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.
Highlights
In forensic sciences, Massively Parallel Sequencing (MPS) surpassed conventional DNA profiling technologies, e.g. capillary electrophoresis-based sequencing, because 1) MPS is capable of obtaining detailed sequence information on conventional genetic markers; 2) MPS has increased multiplexing capabilities; 3) MPS reports massive amounts of data simultaneously from one or many individuals; and 4) MPS provides a higher throughput DNA sequencing procedure[1, 2]
The MPS platforms dedicated for TM forensic genetics are the MiSeq FGx Forensic Genomics System (Illumina) and the HID-Ion Personal Genome ® TM Machine (PGM) (Thermo Fisher Scientific)
The two MPS systems initially showed more than 43% non-concordance at 28 out of the 83 SNPs analyzed (Fig. 1, gray circle with red dot) because the two MPS platforms use different nomenclature in reporting SNP genotypes
Summary
The MPS platforms dedicated for TM forensic genetics are the MiSeq FGx Forensic Genomics System (Illumina) and the HID-Ion Personal Genome ® TM Machine (PGM) (Thermo Fisher Scientific). These platforms are coupled with the commercially available panTM els for human identification, the ForenSeq DNA Signature Prep kit (Illumina) and the HID-Ion AmpliSeq TM TM Identity Panel (Thermo Fisher Scientific). These MPS systems sequence in one reaction 124 (HID-Ion PGM ) ® TM TM and 173 (MiSeq FGx , with additional 59 STR markers) SNP markers, respectively. Percentage of non-concordance between the HID-Ion PGM and MiSeq FGx MPS platforms
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