Characterization of the 172 SNPs Included in the ForenSeq™ DNA Signature Prep Kit in a Population from Northeast Italy

• Published in: International journal of molecular sciences Vol. 26; no. 11; p. 5035
• Main Authors: Saccardo, Chiara, De Leo, Domenico, Turrina, Stefania
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 23.05.2025; MDPI
• Subjects: Analysis; Deoxyribonucleic acid; DNA; DNA Fingerprinting - methods; DNA Fingerprinting - standards; DNA Fingerprinting - statistics & numerical data; Forensic Genetics - methods; Forensic Genetics - standards; Genealogy; Genetic aspects; Genetic markers; Genetic testing; Genomes; Genomics; Haplotypes; High-Throughput Nucleotide Sequencing; Humans; Italy; Mutation; Polymorphism, Single Nucleotide; Razors; Single nucleotide polymorphisms; Italy; United States; California; United States > US; microhaplotypes; MiSeq™ FGx Forensic Genomics System; single nucleotide polymorphisms; massively parallel sequencing; forensic genetics
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms26115035

In this study, 172 Single-Nucleotide Polymorphisms (SNPs) (94 identity-informative SNPs, 56 ancestry-informative SNPs, and 22 phenotypic-informative SNPs) included in the ForenSeq™ DNA Signature Prep kit/DNA Primer Mix B (Verogen) were used for genotyping DNA samples from a population of twenty-one unrelated subjects, native to Northeast Italy. SNP sequencing was performed with the MiSeq FGx™ Forensic Genomics System (Illumina-Verogen), and data were analyzed using the Universal Analysis Software (UAS) v1.2. Raw data underwent further examination with STRait Razor v3 (SRv3) to compare the target SNPs’ genotype calls made with UAS and to identify the presence of microhaplotypes (MHs) due to SNPs associated with the same target SNP’s amplicon. The allele (haplotype) frequencies, Hardy–Weinberg equilibrium, linkage disequilibrium, number of effective alleles (Ae), and relevant forensic statistic parameters were calculated. Among the 172 SNPs evaluated, 45 unique microhaplotypes were found, comprising a novel sequence variant never previously described. The presence of MHs resulted in an 8.00% rise in the typologies of unique sequences, leading to changes in Ae. Notably, for 12 out of the 94 iiSNPs, the values of Ae exceeded 2.00, which is generally associated with a higher expected heterozygosity and increased power of discrimination.