Inter-platform evaluation of the MPSplex large-scale tri-allelic SNP panel for forensic identification

Abstract

MPSplex is a large-scale forensic massively parallel sequencing (MPS) panel with 1,270 tri-allelic SNPs, 44 microhaplotypes (MH) and 55 ancestry-informative bi-allelic SNPs (aiSNPs) designed for missing persons identification. We have evaluated MPSplex with the most widely used MPS platforms in the forensic field: the Illumina MiSeq, the Thermo Fisher Scientific Ion S5 and the Qiagen GeneReader. The tri-allelic SNPs of MPSplex were previously identified from the most polymorphic loci with three common alleles in 1000 Genomes Phase III data and combined with the 44 MH and 55 aiSNPs, then implemented into a QIAseq Targeted DNA Custom Panel (Qiagen), a marker panel which uses Unique Molecular Indices or UMIs. The UMI random-sequence DNA molecules are incorporated onto DNA fragments before the Target Enrichment PCR, allowing the identification of reads that originated from the same template and consequently they can be used to correct the errors that may arise within the PCR or the sequencing process. In this study, we present the results of an inter-platform evaluation of the MPSplex panel, characterizing its performance in different forensic scenarios, which assessed aspects that include sensitivity, genotyping accuracy and mixture analysis. MPSplex aims to provide a tool designed for kinship analysis that can be applied beyond the resolution of first- or second-degree relationships, avoiding the need for much bigger forensic panels designed for genealogy purposes, which usually require significantly more sequencing resources. This study provides evaluation of MPSplex using the MPS systems in routine use for forensic genotyping of large-scale panels of SNPs.