Population Data from Cape Verde: Allele Frequencies of the 26 Most Commonly Used Y-STR Loci for Forensic and Medico-Legal Purposes

Abstract

Y-chromosomal short tandem repeats (Y-STRs) are widely used in forensic genetics due to their specificity to the Y chromosome, proving particularly useful for the identification of male genetic profiles in complex biological mixtures, such as those encountered in sexual assault cases. Despite their utility, the effective forensic application of Y-STRs depends on the population representativeness within genetic reference databases. Before applying the Investigator® Argus Y-28 QS kit (QIAGEN, Hilden, Germany) to the population samples, an internal validation was performed at the Forensic Genetics and Biology Services - North Delegation (INMLCF, I.P.). Direct comparison with the Yfiler® Plus kit demonstrated full concordance of haplotypes, while calibration with certified reference material ensured accurate allele assignment. Robust analytical thresholds were established from negative controls, and sensitivity tests showed that complete and reliable profiles could be obtained from as little as 0.5 ng of DNA, whereas higher concentrations led to artefacts. Additional studies confirmed the precision, reproducibility, and tolerance of the kit to challenging conditions, including UV exposure, supporting its forensic applicability. This dissertation includes two scientific articles published in the journal Genes (MDPI), within the scope of forensic and population genetics. The first article provides a comprehensive review of the application of Y-STRs in sexual crimes, highlighting their advantages, limitations, and the relevance of rapidly mutating Y-STRs (RM Y-STRs) for differentiating closely related male individuals. It also emphasizes the need to increase population representation in databases such as the Y Chromosome Haplotype Reference Database (YHRD), with particular focus on underrepresented groups, such as the Cape Verdean population. The second article presents a population study that characterizes the genetic diversity of the Cape Verdean population residing in Portugal, based on 26 Y-STR loci, including RM Y-STRs. The results reveal a high level of haplotype diversity and reflect the admixed African and European genetic background of this population. The inclusion of these data in the YHRD enhances the statistical robustness of kinship analyses and forensic identification. Together, these two studies reinforce the importance of integrating underrepresented population data into genetic databases and critically applying Y-STR markers in sensitive forensic contexts such as sexual crimes, thus promoting more equitable, rigorous, and scientifically grounded practices in forensic genetics.