Sequence-based genotyping of 58 STRs and 94 iiSNPs with Verogen’s ForenSeq DNA signature prep kit in Mexican-Mestizos from Jalisco state (West, México)

Abstract

Massively parallel sequencing (MPS) allows simultaneous detection of sequence variation of both Single nucleotide polymorphisms (SNPs) and Short tandem repeats (STRs) with different inheritance patterns, such as autosomal (aSTRs), patrilineal Y-linked (Y-STRs), and X-chromosomal (X-STRs). However, to apply these methodologies for Human Identification (HID), population databases with sequence-based (SB) allele frequencies are needed. For this reason, we sequenced 58 STRs (aSTRs, X-STRs, and Y-STRs) and 94 identity informative SNPs (iiSNPs) on 95 Mexican-Mestizo (admixed) individuals from the Jalisco state (West, Mexico), with the Primer Set-A of the ForenSeq™ DNA Signature Prep Kit. For SB allele calling, we used the recent ISFG recommendations for STR sequence nomenclature. The information provided by the SB variation (including flanking regions) in the STRs increased their allelic diversity regarding the length-based (LB) alleles, as follows: 46.2%, 47%, and 18.4% for aSTRs, X-STRs, and Y-STRs, respectively. The combined power of discrimination for aSTRs was virtually 100% based on LB and SB alleles, whereas the combined power of exclusion was 99.9999999977% and 99.9999999999%, respectively. The haplotypes based on X-STRs and Y-STRs show 100% of discriminatory capacity. Our results showed an increase in allele diversity and discriminatory capacity of this genomic system regarding forensic kits based on capillary electrophoresis. This study represents an effort to incorporate more genomic databases from Mexico and Latin America for the forensic application of MPS.