A Novel SNP-STR System Based on a Capillary Electrophoresis Platform.

Hui Jian,Lin Zhang,Ranran Zhang,Li Wang,Meili Lv,Yu Tan,Lagabaiyila Zha,Weibo Liang,Jijun Wang,Shengqiu Qu

doi:10.3389/fgene.2021.636821

Abstract

Various compound markers encompassing two or more variants within a small region can be regarded as generalized microhaplotypes. Many of these markers have been investigated for various forensic purposes, such as individual identification, deconvolution of DNA mixtures, or forensic ancestry inference. SNP-STR is a compound biomarker composed of a single nucleotide polymorphism (SNP) and a closely linked short tandem repeat polymorphism (STR), and possess the advantages of both SNPs and STRs. In addition, in conjunction with a polymerase chain reaction (PCR) technique based on the amplification refractory mutation system (ARMS), SNP-STRs can be used for forensic unbalanced DNA mixture analysis based on capillary electrophoresis (CE), which is the most commonly used platform in worldwide forensic laboratories. Our previous research reported 11 SNP-STRs, but few of them are derived from the commonly used STR loci, for which existing STR databases can be used as a reference. For maximum compatibility with existing DNA databases, in this study, we screened 18 SNP-STR loci, of which 14 were derived from the expanded CODIS core loci set. Stable and sensitive SNP-STR multiplex PCR panels based on the CE platform were established. Assays on simulated two-person DNA mixtures showed that all allele-specific primers could detect minor DNA components in 1:500 mixtures. Population data based on 113 unrelated Chengdu Han individuals were investigated. A Bayesian framework was developed for the likelihood ratio (LR) evaluation of SNP-STR profiling results obtained from two-person mixtures. Furthermore, we report on the first use of SNP-STRs in casework to show the advantages and limitations for use in practice. Compared to 2.86 × 103 for autosomal STR kits, the combined LR reached 7.14 × 107 using the SNP-STR method in this casework example.

Highlights

Microhaplotypes has been revealed the abilities in different forensic application purposes, including individual identification, mixture recognition (Chen et al, 2018; Oldoni and Podini, 2019; Oldoni et al, 2020), and ancestry inference (Bulbul et al, 2018; Chen et al, 2019)
Two single nucleotide polymorphism (SNP) allele-specific forward primers with mismatches introduced using the amplification refractory mutation system (ARMS) technique and one reverse primer were obtained for each SNP-short tandem repeat polymorphism (STR) locus
We developed a novel SNP-STR system based on a capillary electrophoresis (CE) platform

Summary

Introduction

Microhaplotypes has been revealed the abilities in different forensic application purposes, including individual identification, mixture recognition (Chen et al, 2018; Oldoni and Podini, 2019; Oldoni et al, 2020), and ancestry inference (Bulbul et al, 2018; Chen et al, 2019). Indels occur less frequently in the genome than SNPs. indel markers are almost unavailable around the forensic commonly used STRs, such as the expanded CODIS core loci STR set and the Extended European Standard Set (ESS) (Welch et al, 2012; Tan et al, 2018). Indel markers are almost unavailable around the forensic commonly used STRs, such as the expanded CODIS core loci STR set and the Extended European Standard Set (ESS) (Welch et al, 2012; Tan et al, 2018) Based on these reasons, SNP-STRs combine the advantages of both SNPs and STRs, provide more information than DIPSNPs and SNP-SNPs, have more candidates than DIP-STRs, and offer the possibility of gaining better insights into population genetic processes

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Discussion

Conclusion