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Comparative Study
. 2017 Mar 24;7(1):398.
doi: 10.1038/s41598-017-00510-3.

Comparison of Two Massively Parallel Sequencing Platforms using 83 Single Nucleotide Polymorphisms for Human Identification

Dame Loveliness T Apaga  1   2 , Sheila E Dennis  1   2   3 , Jazelyn M Salvador  1   2 , Gayvelline C Calacal  1   2 , Maria Corazon A De Ungria  4   5
Affiliations
Comparative Study

Comparison of Two Massively Parallel Sequencing Platforms using 83 Single Nucleotide Polymorphisms for Human Identification

Dame Loveliness T Apaga et al. Sci Rep. .

Abstract

The potential of Massively Parallel Sequencing (MPS) technology to vastly expand the capabilities of human identification led to the emergence of different MPS platforms that use forensically relevant genetic markers. Two of the MPS platforms that are currently available are the MiSeq® FGx™ Forensic Genomics System (Illumina) and the HID-Ion Personal Genome Machine (PGM)™ (Thermo Fisher Scientific). These are coupled with the ForenSeq™ DNA Signature Prep kit (Illumina) and the HID-Ion AmpliSeq™ Identity Panel (Thermo Fisher Scientific), respectively. In this study, we compared the genotyping performance of the two MPS systems based on 83 SNP markers that are present in both MPS marker panels. Results show that MiSeq® FGx™ has greater sample-to-sample variation than the HID-Ion PGM™ in terms of read counts for all the 83 SNP markers. Allele coverage ratio (ACR) values show generally balanced heterozygous reads for both platforms. Two and four SNP markers from the MiSeq® FGx™ and HID-Ion PGM™, respectively, have average ACR values lower than the recommended value of 0.67. Comparison of genotype calls showed 99.7% concordance between the two platforms.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1
Percentage of non-concordance between the HID-Ion PGM™ and MiSeq® FGx™ MPS platforms. Direct Comparison: Concordance evaluation was performed using raw genotype calls reported by the MPS platforms. Indirect Comparison: Concordance evaluation was performed after reverse complementation of all observed genotypes at the 28 SNP loci from the MiSeq® FGx™ platform. Reverse complementation was necessary because the two MPS systems use different nomenclature in reporting SNP calls.
Figure 2
Figure 2
Distribution of read counts and median coverage of the SNP markers typed with HID-Ion PGM™.
Figure 3
Figure 3
Distribution of read counts and median coverage of the SNP markers typed with MiSeq® FGx™ Forensic Genomics System.
Figure 4
Figure 4
Allele Coverage Ratio of SNPs from the HID-Ion PGM™ and the MiSeq® FGx™ MPS platforms. Gray line marks the 0.67 ACR threshold for balanced heterozygous alleles.
See this image and copyright information in PMC

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