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

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...

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Autores principales: Simayijiang, Halimureti, Morling, Niels, Børsting, Claus
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Taylor & Francis 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9246034/
https://www.ncbi.nlm.nih.gov/pubmed/35784409
http://dx.doi.org/10.1080/20961790.2020.1779967
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author Simayijiang, Halimureti
Morling, Niels
Børsting, Claus
author_facet Simayijiang, Halimureti
Morling, Niels
Børsting, Claus
author_sort Simayijiang, Halimureti
collection PubMed
description 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 POINTS: Sequencing 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.
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spelling pubmed-92460342022-07-01 Sequencing of human identification markers in an Uyghur population using the MiSeq FGx(TM) Forensic Genomics System Simayijiang, Halimureti Morling, Niels Børsting, Claus Forensic Sci Res Original Articles 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 POINTS: Sequencing 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. Taylor & Francis 2020-09-10 /pmc/articles/PMC9246034/ /pubmed/35784409 http://dx.doi.org/10.1080/20961790.2020.1779967 Text en © 2020 The Author(s). Published by Taylor & Francis Group on behalf of the Academy of Forensic Science. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Articles
Simayijiang, Halimureti
Morling, Niels
Børsting, Claus
Sequencing of human identification markers in an Uyghur population using the MiSeq FGx(TM) Forensic Genomics System
title Sequencing of human identification markers in an Uyghur population using the MiSeq FGx(TM) Forensic Genomics System
title_full Sequencing of human identification markers in an Uyghur population using the MiSeq FGx(TM) Forensic Genomics System
title_fullStr Sequencing of human identification markers in an Uyghur population using the MiSeq FGx(TM) Forensic Genomics System
title_full_unstemmed Sequencing of human identification markers in an Uyghur population using the MiSeq FGx(TM) Forensic Genomics System
title_short Sequencing of human identification markers in an Uyghur population using the MiSeq FGx(TM) Forensic Genomics System
title_sort sequencing of human identification markers in an uyghur population using the miseq fgx(tm) forensic genomics system
topic Original Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9246034/
https://www.ncbi.nlm.nih.gov/pubmed/35784409
http://dx.doi.org/10.1080/20961790.2020.1779967
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