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Single nucleotide polymorphism typing with massively parallel sequencing for human identification

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Abstract

The Ion AmpliSeq™ HID single nucleotide polymorphism (SNP) panel, a primer pool of 103 autosomal SNPs and 33 Y-SNPs, was evaluated using the Ion 314™ Chip on the Ion PGM™ Sequencer with four DNA samples. The study focused on the sequencing of DNA at three different initial target quantities, related interpretation issues, and concordance of results with another sequencing platform, i.e., Genome Analyzer IIx. With 10 ng of template DNA, all genotypes at the 136 SNPs were detected. With 1 ng of DNA, all SNPs were detected and one SNP locus in one sample showed extreme heterozygote imbalance on allele coverage. With 100 pg of DNA, an average of 1.6 SNP loci were not detected, and an average of 4.3 SNPs showed heterozygote imbalance. The average sequence coverage was 945–600× at autosomal SNPs and 465–209× at Y-SNPs for 10 ng–100 pg of DNA. The average heterozygote allele coverage ratio was 89.6–61.8 % for 10 ng–100 pg of DNA. At 10 ng of DNA, all genotypes of the 95 SNPs shared between the two different sequencing platforms were concordant except for one SNP, rs1029047. The error was due to the misalignment of a flanking homopolymer. Overall, the data support that genotyping a large battery of SNPs is feasible with massively parallel sequencing. With barcode systems, better allele balance, and specifically designed alignment software, a more comprehensive rapid genotyping and more cost-effective results may be obtained from multiple samples in one analysis than are possible with current typing and capillary electrophoresis systems.

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Acknowledgments

This project was supported in part by Award No. 2012-DN-BX-K033, awarded by the National Institute of Justice, Office of Justice Programs, US Department of Justice. The opinions, findings, and conclusions or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect those of the US Department of Justice. We would like to thank Life Technologies for providing its technical expertise and contributing to the sample preparation and sequencing chemistries used in this study. In addition, we would like to thank Illumina Inc for its contributions for generating the in-house SNP panel.

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Authors and Affiliations

  1. Institute of Applied Genetics, Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA

    Seung Bum Seo, Jonathan L. King, David H. Warshauer, Carey P. Davis, Jianye Ge & Bruce Budowle

  2. Center of Excellence in Genomic Medicine (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia

    Bruce Budowle

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  1. Seung Bum Seo
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  2. Jonathan L. King
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  3. David H. Warshauer
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  4. Carey P. Davis
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  5. Jianye Ge
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  6. Bruce Budowle
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Corresponding author

Correspondence to Bruce Budowle.

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Seo, S.B., King, J.L., Warshauer, D.H. et al. Single nucleotide polymorphism typing with massively parallel sequencing for human identification. Int J Legal Med 127, 1079–1086 (2013). https://doi.org/10.1007/s00414-013-0879-7

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  • DOI: https://doi.org/10.1007/s00414-013-0879-7

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