DNA Phenotyping: The prediction of human pigmentation traits from genetic data

Phenotyping is the ability to assign characteristics to an organism based on certain measurable parameters. In the case of DNA phenotyping, it is limited to the sole use of DNA to determine a phenotype such as an externally visible characteristic. In a forensic setting, it encompasses the ability of a forensic investigator to predict the physical appearance of an individual using molecular analyses from biological samples left at a crime scene, termed DNA ‘intelligence’. It is able to provide investigative leads to find unknown perpetrators or identify missing persons in cases where all other means of inquiry, including conventional DNA profiling, are non-informative. In a non-forensic setting, it permits the prediction of the physical appearance of our ancestors, historical persons or any other deceased individual for whom the identification of appearance traits may be interesting, and it sheds light on human evolution. In this thesis, DNA variants highly associated with human eye and hair colour pigmentation traits were explored for their potential and contribution towards accurate prediction systems using sensitive laboratory assays together with statistical models. This thesis describes the design, performance and developmental validation of the new IrisPlex and HIrisPlex systems. IrisPlex represents a sensitive single multiplex genotyping assay together with a statistical model that is capable of predicting eye colour using 6 SNPs from 6 genes with high degrees of blue and brown eye colour accuracy and is reliable independent of bio-geographic ancestry knowledge. It also describes the HIrisPlex system, which is made up of a sensitive single multiplex genotyping assay together with two prediction models, one for eye colour and the other for hair colour. Targeting 24 of the most eye and/or hair colour informative DNA variants, this system has the ability to simultaneously predict both the eye and hair colour of an individual from a DNA sample. HIrisPlex displays accuracies of > 94% for eye colour category prediction together with accuracies of 79% on average for hair colour categories and is reliable independent of ancestry knowledge. Finally this thesis describes examples of the HirisPlex application using aDNA samples up to 800 years old. From this data, a historical figure from Polish history, General Sikorski was revealed to have blue eyes and blond hair, confirming historical records. There are several chapters that demonstrate interesting applications of eye and hair colour DNA phenotyping using the IrisPlex and HirisPlex systems in an evolutionary, anthropological and historical context. These DNA-based prediction systems are also being used worldwide in accredited forensic laboratories.