Freckle On: Predicting Freckles from DNA

Credit for Source Photo: Freckles by Max Pixel

DNA phenotyping is becoming a popular approach in predicting physical appearances from DNA in cases where there are no suspects and no database hits from samples found at crime scenes.  This genetic-based approach translates genotype DNA evidence into phenotype physical appearance predictions, which can narrow down suspect lists and solve human remains cases where individuals cannot be readily identified. First, author Magdalena Kukla-Bartoszek and her team at the Malopolska Center of Biotechnology studied genes associated with human pigmentation and their impact on freckle presence. Their final prediction model correctly predicted individuals that were non-freckled and heavily freckled about 70% of the time. Though not accurate enough for immediate field implementation, the significance of pigmentation genes in predictive DNA analysis of freckles cannot be underestimated.

Forensic DNA phenotyping is the use of DNA to predict physical characteristics of an individual.  This area of forensic genetics explores variations in our DNA sequence that potentially predicts ancestry, physical appearance and age.  Pigmentation is a highly studied area within forensic genetics where predictions of freckles complements the description of an individual’s pigmentation.  A previous study used 5 genes as predictors for freckles and identified individuals based on freckled versus non-freckled with 66%  accuracy.  Kukla-Batoszek and her collaborators took this same model further by increasing the number of predictor genes to distinguish between freckle intensity, or the abundance of freckles. (Fig 1) There are 4 main genes: IRF4, BNC2, OCA2, and MC1R with many variants that associate with the presence of freckles.  Though geneticists still search for more genes that impact the freckle phenotype, the variants that they are still finding within these four genes have proven to be most helpful when developing prediction models.  Women and people with lighter pigmentations are more likely to have freckles than their counterpoints, and red-haired individuals have an even higher probability.  

Figure 1: The number of freckles an individual has determines which category they belong in.  Photo Credit: Freckles & Moles by Izzie Button on Flickr

The authors identified 19 DNA variations called single nucleotide polymorphisms (SNPs)  associated with the freckle phenotype, in addition to twelve contributing predictors that increased the accuracy of matching an individual to the non-freckled or freckled category.  The team studied the effects of the variations in 960 individuals of Polish descent who often express light pigmentation to determine the accuracy of their model.

The overall prediction accuracy of an individual having freckles increased from the previous study by 8% to an overall 77%.  The heavily freckled phenotype increased in accuracy by 12% when compared to the previous study.  Variations associated with the medium freckled phenotype are more complex due to the influence of age (freckles decrease as we get older) and mutations that affect freckle-associated genes like the MC1R gene.  (Fig 2) Most cases of freckles are caused by the MCR1 gene, and mutations in this gene have been associated with the appearance and intensity of freckles.  MC1R’s job is to make sure there is a balance of pigments in the skin, so if one of the two copies inherited from your parents are broken, you get freckles.

Figure 2: Percentage of accurate DNA to phenotype predictions of freckled individuals.  Source: Catherine Allen, adapted from Kukla-Bartoszek et. al, FSI Genetics, 2019, Volume 42, P252-259

Kukla-Batoszek and team’s model identified unknown individuals correctly 60.3% of cases to one of the three freckle categories.  When looking at non-freckled compared to freckled predictions, the accuracy increased to 70.5%. These are lower accuracy values than would be used by any method in the field, for good reason; only 7/10 times would the individual be correctly identified as having freckles or not. In addition, other pigmentation phenotypes such as eye, skin and hair color have much greater accuracy than the current freckle prediction models. Prediction accuracy is important because an incorrect prediction can mislead an investigation by excluding (or including) the wrong suspects.

We need a greater understanding of the fundamental genetics of freckles if they are to be used as predictors, especially when trying to match individuals who have medium intensity freckles.  Many DNA variations exist that alter expected outcomes of the freckle phenotype, which complicate genotype-to-phenotype predictions.  However, when paired with other pigmentation predictors like eye and skin color, the freckle phenotype can prove useful in narrowing down suspect lists.  Before field implementation though, forensic scientists must include rigorous statistical checks to prevent the wrong prediction misleading us away from the actual perpetrator and towards an innocent person.

TitleDNA-based predictive models for the presence of freckles
AuthorsMagdalena Kukla-Bartoszek, Ewelina Pośpiech, Anna Woźniak, Michał Boroń, Joanna Karłowska-Pik, Paweł Teisseyre, Magdalena Zubańska, Agnieszka Bronikowska, Tomasz Grzybowski, Rafał Płoski, Magdalena Spólnicka, Wojciech Branicki
JournalForensic Science International Genetics
PublisherElsevier B.V.

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