Choice between DNA primer sets (A or B) of the ForenSeq kit: forensic evaluation in a Mexican admixed population sample

• Published in: International journal of legal medicine 2024-11
• Main Authors: Aguilar-Velázquez, José Alonso, García-Aceves, Mayra Elizabeth, Córdova-Mercado, Miranda Fabiola, Guardado-Estrada, Mariano, Peña-Durán, Emiliano, Villavicencio-Queijeiro, Alexa, Salas-Salas, Orlando, Coronado-Ávila, Carolina Elena, Cárdenas-Monroy, Christian Adrián, Ramos-González, Benito, Rangel-Villalobos, Héctor
• Format: Article
• Language: English
• ISSN: 0937-9827; 1437-1596; 1437-1596
• DOI: 10.1007/s00414-024-03366-1

Massively parallel sequencing (MPS) overcomes many PCR-CE limitations to analyze STRs and allow simultaneous inclusion of SNPs in forensic cases. By MPS, the ForenSeq™ DNA Signature Prep kit analyzes 27 aSTRs, 7 X-STRs, 24Y-STRs, and 94 identity-informative SNPs (iiSNPs) with the DNA Primer Set-A (DPS-A). Optionally, the DNA Primer Set-B (DPS-B) adds to the analysis 56 ancestry-informative SNPs (aiSNPs) and 24 phenotype-informative SNPs (piSNPs), but diminishes from 96 to 32 the number of samples per sequencing run. We assessed the forensic informativity provided by the loci analyzed by these two DPS in admixed individuals from Mexico City (Center, Mexico). For STRs, we report length-based (LB) and sequence-based (SB) allele frequencies and forensic parameters of the 152 identity informative markers (DPS-A). For aSTRs, the combined PD of SB genotypes (PD ~ 100%) was ~ 2949 times larger than that from LB. Conversely, the observed phenotype distribution offered low PD levels (PD = 6.6% and 10.4%), whereas piSNPs predicted accurately only the modal brown eye and dark hair colors, respectively. Similarly, aiSNPs detected a large prevalence of admixed individuals (97.3%; PD = 5.4%). Although few individuals were inferred as Europeans and Native Americans (1.37% each), they were self-declared as admixed, which result confusing for HID purposes. In brief, SB genotypes increased significantly the informativity of STRs to solve complex cases (DPS-A), whereas aiSNPs and piSNPs added mostly irrelevant information (DPS-B). We provide useful cost-benefit criteria in one Latin American population to choose DPS-A (96 samples) instead of DPS-B (32 samples) of the Forenseq kit.