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Inter-platform evaluation of the MPSplex large-scale tri-allelic SNP panel for forensic identification
Univ Santiago de Compostela, Spain.
Int Commiss Missing Persons, Netherlands.
Int Commiss Missing Persons, Netherlands.
Linköping University, Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet & Forens Toxicol, Linköping, Sweden.
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2025 (English)In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 77, article id 103233Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
ELSEVIER IRELAND LTD , 2025. Vol. 77, article id 103233
Keywords [en]
Forensic genetics; Tri-allelic SNPs; Unique Molecular Indices (UMIs); Missing persons identification; Massively parallel sequencing
National Category
Genetics and Genomics
Identifiers
URN: urn:nbn:se:liu:diva-212296DOI: 10.1016/j.fsigen.2025.103233ISI: 001439937600001PubMedID: 40037007Scopus ID: 2-s2.0-85219083650OAI: oai:DiVA.org:liu-212296DiVA, id: diva2:1945327
Note

Funding Agencies|Consellera de Cultura, Educacio n e Ordenacio ; Emprego e Industria from Xunta de Galicia, Spain [ED481A-2020/039, PID2019-107876RB-I00]; Ministerio de Educacio n, Cultura y Ciencia, Spain [MCIN/AEI/10.13039/501100011033, PID2022-141224OB-I00, MCIN/AEI/10.13039/501100011 033, IJC2020-042638-I]; Gobierno de Espan [a MCIN/AEI/10.13039/501100011033]; European Union; Hague, Netherlands

Available from: 2025-03-18 Created: 2025-03-18 Last updated: 2025-03-18

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