensic DNA Phenotyping (FDP) provides the ability to predict externally visible characteristics from minute amounts of crime scene DNA, which can help find unknown perpetrators who are typically unidentifiable via conventional forensic DNA profiling. Fundamental human genetics research has led to a better understanding of the specific DNA variants responsible for physical appearance characteristics, particularly eye, hair, and skin color. Recently, we introduced the HIrisPlex-S system for the simultaneous prediction of eye, hair, and skin color based on 41 DNA variants generated from two forensically validated SNaPshot multiplex assays using capillary electrophoresis (CE). Here we introduce massively parallel sequencing (MPS) solutions for the HIrisPlex-S (HPS) system on two MPS platforms commonly used in forensics, Ion Torrent and MiSeq, that cover all 41 DNA variants in a single assay, respectively. Additionally, we present the forensic developmental validation of the two HPS-MPS assays. The Ion Torrent MPS assay, based on Ion AmpliSeq technology, illustrated the successful generation of full HIrisPlex-S genotypic profiles from 100 pg of input control DNA, while the MiSeq MPS assay based on an in-house design yielded complete profiles from 250 pg of input DNA. Assessing simulated forensic casework samples such as saliva, hair (bulb), blood, semen, and low quantity touch DNA, as well as artificially damaged DNA samples, concordance testing, and samples from numerous species, all illustrated the ability of both versions of the HIrisPlex-S MPS assay to produce results that motivate forensic applications. By also providing an integrated bioinformatics analysis pipeline, MPS data can now be analyzed and a file generated for upload to the publically accessible HIrisPlex online webtool (https://hirisplex.erasmusmc.nl). In addition, we updated the website to accept VCF input data for those with genome sequence data. We thus provide a user-friendly and semi-automated MPS workflow from DNA sample to individual eye, hair, and skin color prediction probabilities. Furthermore, we present a 2-person mixture separation tool that not only assesses genotype reliability with regards genotyping confidence but also provides the most fitting mixture scenario for both minor and major contributors, including profile separation. We envision this MPS implementation of the HIrisPlex-S system for eye, hair, and skin color prediction from DNA as a starting point for further expanding MPS-based forensic DNA phenotyping. This may include the future addition of SNPs predictive for more externally visible characteristics, as well as SNPs for bio-geographic ancestry inference, provided the statistical framework for DNA prediction of these traits is in place.

The visibilities and invisibilities of race entangled with forensic DNA phenotyping technology

Forensic DNA phenotyping (FDP) technology represents a set of techniques that aim to predict physical features of criminal suspects, such as eye, skin and hair colour, and also ethnicity through the inference of biogeographic ancestry from their biological samples. In contrast to other forensic technologies, FDP is not used for identification purposes but valued for its potential intelligence value. Since features predicted by FDP relate to common traits shared by different population groups, critical voices highlight that this technology may (re)create dynamics of collectivisation of suspect populations.Looking at the criminal justice system, this paper aims to explore the diverse understandings of FDP by professionals working in forensic laboratories and by the members of police forces, alongside the automatic exchange of genetic profiles to fight cross-border crime. Their perceptions are explored according to the perceived potential investigative value and potential threats of FDP. Furthermore, we discuss how racial issues are implicitly and explicitly present in these narratives. Results show that FDP may be ushering in a new assemblage of racial issues along three entangled dimensions: the differentiating power of externally visible characteristics, the comparison between genetic and eyewitness testimonies, and the collectivisation of suspicion.

DNA-based predictive models for the presence of freckles

Freckles or ephelides are hyperpigmented spots observed on skin surface mainly in European and Asian populations. Easy recognition and external visibility make prediction of ephelides, the potentially useful target in the field of forensic DNA phenotyping. Prediction of freckles would be a step forward in sketching the physical appearance of unknown perpetrators or decomposed cadavers for the forensic DNA intelligence purposes. Freckles are especially common in people with pale skin and red hair and therefore it is expected that predisposition to freckles may partially share the genetic background with other pigmentation traits. The first proposed freckle prediction model was developed based on investigation that involved variation of MC1R and 8 SNPs from 7 genes in a Spanish cohort [19]. In this study we examined 113 DNA variants from 46 genes previously associated with human pigmentation traits and assessed their impact on freckles presence in a group of 960 individuals from Poland. Nineteen DNA variants revealed associations with the freckle phenotype and the study also revealed that females have ∼1.8 higher odds of freckles presence comparing to males (p-value = 9.5 × 10−5). Two alternative prediction models were developed using regression methods. A simplified binomial 12-variable model predicts the presence of ephelides with cross-validated AUC = 0.752. A multinomial 14-variable model predicts one of three categories – non-freckled, medium freckled and heavily freckled. The two extreme categories, non-freckled and heavily freckled were predicted with moderately high accuracy of cross-validated AUC = 0.754 and 0.792, respectively. Prediction accuracy of the intermediate category was lower, AUC = 0.657. The study presents novel DNA models for prediction of freckles that can be used in forensic investigations and emphasizes significance of pigmentation genes and sex in predictive DNA analysis of freckles.

Shifting Ethical Boundaries in Forensic Use of DNA

Abstract In this paper we explore shifts in how the law and ethics allow European law enforcement officers to use forensic genetic technologies. We do so by reviewing three technologies, ‘traditional’ (STR-based) forensic DNA profiling, forensic DNA phenotyping and the searching of genetic genealogy databases. In particular, we discuss changes in how ethical boundaries have been placed around what is seen as an appropriate use of genetic technologies in European criminal justice systems. While the ‘type’ of DNA that law enforcement officers are permitted to analyse offers a useful ethical reference point, for newer forensic genomic technologies, ethical scrutiny, we argue, would also look at the specific purpose or use of the technology.

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.

Update on the predictability of tall stature from DNA markers in Europeans

Predicting adult height from DNA has important implications in forensic DNA phenotyping. In 2014, we introduced a prediction model consisting of 180 height-associated SNPs based on data from 10,361 Northwestern Europeans enriched with tall individuals (770 > 1.88 standard deviation), which yielded a mid-ranged accuracy (AUC = 0.75 for binary prediction of tall stature and R2 = 0.12 for quantitative prediction of adult height). Here, we provide an update on DNA-based height predictability considering an enlarged list of subsequently-published height-associated SNPs using data from the same set of 10,361 Europeans. A prediction model based on the full set of 689 SNPs showed an improved accuracy relative to previous models for both tall stature (AUC = 0.79) and quantitative height (R2 = 0.21). A feature selection analysis revealed a subset of 412 most informative SNPs while the corresponding prediction model retained most of the accuracy (AUC = 0.76 and R2 = 0.19) achieved with the full model. Over all, our study empirically exemplifies that the accuracy for predicting human appearance phenotypes with very complex underlying genetic architectures, such as adult height, can be improved by increasing the number of phenotype-associated DNA variants. Our work also demonstrates that a careful sub-selection allows for a considerable reduction of the number of DNA predictors that achieve similar prediction accuracy as provided by the full set. This is forensically relevant due to restrictions in the number of SNPs simultaneously analyzable with forensically suitable DNA technologies in the current days of targeted massively parallel sequencing in forensic genetics.

Prediction of skin color, tanning and freckling from DNA in Polish population: linear regression, random forest and neural network approaches

Predicting phenotypes from DNA has recently become extensively studied field in forensic research and is referred to as Forensic DNA Phenotyping. Systems based on single nucleotide polymorphisms for accurate prediction of iris, hair and skin color in global population, independent of bio-geographical ancestry, have recently been introduced. Here, we analyzed 14 SNPs for distinct skin pigmentation traits in a homogeneous cohort of 222 Polish subjects. We compared three different algorithms: General Linear Model based on logistic regression, Random Forest and Neural Network in 18 developed prediction models. We demonstrate Random Forest to be the most accurate algorithm for 3- and 4-category estimations (total of 58.3% correct calls for skin color prediction, 47.2% for tanning prediction, 50% for freckling prediction). Binomial Logistic Regression was the best approach in 2-category estimations (total of 69.4% correct calls, AUC = 0.673 for tanning prediction; total of 52.8% correct calls, AUC = 0.537 for freckling prediction). Our study confirms the association of rs12913832 (HERC2) with all three skin pigmentation traits, but also variants associated solely with certain pigmentation traits, namely rs6058017 and rs4911414 (ASIP) with skin sensitivity to sun and tanning abilities, rs12203592 (IRF4) with freckling and rs4778241 and rs4778138 (OCA2) with skin color and tanning. Finally, we assessed significant differences in allele frequencies in comparison with CEU data and our study provides a starting point for the development of prediction models for homogeneous populations with less internal differentiation than in the global predictive testing.

Performance of four models for eye color prediction in an Italian population sample

Forensic DNA phenotyping (FDP) has recently provided important advancements in forensic investigations, by predicting the physical appearance of a subject from a biological sample, using SNP markers. The majority of operable prediction models have been developed for iris color; however, replication studies to understand their applicability on a worldwide scale are still limited for many of them.In this work, 4 models for eye color prediction (IrisPlex, Ruiz, Allwood and Hart models) were systematically evaluated in a sample of 296 subjects of Italian origin. Genotypes were determined by a custom NGS-based panel targeting all the predictive SNPs included in the 4 tested models.Overall, 60–69% of the Italian sample could be correctly predicted with the IrisPlex, Ruiz and Allwood models, applying the recommended threshold. The IrisPlex model showed the lowest frequency of errors (17%), but also the highest number of inconclusive results (18%). In the absence of the threshold, the highest proportion of correct predictions was again obtained with the IrisPlex model (76%), followed by the Allwood (73%) and the Ruiz (65%) models. Lastly, the Hart predictive algorithm had the lowest error rate (2%), but the majority of predictions (87%) were restricted to the less informative categories of “not-blue” and “not-brown”, and correct color predictions were obtained only for 11% of the sample.As observed in previous studies, the majority of incorrect and undefined predictions were ascribable to the intermediate category, which represented 25% of the Italian sample. An adjustment of the IrisPlex (multinomial logistic regression) and Ruiz models (Snipper Bayesian classifier) with Italian allele frequencies gave only minor improvements in predicting intermediate eye color and no remarkable overall changes in performance. This suggests an incomplete knowledge underlying the intermediate colors. Considering the impact of this phenotype in the Italian sample as well as in other admixed populations, future improvements of eye color prediction methods should include a better genetic and phenotypic characterization of this category.

&lt;p&gt;DNA phenotyping: current application in forensic science&lt;/p&gt;

&lt;p&gt;DNA phenotyping: current application in forensic science&lt;/p&gt;

A law enforcement intelligence framework for use in predictive DNA phenotyping

ABSTRACTAnalysis of information about physical characteristics, biogeographical ancestry or common genetic ancestors from crime scene DNA is a technique aimed at informing an intelligence process, rather than obtaining evidence for a criminal trial. This intelligence supports tactical or operational decision-making. Like other forms of intelligence there is a risk for it to be misconstrued or for its investigative value to be misunderstood. The potential for intelligence derived from DNA to divert investigative resources or result in unnecessary intrusions into individual privacy can be mitigated by applying an appropriate intelligence doctrine. Establishing an appropriate framework could reduce the need for government regulation of these emerging capabilities in the context of law enforcement use.

Del perfil al retrato genético: dependencia de trayectoria en las tecnologías del ADN

Este artículo busca mostrar la pertinencia de la historia para explicar el desarrollo de las tecnologías del adn forense y la estandarización de su uso en el ámbito judicial. Nuestra descripción de la trayectoria que ha seguido el perfil genético y de las tareas epistémicas que se le han asignado desde 1984 hasta el presente, nos permite caracterizarlo como una entidad histórica, que posee dependencia de trayectoria. Ofrecemos también una reflexión sobre el lugar que ocupa la novedosa técnica del fenotipado a partir de adn en esta trayectoria. Al enfatizar la relevancia de la contingencia en las trayectorias del adn forense tomamos posición respecto de la relación entre la historia y la filosofía de la ciencia, pues su inclusión como un recurso explicativo de los desarrollos tecno-científicos implica reconocer que se tratan de procesos dinámicos en los que las secuencias de sucesos están causalmente relacionadas.

Forensic DNA phenotyping: the geneticist's guide to solving murder mysteries

The Science Communication Competition is now in its eighth year. As in previous years, it aims to find young talented science writers and give them the opportunity to have their work published in The Biochemist. In 2015, a new branch of the competition was launched to include video entries. Overall this year's competition attracted 47 entries and these were reviewed by our external panel of expert judges. The third prize in the written category was awarded to Corina Lagewaard from the University of Tasmania, whose article is presented here. The third prize in the video category went to Julia Schulz from the University of Kentucky. Julia's video, “The BloodBrain Barrier – Protecting the Body's Control Center”, can be viewed at bit.ly/scicomm32018.

Forensic DNA phenotyping in Europe: views “on the ground” from those who have a professional stake in the technology

Forensic DNA phenotyping (FDP) is an emerging technology that seeks to make probabilistic inferences regarding a person’s observable characteristics (“phenotype”) from DNA. The aim is to aid criminal investigations by helping to identify unknown suspected perpetrators, or to help with non-criminal missing persons cases. Here we provide results from the analysis of 36 interviews with those who have a professional stake in FDP, including forensic scientists, police officers, lawyers, government agencies and social scientists. Located in eight EU countries, these individuals were asked for their views on the benefits and problems associated with the prospective use of FDP. While all interviewees distinguished between those phenotypic tests perceived to either raise ethical, social or political concerns from those tests viewed as less ethically and socially problematic, there was wide variation regarding the criteria they used to make this distinction. We discuss the implications of this in terms of responsible technology development.