Phenotyping: The hidden mugshot in a culprit’s DNA - European Biotechnology Magazine (2024)

Police investigators today begin searches for perpetrators with conventional DNA profiling - comparing a genetic signature from sperm or hair left at a crime scene with a database of identified offenders. But that doesn’t finger culprits who have never been registered. A growing technology called ‘DNA phenotyping’ is now aimed at interpreting genomic clues about a suspect’s possible external appearance. The science behind it is new, and investigators have to navigate the statistical uncertainties - as well as ethical and legal questions - the technology is raising all over Europe.

The age of forensic DNA phenotyping (FDP) in Europe began in 1999 with the brutal rape and murder of a 16-year-old girl in the Netherlands. As police investigations bogged down and rumours flourished in the local community about asylum seekers from Iraq and Afganistan housed in the area, forensic geneticist Peter de Knijff decided to break Dutch law. With permission from local police, he analysed the DNA in semen found at the crime scene in an attempt to identify the perpetrator’s bio­geographical ancestry. That move would open a door into a new era of criminal investigation – drawing up a mugshot based purely on an individual’s genetic code. The move was and would continue to be a controversial act of scientific progress that opened a Pandora‘s box of ethical and legal implications.

The missing legal framework in Europe

At the time of de Knijff‘s decision, Dutch law forbade an explicit analysis of culprit DNA to determine ancestry, physical health or other genetically encoded characteristics. Forensic analysis of DNA was restricted to determining a person’s individual identity via a DNA profiling assay. This legal situation remains the standard in many countries in Europe today. While Germany and Belgium, for example, explicitly prohibit deriving physical traits other than gender from DNA, countries like Spain still have no legal provisions, but in practice still restrict DNA forensics to non-coding DNA. Others (like Britain) regularly use the legal vacuum to deduce ethnic origin and hair colour from crime-scene DNA, even though a 2001 resolution from the European Council regarding the exchange of DNA analysis results urges member states to only take non-coding chromosome zones into account. These provide no information about hereditary characteristics.

In the Netherlands, de Knijff‘s legal violation opened a societal debate that led to an amendment of the law in 2003. It now allows forensic geneticists to search crime-scene DNA for clues to a culprit‘s physical appearance and ancestry, but still strictly prohibits the deduction of any health­-related information.

Law still trumps science

The problem is that forensic science continues to trail behind when it comes to exploiting new legal freedoms in the area of genetics. That’s mostly because researchers still don’t know much about the genetics of most externally visible characteristics (EVCs) in humans such as eye, hair and skin colour, hair structure or baldness, height, earlobe shape and so on. “We know much more about the genetic basis of human diseases than about the genetics of the normal characteristics of the human appearance,” says Manfred Kayser, head of the Department of Genetic Identification at the Medical Center of Rotterdam‘s Erasmus University. Funded in 2004 as a response to the change in legal frameworks, the Netherland’s National Forensic Institute – supported by the university – has sought to create a centre where the necessary basic research could be carried out in the quest to develop useful new tests for forensic application. That’s a unique concept in Europe, since forensic institutes usually have neither the capacity nor budgets to be deeply involved in scientific research. A scholar from the lab of renowned genetic anthropologist Mark Stoneking, Kayser proved an ideal fit for the job. He spent the last decade of his research career building a huge scientific database that collected subtle genetic variations on single nucleotide poly­morphisms (SNPs), which are correlated with specific EVCs. And the geneticist has already translated the research into a forensic test format.

The first of these tests, called “Irisplex”, estimates eye colour based on an individual’s DNA. It has already received approval from Dutch officials for use in criminal investigations. Kayser’s most recent development “Hirisplex”, which extends the prediction to both eye and hair colour, is still awaiting official approval.

Genetics – we don’t know enough

Aside from these two pigmentation tests, forensic genetics still doesn’t offer investigators much additional information, as we still know too little about genes and predictive DNA markers. Kayser believes, however, that the scientific foundations for predicting baldness, hair structure and skin colour have been largely mapped out, making new forensic tests for these EVCs likely soon. “The problem is that – like with the prediction of eye and hair colour – we are only able to differentiate gross categories of skin colour.” Fine nuances between blue and grey eyes, for example, or blonde and brown hair, or darker or lighter skin, are in reality smooth transitions. Finding the genetic variations, SNPs or other types of genetic markers responsible for such slight differences will be both very laborious and extremely expensive. The reason for the high costs is that the scientific foundation of any forensic genetic test are genome-wide association studies (GWAS). These analyses scan the genomes of as many people as possible to find correlations between the approximately 15 million human SNPs and a specific EVC (such as height). Twin studies suggest that height is 80% nature and 20% nurture. A recent GWAS of 250,000 individuals found 697 SNPs associated with height – by far the largest genetic dataset of any human EVC. But as it turns out, these hundreds of SNPs still just explain 16% of humanity’s observed height differences.

Tossing a coin

In other words, geneticists still don’t even know enough about the genes involved in normal height development, which clearly makes developing a forensic test impossible. In 2009, genomics expert Yurii Aulchenko tried to predict body height with the 54 height­-associated SNPs known at the time – and failed. According to Kayser, prediction values from the study didn’t really beat a coin toss. “Currently available genetic know­ledge on body height clearly illustrates on the one hand just how much genetic information on height is still missing, and on the other hand that accurate DNA prediction of normal height is not around the corner, and if ever possible will likely involve many thousands of SNPs,” Kayser wrote in a recent FDP review (http://dx.doi.org/10.1016/j.fsigen.2015.02.003).

The same is true for other human EVCs. That’s why if US companies like Human Longevity or Parabon Nanolabs claim to be able to reconstruct a “snapshot” of a culprit’s face from DNA, Kayser is highly sceptical. Especially because these firms have yet to publish peer­reviewed papers describing the science behind their predictive technologies. And of course the tests lack any independent validation. “Based on currently published and publicly available scientific state-of-the-art, it’s very unlikely that this works,” Kayser says. The appearance of a human face is determined by hundreds – if not thousands – of genetic variants, but only about a dozen are known so far, according to the scientist. That said, Kayser still thinks that a reliable, validated DNA-based mugshot might be a possibility in the future. “Twins’ faces look very much alike,” he reminds. “And as their DNA is almost identical, we know that a face’s uniqueness has to be hidden in the genome – although we don’t yet know where.”

When it comes to deducing bio­geographical ancestry from DNA traces, as the Dutch forensic scientist de Knijff did back at the turn of the millennium, geneticists have grown much more confident. Specific SNPs now allow them to trace ancestry back to the broad continental regions Europe, Africa, East Asia, Oceania or the Americas with a certainty of 99.9%, according to the “Joint Trace Commission“ head Peter Schneider at the University of Cologne. Even though the perpetrator from the 1999 case in the Netherlands has never been identified, de Knijff’s analysis revealed that the murdered Dutch girl was raped by a man from northwestern Europe origin. But Schneider reiterates that a more specific result – pinning crimes to a particular national origin with science – is still not possible. That’s because nationalities and borders have political and cultural, not biological roots. To pinpoint ancestry to certain regions with enough predictability, investigators would have to check thousands of SNPs. That presents a technical problem, he adds, since DNA isolated at crime scenes is usually too fragmented for this kind of analysis.

Clues from the ageing genome

Scientists are at least able to give investigators more precise clues about a suspect’s age based on forensic DNA evidence. Since methylation of the DNA component cytosine changes at certain positions (CpGs) in the genome, this particular marker can be used to predict age with a relatively high degree of probability. In his review, Kayser writes that two CpG markers explained 73% of age variation, and predicted individual ages with an average accuracy of about five years. Looking at more than 100 CpGs leads to a deviation from real age of just over three years, and Schneider concludes that age can be accurately predicted within a range of 4-5 years. He adds that such analyses could already be performed, even within restrictive legislation environments like Germany, because methylation analysis and age deduction reveal none of an individual’s personal information. Age information would be tremendously valuable to investigators, since “the predictability of age has a higher criminal and practical value than predictions about eye or hair colour.”

DNA – the best witness

Even though forensic DNA pheno­typing is still in its infancy as an applicable technology, both Schneider and Kayser expect advances will soon help it develop into a versatile tool for investigators. Next-generation sequencing technologies (NGS) are already making it easier to analyse large numbers of SNPs. “Although studies showing the multi­plexing analysis of thousands of SNPs via targeted NGS are still pending, over 500 SNPs can already be successfully combined in a single targeted sequencing run using the Ion Torrent Personal Genome Machine,” says Kayser. Such tests can also help verify witness testimonies, which are often questionable or subjectively biased. That‘s because a results from a forensic DNA phenotyping test comes with a scientif­ically sound degree of probability. With HIrisplex, for example, investigators can be 95% sure that a perpetrator’s eyes are indeed blue, although predicting grey or green eyes is less certain (approximately 15-30%). Witness statements, on the other hand, provide no empirical data about the true value of a testimony, so the test is at least a solid starting point.

But critics say that overeager police officers might still face difficulties in dealing with the probabilistic nature of FDP results, and could end up on the wrong track if they take current DNA analysis results without a grain of salt. And other uncertainties remain. Tests can for example make predictions about genetically-based EVCs, but a suspect’s external appearance could still easily be changed by cosmetics, plastic surgery, coloured contact lenses, dyed hair, a deep tan or even disease. Hair colour also alters with age, and science still hasn’t developed a tool for predicting exactly how.

Regulating FDP

So FDP results raise both ethical and scientific challenges. Deducing information from DNA about characteristic features has long been a general legal question in its own right. Experts argue that such tests could actually infringe an individual‘s right to privacy when it comes to administrating their own personal information. This is certainly true for health-related information that even culprits may be un­aware off – such as genetic risk factors for disease. When it comes to personal appearance, however, Kayser believes that privacy issues – including the right not to know – don’t apply: “This simply is because appearance traits are not only known to the person itself, but to everybody who has ever seen this person, including the police.” Kayser therefore argues that in legal terms, FDP is comparable to testimony from a human witness, as it delivers the same type of information that human eyewitnesses do. And since there is no specific law regulating the use of testimony from eyewitnesses, Kayser asks,why does one need it for DNA?

On the other hand, Kayser gives reasons why at least some amount of regulation might be necessary, particularly when it comes to predicting ancestry from DNA. To a certain degree, eyewitnesses can make broad assumptions about a culprit’s descent on a continental level. That information can therefore not be considered private information, Kayser argues: But “mixed ancestry such as between continents may not necessarily be visible.“ Therefore, privacy issues – including the right not to know – could apply for genetic ancestry testing. The respective law in the Netherlands, which is generally considered the most progressive in Europe, doesn’t take this problem into account. Neither does legislation in other EU states that don’t regulate FDP specifically but already do practise ancestry testing in investigations.

In German law, any forensic use of DNA is restricted to “non-coding markers“. But this leaves a loophole for FDP, according to Kayser, because many SNPs used by FDP analysis are located in such “non-coding” regions of the genome. “A distinction between coding and non-coding parts appears outdated, and should therefore not be used any longer when regulating the application of DNA via legislation,” Kayser says.

European legislation needs an update, it seems, as forensic DNA phenotyping is coming whether lawmakers want it or not. Only by setting down the rules for what police investigators should or should not know about a culprit’s genetic predispositions will societies be able to harness these coming technologies to solve crimes.

Phenotyping: The hidden mugshot in a culprit’s DNA - European Biotechnology Magazine (2024)

FAQs

How accurate is DNA phenotyping? ›

FDP can already identify a source's gender with 100% accuracy, and likely hair color, iris color, adult height, and a number of other EVCs with accuracy rates approaching 70%.

Is DNA phenotyping ethical? ›

According to ncbi.nlm.nih.gov, “Forensic DNA phenotyping has shown that preserving privacy and protecting against discrimination are major ethical and regulatory considerations.” As science grows, so will the concerns. This could lead to major violations of ethics and people's privacy.

What can DNA phenotyping tell us about a person? ›

Another commonly used term for DNA phenotyping is molecular photofitting. The technique is primarily used to predict a person's physical appearance and/or ancestry for forensic purposes. Using a genome-wide association study (GWAS) approach, genetic variants associated with the target trait are discovered.

What are the disadvantages of DNA phenotyping? ›

The main disadvantage lies in the fact that this type of examination is uniquely comparative, requiring a pair of unknown/reference samples to be compared. In the absence of such a pair, the only possibility would be searching a DNA database containing suspects' profiles.

Can you tell what someone looks like from their DNA? ›

There are a variety of things you can predict fairly accurately from DNA: sex, ancestry, freckles, and (natural) skin, hair, and eye color.

Can you tell skin color from DNA? ›

An AncestryDNA ® + Traits test can tell you more about your genes and your skin pigmentation.

Can phenotyping predict age? ›

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.

Who uses DNA phenotyping? ›

Just as an eye-witness may describe the appearance of a person of interest, the DNA left at a crime scene can be used to discover the physical appearance of the person who left it. This allows DNA phenotyping to be used as an investigative tool to help guide the police when searching for suspects.

Why are people against DNA testing? ›

Several. There is the fear that the data will be used against the owner, particularly in insurance obligations. Then there is the fear that family secrets could be exposed which could affect the whole family around him. Once out of the bag, such issues are impossible to rebag.

What determines what a person looks like? ›

DNA contains all the information needed to build your body. Did you know that your DNA determines things such as your eye color, hair color, height, and even the size of your nose? The DNA in your cells is responsible for these physical attributes as well as many others that you will soon see.

Can you tell personality traits from DNA? ›

Scientists estimate that 20 to 60 percent of temperament is determined by genetics. Temperament, however, does not have a clear pattern of inheritance and there are not specific genes that confer specific temperamental traits.

How can you tell if someone is using DNA? ›

Each person's nuclear DNA is unique—except for identical twins, who have the same DNA. When a sufficient nuclear DNA profile from the victim's remains matches the nuclear DNA profile from a sample known to have come from the victim, we can be very sure of the identity of the victim.

When was DNA phenotyping invented? ›

A SHORT INTRODUCTION TO FORENSIC DNA PHENOTYPING. Following the discovery of the 'genetic fingerprint' by Alec Jeffreys in 1984,1 the analysis of DNA became quickly one of the most prominent investigative tools for the police.

What issues might DNA phenotyping raise? ›

The most prominent concerns are related to privacy, discrimination and interpretation of findings.

Do you agree with using DNA phenotyping for solving crimes? ›

It's probabilistic in nature and doesn't provide concrete evidence. In criminal proceedings, the standard for proving guilt beyond a reasonable doubt is typically very high. DNA phenotyping predictions, which rely on probabilities and statistical likelihoods, might not meet this high standard on their own.

Is DNA profiling highly reliable? ›

While DNA testing is not completely foolproof, it is more than 99% accurate. In fact, there is only a one in one billion chance that the DNA test results of two individuals will match. Errors in testing are often the result of mix-ups in the lab or the contamination of samples.

How accurate are DNA ethnicity estimates? ›

“We're talking about 99.9 percent accuracy for these arrays,” Erlich says. But even with that high level of accuracy, when you process 1 million places in the genome, you might get 1,000 errors. Those small errors alone can help explain why one twin might have slightly different results from another.

Can DNA matching be wrong? ›

Faced with unexpected results, DNA testing clients sometimes wonder, “Can my DNA test be wrong?” Here's the answer: usually not, and very rarely yes. Most of the time, when you see a result you do not expect, it is your DNA trying to tell you something about your family relationships.

Is DNA matching 100% accurate? ›

A provider will take a blood sample after your eighth week of pregnancy. They send the samples to a lab, where a specialist analyzes trace amounts of the fetus's DNA in the blood sample and compares it to the DNA in a cheek swab from the potential non-birthing parent. An NIPP is 99.9% accurate and very safe.

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