The Use of Forensic DNA Phenotyping in Predicting Appearance and Biogeographic Ancestry

Background: Persons whose identifying DNA profile (STR profile) is not yet known to the ingvestigating authorities cannot be identified by standard forensic DNA analysis (STR profiling) as it is now practiced. In view of the current public debate, particularly in Germany, on the legalization of so-called forensic DNA phenotyping, we present its scientific basis, societal aspects, and forensic applications and describe the analytic techniques that are now available.

Methods: This review is based on pertinent publications that were retrieved by a selective search in PubMed and in public media, and on the authors’ own research.

Results: Forensically validated DNA test systems are available for the categorization of eye, hair, and skin color and the inference of continental biogeographic ancestry. As for statistical measures of test accuracy, the AUC (area under the curve) values lie in the range 0.74–0.99 for eye color, 0.64–0.94 for hair color, and 0.72–0.99 for skin color, depending on the predictive model and color category used.The corresponding positive predictive values (PPV) are lower. Empirical social-scientific research on forensic DNA phenotyping has shown that preserving privacy and protecting against discrimination are major ethical and regulatory considerations.

Conclusion: All three methods of forensic DNA phenotyping—the predition of externally visible characteristics, biogeographic ancestry, and the estimation of age from crime scene DNA—require a proper regulatory framework and should be used in conjunction with each other. Before forensic DNA phenotyping can be implemented in forensic practice, steps must be taken to minimize the risks of violation of privacy and of ethnic discrimination and to ensure that these methods are used transparently and proportionately.

Cite this as:
Schneider PM, Prainsack B, Kayser M: The use of forensic DNA phenotyping in predicting appearance and biogeographic ancestry. Dtsch Arztebl Int 2019; 116: 873–80. DOI: 10.3238/arztebl.2019.0873

The legalization of forensic DNA phenotyping has been publicly debated in Germany and Switzerland in the past few years while the technology has already been implemented in a few other countries. Forensic DNA phenotyping goes beyond standard forensic DNA profiling, where short tandem repeat (STR) polymorphisms are used to identify individuals from DNA obtained at crime scenes and other DNA markers are used for sex determination. In more novel forensic DNA phenotyping, however, information from crime scene DNA about externally visible characteristics and biogeographic ancestry (i.e., the inferred geographic region(s) of origin of a person’s biological ancestors) are collected. Estimating a person’s age from DNA found at the crime scene is also part of forensic DNA phenotyping and is currently debated as well, but will only be peripherally considered in this review, as it differs from the other two types of forensic DNA phenotyping in its scientific, including molecular, basis, analytical methods, and sample requirements (Box). Genetic diseases and their predispositions are excluded from forensic DNA phenotyping, as it is held that their forensic use would disproportionately violate privacy.

Box

DNA-based age estimation by methylation analysis

The public debate about the legalisation of forensic DNA phenotyping arose after many years of research into the genetic basis of physical appearance and the genetic correlates of biogeographic ancestry, followed by the development of suitable analytical techniques that could be used forensically for the DNA-based prediction from human biological samples obtained at crime scenes (1, 2, 3). Such DNA test systems are needed because of the general limitations of forensic STR-profiling. The latter can only yield an individual identification by a direct comparison of the crime-scene STR-profile with the STR-profile of a suspect in the case, or of a person whose STR-profile is stored in a nationwide forensic DNA database (e.g, the DNA database of the Federal Criminal Police Office [Bundeskriminalamt], the German counterpart to the F.B.I.). Positive identification is possible only if there is a match, i.e., absolute agreement of the STR-profile of the crime scene sample with that of a known person.

In criminal cases without a STR-profile match, forensic DNA phenotyping can be a helpful component of a targeted police investigation to find the unknown person who left DNA traces behind at a scene of crime. The goal of forensic DNA phenotyping is to narrow down the number of potential crime scene trace donors in such cases to a smaller group of persons who most likely have the externally visible characteristics and biogeographic ancestry that were inferred from the crime-scene DNA. Ultimately, however, only forensic STR-profiling can enable the individual identification of a (known) person (exception: monozygotic twins), thus providing evidence presentable in court. Forensic DNA phenotyping is therefore an investigative tool rather than an instrument to identify a specific person.

As of December 2019, forensic DNA phenotyping is explicitly regulated and permitted by law in two EU member states (the Netherlands and Slovakia), and practiced in compliance with existing laws in seven more (the United Kingdom, Poland, the Czech Republic, Sweden, Hungary, Austria, and Spain) (eTable) (4). In Switzerland, it is forbidden under current law, but the legalization of forensic DNA phenotyping is currently being considered. In Germany, in November 2019, the Bundestag (Parliament) and Bundesrat (Federal Council) approved a change in the law to permit forensic DNA phenotyping (with the exception of the DNA-based inference of biogeographic ancestry; cf. eTable for details).

eTable

Overview of the legal situation concerning forensic DNA phenotyping in Germany, Austria, Switzerland, and other EU member states for which definitive information is available (updated and revised from [4]; current as of December 2019)

DNA-based prediction of externally visible characteristics

Of all externally visible characteristics, eye, hair, and skin color can currently be predicted from crime-scene DNA on the level of commonly used color categories (Table 1). This is now possible because genes and predictive DNA markers (single-nucleotide polymorphisms, SNPs) have been identified that are either causal for these features or associated with them. Forensic DNA tests for the analysis of these DNA markers have been developed and validated, along with suitable statistical predictive models (Table 1).

Table 1

Curently available forensic DNA test systems*1 for eye, hair, and skin color

The development of any statistical predictive model, e.g., for eye color, based on a model reference dataset consisting of genotypes and associated phenotypes is followed by statistical validation of the model, yielding parameters of test accuracy. Test accuracy reflects the average accuracy with which a DNA test can predict a particular externally visible characteristic, e.g., blue eyes, and can be expressed by a variety of statistical parameters (Table 1). As recommended by Caliebe et al. (5), test accuracy estimates in forensic DNA phenotyping, rather than for medical diagnostic tests, should be expressed in positive and negative predictive values (PPV and NPV). Differences in test accuracy (Table 1) reflect differences in the information content and number of DNA markers employed in the DNA tests used, as well as in the underlying reference data used in the statistical predictive models.

Test accuracy (Table 1) should not be confused with the accuracy of individual test results (eFigure). The latter are obtained for individual persons in a specific case by applying a particular DNA test and statistical model, and are generally expressed as probability values (5) (eFigure). What probability of a particular externally visible characteristic suffices for its useful inclusion in a police investigation is not a scientific question but, rather, an operative decision of the investigating authority: what is the individual probability threshold that would justify including this feature in a police investigation when all relevant aspects of the case at hand have been considered, and what significance should be attached to this information during the investigation?

eFigure

Illustration of individual test results from DNA-based prediction of eye, hair, and skin color

As can be seen from the test accuracy values provided in Table 1, the currently available DNA tests and statistical models permit some categories of eye, hair, and skin color to be more accurately predicted, on average, than others: blue and brown eyes are more accurately predictable than eyes that are neither brown nor blue, red and black hair more accurately than blond and brown hair, and dark skin colors more accurately than light ones. There are multiple reasons for this. For instance, the lesser accuracy in predictability of blond and brown hair results from the fact that blond hair may darken during childhood and adolescence. Some brown-haired adults who had blond hair as children display a high individual probability value for brown hair, others for blond hair (6). Thus, any test result with a high probability of blond hair allows either of two interpretations: the person is either a blond adult or a brown-haired adult who had blond hair as a child. Persons whose eyes are neither blue nor brown only rarely have a high individual probability value for their true, intermediate eye-color category; typically, they have similar individual probability values for both the blue eye and the brown eye color categories.

In general, genetic predictive models for pigmentation traits need not be assumed to be population-dependent (5); however, the degree of population-independence does depend on the causality of the DNA markers used and on the extent and population distribution of contributory non-genetic factors (5). Current DNA tests for pigmentation traits (Table 1) include both causal and non-causal DNA markers. Heritability estimates of all pigmentation traits are very high; environmental influences such as age (eye and, especially, hair color) and solar radiation (hair and, especially, skin color) do exist, but their contribution is relatively minor. To minimize potential population effects, data from multiple populations are combined e.g. in the IrisPlex, HIrisPlex, and HIrisPlex-S models (6–8) (https://hirisplex.erasmusmc.nl/) (Table 1).

Forensic DNA tests for the more fine-grained prediction of eye, hair, and skin color are not yet available, nor is there any such test for age-related loss of hair color (2). DNA-based prediction of other externally visible characteristics (e.g., hair structure, hair loss, and body height) is not yet possible with test accuracies comparable to those achieved for eye, hair, and skin color (2, 9, 10), and such tests will, therefore, not be discussed any further in this review.

DNA-based inference of biogeographic ancestry

Biogeographic ancestry does not in any way correspond to such concepts as ethnic origin or “race”; ethnicity and “race” are shaped by a multitude of factors that are not genetic. For the same reason, biogeographic ancestry cannot be equated with language, religion, or other manifestations of culture or tradition. It solely concerns the geographical region(s) from which a person’s biological ancestors originated.

The DNA-based inference of a person’s biogeographic ancestry is based on the genetic features that person has inherited from his or her biological ancestors. The farther apart the geographic regions of origin of two persons lie, the greater the genetic differences between them. These differences are due to mutations, migrations over the course of human history, local selection, genetic isolation, other effects (including random ones), and heredity. This is why there are DNA markers that are seen only in population groups from particular geographical regions, or that are very common in one geographical region and rare in others; these are called ancestry-informative DNA markers (3).

Ancestry-informative DNA markers can be passed on from one generation to the next in three different ways, which means that they display biogeographic ancestry in three different ways. Markers located on the autosomes are inherited from both parents and thus reflect the geographic origins of both. Markers located on the Y-chromosome are passed on only from father to son and thus exclusively reflect the geographical origin of a (male) person’s ancestors in the purely male (paternal) lineage. Mitochondrial DNA markers are passed on only from mother to child and thus exclusively reflect the geographical origin of a (male or female) person’s ancestors in the purely female (maternal) lineage. The autosomal DNA is reassorted in each generation through the processes of DNA recombination, meiosis and fertilization, with the result that only half of the total parental autosomal DNA, and thus only half of the autosomal DNA markers, are still present in each offspring. In contrast, the Y-chromosomal (Y-) and mitochondrial (mt-) DNA markers are passed along essentially unchanged over many generations in the male and female lineages, respectively.

DNA-based inference of biogeographic ancestry should, therefore, include ancestry-informative DNA markers of all three kinds—autosomal, Y-chromosomal (in case of males), and mitochondrial. If all of a person’s biological ancestors came from the same geographical region, then these three kinds of DNA markers will, in the ideal case, all lead to the same conclusion as to that person’s biogeographic ancestry. For a person whose biological ancestors ancestors came from different regions, the autosomal DNA markers can be used to make quantitative inferences about that person’s mixed biogeographic ancestry, while the Y- and mt-DNA markers separately and uniquely reflect the biographic ancestry of that person in the male and female lineages, respectively. Nonetheless, the currently available forensic DNA test systems often enable only limited inference of a mixing of ancestors from different geographic regions if such mixing occurred many generations ago.

Ancestry-informative DNA markers selected from population genetic studies around the world (mostly SNPs) have been used to develop and validate numerous forensic DNA test systems; these are highly reliable because of the number and diversity of the DNA markers used with respect to the populations that are to be distinguished from one another (Table 2). With the aid of these test systems, crime scene samples can be used to determine the biogeographic ancestry of any person at the level of detail of the continental regions Europe, sub-Saharan Africa, East Asia, South Asia, Oceania, and the Americas (where the indigenous populations of each region are meant) (Tables 2 and 3).

Table 2

A selection of available DNA test systems*1 for continental biogeographic ancestry

Table 3

Individual test results from the DNA-based inference of continental biogeographic ancestry. An illustrative example with eight test subjects chosen according to actual region of origin *1

Such DNA tests may be less reliable, however, in the determination of a person’s subcontinental ancestry, as the effects of migration within continents markedly lessen the ancestry informativeness of DNA markers. Increasing the number of ancestry-informative DNA markers to be analyzed in samples from crime scenes, which is now possible with a method called “targeted massively parallel sequencing” (MPS) (Table 2), can make the determination of subcontinental ancestry possible (11), as can certain Y or mtDNA markers (5, 12).

The quality of DNA-based biogeographic ancestry inference depends not only on the geographical informativeness of the DNA markers that are employed, but also in large measure on the population genetic data used as a reference. Thus, DNA-based ancestry inference can only accurately describe the geographical spectrum of ancestry of a tested person if that spectrum of ancestry is well represented in the population genetic reference data set used. It follows that, whenever such test results are reported, the reference data used should be described as well.

Ethical aspects of forensic DNA phenotyping

A number of publications on the ethical, societal, and regulatory aspects of forensic DNA analysis in general (13), and of forensic DNA phenotyping in particular (14), provide valuable assistance for the ethical assessment of these technological developments and for considerations of the appropriate regulatory framework. An analysis of the social-scientific, judicial, and ethical literature as part of the VISAGE research project (www.visage-h2020.eu), as well as interviews with experts and members of civil society organizations (15), have led to the identification of the following major concerns about forensic DNA phenotyping: discrimination against minority groups, invasion of privacy, conflict with data protection (confidentiality) laws, and exaggerated expectations on the part of users and the general public.

Many experts see the greatest problem in the risk that forensic DNA phenotyping will be used in a way that discriminates against minority groups, particularly in societies where racism and xenophobia are now on the rise. Even those who support the use of forensic DNA phenotyping in specific cases emphasise that these methods should not be used in police investigations until appropriate measures have been taken to ensure that they are used transparently and proportionately. The training of forensic DNA experts and investigators is essential to ensure that the laboratory findings are correctly generated, interpreted, documented, and transmitted to the investigating authorities, and that the authorities understand them correctly and use them properly.

Practical use of forensic DNA phenotyping

Forensic DNA phenotyping can be used even in criminal cases where there are no eyewitnesses; a further advantage over eyewitness testimony is that the estimated individual probability values are always accompanied by case-specific, individual error estimates that the police can take into account in their investigation. For example, if there is an estimated 95% probability of blue eyes (5% error rate), an investigator can consider this figure more reliable than one with an 80% probability (20% error rate) in another case. In contrast, the error rate of an eyewitness report in any particular case is impossible to assess. It is well known that eyewitnesses can testify falsely for a variety of reasons. For example, in the U.S.A., the Innocence Project revealed that 70% of the 350 erroneous verdicts retrospectively identified by STR profile analysis had been reached because of false eyewitness reports (16).

DNA-based predictions of externally visible characteristics and the biographical inference of ancestries that are rare in the area where a crime was committed will be more helpful to police investigations than predictions of features and origins that are common there. At the same time, DNA-based predictions of regionally common features can, indeed, provide useful clues while removing unfounded suspicion from minority groups, as happened in the investigation of the rape and murder of Marianne Vaastra in the Netherlands in 1999 (17). Only rarely do the authorities reveal publicly, after the conclusion of a case, that forensic DNA phenotyping was successfully used; this was done in another Dutch rape and murder case, that of Milica van Doorn of 1992 (18).

As STR profile analysis has a relatively high chance of directly identifying a culprit who has already left genetic traces behind elsewhere, an STR profile analysis is generally performed first in every case. For example, in Germany, every third or fourth search for matches with DNA traces from a crime scene in the national forensic DNA database finds a match (19). In cases where STR profile analysis yields no match, an adequate amount of DNA must be available from the scene of the crime for forensic DNA phenotyping to be performed. However, many samples from crime scenes, such as the now commonly obtained skin contact traces, which contain very small quantities of DNA, are consumed for STR-profiling. Moreover, there must be an unequivocal connection between the DNA traces found at the scene of the crime and the crime itself. Thus, the DNA trace is required to have been obtained directly from the victim or from an object used to commit the crime, both to justify the expense of forensic DNA phenotyping and to assure its proportionality as well as that of any subsequent DNA mass screening (as per section 81h StPO [Code of Criminal Procedure] in German law). Lastly, forensic DNA phenotyping makes use mainly of DNA traces from crime scenes that are derived from a single individual (which can be determined from the preceding STR-profiling results). Mixed DNA traces derived from two or more persons often do not enable the unequivocal identification of phenotypic features.

Certain externally visible characteristics depend on biogeographic ancestry. People with blond hair, blue eyes, and light skin are always at least partly of European ancestry. People with brown eyes, black hair, and skin of intermediate lightness are found among the indigenous populations of Europe, Asia, and the Americas; these three continental regions of origin can be reliably distinguished from each other by the DNA-based inference of biogeographic ancestry. Moreover, information on geographic origin is of investigative value in itself. It follows that a combined DNA analysis of externally visible characteristics and biogeographic ancestry can increase the informational yield of a criminal investigation. An additionally performed DNA-based estimation of age (20) (Box) further increases this yield, both because information on age is of investigative value in itself, and because some of the individual’s externally visible characteristics may be affected by age (e.g., hair color or hair loss). It is therefore strongly recommended that all three techniques of forensic DNA phenotyping, i.e., the prediction of externally visible characteristics, biogeographic ancestry and the estimation of age from DNA should be used together in forensic practice, within an appropriate legal regulatory framework.

Acknowledgements

We thank Arwin Ralf and Theresa Gross for their help in the creation of the figures and tables, Walther Parson, Ingo Bastisch, Martina Unterländer, Richard Scheithauer, and Markus Rothschild for helpful comments, and Markus Rothschild for his initiative and practical support. The authors’ scientific work related to the topic of this article was financially supported by the University Hospital of Cologne (PMS), King’s College London (BP), the University of Vienna (BP), Erasmus MC University Medical Center Rotterdam (MK), and the European Union Research and Innovation Program HORIZON 2020, contract no. 740580 (VISAGE).

Conflict of interest statement
Prof. Schneider has appeared as an invited speaker at scientific meetings, with reimbursement of meeting participation fees and of travel and accommodation expenses by Thermo Fisher Scientific and Promega. He serves in criminal proceedings as a court-appointed expert on the analysis of DNA traces.

Prof. Kayser is a co-inventor of patent no. EP2195448A1 (“Method to predict iris color”) but receives no license fees or royalties from this. He has appeared as an invited speaker at scientific meetings, with reimbursement of meeting participation fees and of travel and accommodation expenses by Thermo Fisher Scientific, Promega, and the Wenner-Gren Foundation. He is commissioned to provide medicolegal expert reports on DNA trace analysis for the investigative authorities in multiple countries.

Prof. Prainsack and Prof. Kayser served until April 2018 as members of the Scientific Advisory Board of Identitas Inc., without receiving honoraria or other payments for this activity.

Manuscript received on 24 May 2019; revised version accepted on 19 November 2019.

Translated from the original German by Ethan Taub, M.D.

Corresponding author
Prof. Dr. rer. nat. Manfred Kayser
Department of Genetic Identification
Erasmus MC University Medical Center Rotterdam
PO Box 2040
3000 CA Rotterdam, the Netherlands

Cite this as:
Schneider PM, Prainsack B, Kayser M: The use of forensic DNA phenotyping in predicting appearance and biogeographic ancestry. Dtsch Arztebl Int 2019; 116: 873–80. DOI: 10.3238/arztebl.2019.0873

►Supplementary material

eTable and eFigure:
www.aerzteblatt-international.de/19m0873

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