Assessment of a microhaplotype panel for human identification and ancestry inference in Brazil

Microhaplotypes (MHs) comprise multiple single nucleotide polymorphisms (SNPs) in DNA segments of up to 300 bp in length. These SNP combinations result in numerous allelic variations (i.e., haplotypes). They are an emerging type of genetic marker with the potential to be an alternative to Short Tandem Repeats (STRs), Single Nucleotide Polymorphisms (SNPs), and Insertion/deletion polymorphisms (InDels) in population genetic studies and forensic cases involving degraded DNA or mixed contributors. This study is the first to evaluate a microhaplotype panel in an admixed Brazilian population. We assessed 130 MH markers in 344 individuals from Ribeirão Preto (State of São Paulo, Brazil) regarding their human identification and ancestry prediction application. DNA was extracted, and samples were genotyped using the Infinium Multi-Ethnic Global-8 array (MEGA) Kit (Illumina). The Sanger and Michigan imputation tools inferred SNPs missing in the MEGA assay. The linkage disequilibrium analysis indicated that 108 out of the 128 microhaplotypes behave independently at a population level, and the combined match probability for these 108 MHs was 4.4 × 10^-81. Compared to widely used STR panels, including the 20 CODIS loci, the 108 MHs evaluated showed substantially higher discriminatory power [1 - (2.9 × 10^-28) vs. 1 - (4.4 × 10^-81). Although STRs remain the global standard in forensic genetics, these findings emphasize the potential of MHs to improve individual identification, particularly in complex or degraded samples. Analyses of 126 MHs differentiated the populations from Africa, East Asia, America (Native Americans), and Europe. This microhaplotype panel provides a powerful complementary tool for individual identification alongside the markers currently used in forensic genetics.