Ancestry analysis in forensic geneticsnew markers and methodology

Abstract

The analysis of human population variation is an area of considerable interest in the forensic genetics field – ancestry informative assays can provide investigative leads from DNA evidences in cases where the source individual is not known or is unable to declare its ancestry. Short tandem repeat (STR) markers, commonly used in human identification applications, are not ideal for ancestry prediction as they are highly variable between individuals and have low inter-population variation. Binary loci with large allele frequency differences between populations have been proposed as an alternative to estimate biogeographic origin. Autosomal markers have emerged as amongst the best ancestry markers, providing valuable complementary data to Y-chromosome and mitochondrial DNA. This thesis describes five complementary ancestry informative assays that, when combined, can differentiate up to six population groups: Africa, East Asia, Oceania, Native America and two Eurasian groups (Europe and Central South Asia). Nevertheless, the differentiation of the more closely related Middle East group is prone to higher classification errors – higher numbers of markers have to be analysed. The described assays provide ancestry informative genotypes in sensitive tests designed to work with limited DNA samples. Three analyse single nucleotide polymorphisms (SNPs) using SNaPshot® technology. The others analyse insertion deletion polymorphisms (Indels) and STRs using direct PCR-to-CE techniques that offer the possibility to detect mixed profiles. The emergence of next generation sequencing (NGS) technologies allows the analysis of more markers in a single assay, improving the differentiation of closely related populations. Furthermore, the enlarged multiplex scales enhance population divergence balance, enabling the analysis of admixed individuals without biased estimation of co-ancestry proportions. However, although initial validation of a NGS platform is presented in this thesis, further evaluations have to be performed prior to the inclusion of such technology in routine casework.