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

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.

Performance Comparison of Massively Parallel Sequencing (MPS) Instruments Using Single-Nucleotide Polymorphism (SNP) Panels for Ancestry

“…Nevertheless, the ancestry inference was concordant for samples run on both systems. The results obtained in this study validate the inferences made on studies reported earlier for the PGM 9,20–24,26–32 in that the introduction of the automated workflow for higher throughput did not alter the predictions provided by the manufacturer’s plugin. With ever-increasing demands on the analyst, it is feasible that the S5 could be implemented to streamline operations, saving hours of labor to perform priority tasks.…”

Assessment of the Precision ID Identity Panel kit on challenging forensic samples

“…The use of a threshold for the "locus call" (e.g., its genotyping) has been debated from the very beginning of the application of PCR-MPS technologies in Forensic Genetics, and a minimum of 20 x has been suggested as a reliable threshold [12]. To date, a wide range of thresholds, from 6 x to 200 x, have been used in different studies characterizing the Precision ID Identity Panel [12][13][14]23,[26][27][28] as well other SNP-based methods [39][40][41]. In the present study, the definition of this threshold has been empirically defined as follows.…”

Validation and interpretation of IGH and TCR clonality testing by Ion Torrent S5 NGS for diagnosis and disease monitoring in B and T cell cancers

“…Given the reported higher sensitivity and specificity of NGS methods for IGH and TCR clonality testing, we decided to move from a method that used PCR fragment analysis by capillary electrophoresis (Invivoscribe, Inc) to an NGS-based method. Here we describe how we validated the NGS LymphoTrack assays [ 9 , 10 , 22 ] (Invivoscribe, Inc) with the Ion Torrent S5 sequencing instrument, which employs a different sequencing chemistry than the Illumina platforms [ 23 , 24 ] and has not been previously reported for use with NGS clonality studies to our knowledge. We also discuss the pitfalls in comparing to other molecular methodologies and to clinical measurements of disease and in interpreting results.…”