Forensic applications of compound genetic markers: trends and future directions

A compound marker integrates two or more genetic markers into a single assay. The application of compound markers enhances the predictive accuracy of genetic testing by leveraging the strengths of different genetic variations while mitigating the limitations of individual markers. Compound markers include SNP-SNPs, SNP-STRs, DIP-SNPs, DIP-STRs, Multi-In/Dels, CpG-SNPs, CpG-STRs/CpG-In/Del, and Methylation-Microhaplotypes. Currently, no commercially available multiplex kit can amplify two or more different genetic markers simultaneously in a single reaction. Though compound marker panels for next-generation sequencing (NGS) platforms have been designed, however, reports are scarce on compound markers for genetic studies at a global scale, particularly for African populations. The African population is the most genetically diverse, but is underrepresented due to funding constraints and the need for novel techniques to address diverse and admixed ancestral backgrounds. With the emerging application of NGS in forensic investigations, human identification is not limited to traditional STR typing, as a single NGS run can simultaneously target autosomal STRs, sex determination markers, SNP markers, and InDel/DIP markers. Additional applications of compound markers include mixture deconvolution, detection of minor donors in unbalanced DNA samples, paternity testing, amplification of highly degraded DNA samples and inference of biogeographic ancestry. The workflow of genotyping compound markers through CE and NGS has not yet been integrated into forensic laboratories because it requires the development and internal validation of genetic markers and analytical protocols. Furthermore, it is essential to address the ethical and legal considerations related to the responsible use of genetic data generated from compound markers. The current review explores the application of compound markers, identification of new micro and macrohaplotypes, and considerations for integrating NGS to facilitate forensic investigations.