Single nucleotide polymorphisms : from forensic identification to DNA phenotyping

Tese de doutoramento, Biologia (Genética), Universidade de Lisboa, Faculdade de Ciências, 2017Single nucleotide polymorphisms or SNPs present low mutation rates and its biology permits for an automated analysis, with a relatively simple interpretation due to the fact of the techniques used to analyze these markers originating few artifacts. This allows to attain additional genetic information that can offer great value to the geneticist and for the discovery of the truth in civil or criminal cases. For all these, in recent years we have witnessed the rapid development of SNP methodology as a tool in forensic genetics. These markers can be characterized in four forensically relevant classes, one of which consists of SNPs useful in individual identification and other consists in polymorphisms used to identify family lineages, allowing the obtainment of additional genetic information to complement those usually achieved through STR analysis. Thus, SNP study in these situations relates to the need of additional genetic information due to the existence of STR incompatibilities in the studied systems or due to the lack of sample from individuals essential to the analysis of kinship casework. SNP study is also of great importance when incomplete amplification or no amplification of the studied STR systems is observed, resulting from the small quantity and / or poor quality of the analyzed DNA. The two remaining SNP classes cannot provide individual or family identification but they present large forensic interest because they allow inferring about characteristics of the sample donor. The first of these classes is composed by SNPs that provide biogeografical ancestry information and the remainder class consists of markers that provide information about phenotypic characteristics. This type of information can be especially important when no information is known about the sample donor and not even his or her genetic profile has entered into DNA databases, in a way that these will provide valuable clues to the discovery of the individual yet to be identified. The application of these markers to forensics is being studied by several research groups worldwide so that their use can become a reality in the near future. However, since forensic genetics is founded on scientific knowledge and based on human genetic diversity, it is important to study these in the populations in which this type of analysis can be used. Thus, it is important to study the SNP loci in the Portuguese population so that these markers can be used to carry out forensic testing in cases involving Portuguese individuals. The purpose of this work was to contribute to this development, both through the verification of SNP multiplexes in the Portuguese population and through the modification and improvement of these tools in order to obtain more and better Information with them. Thus, this work intended to study and optimize individual identification SNP multiplexes to be used on kinship testing and on individual identification and to study a phenotype informative SNP multiplex for application in the resolution of cases where there is no suspect’s sample for comparison. Initially, based on the 52-plex developed by the SNPforID consortium, it was developed and optimized a set of 20 loci set for individual identification so that these could be used as an additional tool to STR investigation in the study of paternity testing and kinship analysis. Later, it was studied the population and forensic parameters of the 52-plex in the Portuguese population and the effectiveness of this multiplex in the analysis of complex samples such as bone, tooth or crime scene’s samples from which it was not obtained a complete genetic profile when applying a commercial STR kit. Another main objective was to study the application of IrisPlex in Portuguese population. This is a multiplex designed to infer about the eye color of a sample donor. In addition, since that when this thesis project was carried out it was verified that the markers that make up this multiplex, besides being related to eye color determination are also involved in hair and skin color, due to the main genes involved in the 3 mechanisms being the same, it was also decided to supplement this multiplex with additional markers in order to verify if the resulting tool could provide additional information on these other externally visible characteristics. Thus, this doctoral thesis presents the results obtained through the analysis of SNPs and of its applicability to the Portuguese population, focusing on the individual identification loci and on the markers used for forensic DNA phenotyping. The results obtained are presented in chapters II to V, in the form of scientific articles which have been or will be published in indexed and peer-reviewed international scientific publications. In the future, SNP analysis will certainly be used more quite often in criminal and identity investigation casework, namely through the analysis of identity investigation and of forensic DNA phenotyping SNPs