Sequencing of human identification markers in an Uyghur population using the MiSeq FGxTM Forensic Genomics System

Halimureti Simayijiang; Niels Morling; Claus Børsting

doi:10.1080/20961790.2020.1779967

Sequencing of human identification markers in an Uyghur population using the MiSeq FGx^TM Forensic Genomics System

Forensic Sci Res. 2020 Sep 10;7(2):154-162. doi: 10.1080/20961790.2020.1779967. eCollection 2022.

Authors

Halimureti Simayijiang^{1

2}, Niels Morling¹, Claus Børsting¹

Affiliations

¹ Faculty of Health and Medical Sciences, Section of Forensic Genetics, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark.
² Faculty of Criminal Science and Technology, Xinjiang Police College, Xinjiang, China.

Abstract

Massively parallel sequencing (MPS) offers a useful alternative to capillary electrophoresis (CE) based analysis of human identification markers in forensic genetics. By sequencing short tandem repeats (STRs) instead of determining the fragment lengths by CE, the sequence variation within the repeat region and the flanking regions may be identified. In this study, we typed 264 Uyghur individuals using the MiSeq FGx™ Forensic Genomics System and Primer Mix A of the ForenSeq™ DNA Signature Prep Kit that amplifies 27 autosomal STRs, 25 Y-STRs, seven X-STRs, and 94 HID-SNPs. STRinNGS v.1.0 and GATK 3.6 were used to analyse the STR regions and HID-SNPs, respectively. Increased allelic diversity was observed for 33 STRs with the PCR-MPS assay. The largest increases were found in DYS389II and D12S391, where the numbers of sequenced alleles were 3-4 times larger than those of alleles determined by repeat length alone. A relatively large number of flanking region variants (28 SNPs and three InDels) were observed in the Uyghur population. Seventeen of the flanking region SNPs were rare, and 12 of these SNPs had no accession number in dbSNP. The combined mean match probability and typical paternity index based on 26 sequenced autosomal STRs were 3.85E-36 and 1.49E + 16, respectively. This was 10 000 times lower and 1 000 times higher, respectively, than the same parameters calculated from STR repeat lengths.Key PointsSequencing data on STRs and SNPs used for human identification are presented for the Uyghur population.STRinNGS v.1.0 was used to analyse the flanking regions of STRs.The concordance between PCR-CE and PCR-MPS results was 99.86%.Detection of sequence variation in STRs and their flanking regions increased the allelic diversity.

Keywords: ForenSeq™ DNA Signature Prep Kit; Forensic sciences; Uyghur; forensic genetics; massively parallel sequencing (MPS); short tandem repeat (STR); single nucleotide polymorphism (SNP).

Grants and funding

The study was supported by a research grant to Halimureti Simayijiang from the Xinjiang Police College, the Department of Education of the Xinjiang Uyghur Autonomous Region, and Ellen and Aage Andersen’s Foundation.