title: Effects of the Ion PGM™ Hi-Q™ sequencing chemistry on sequence data quality.
abstract: Massively parallel sequencing (MPS) offers substantial improvements over current forensic DNA typing methodologies such as increased resolution, scalability, and throughput. The Ion PGM™ is a promising MPS platform for analysis of forensic biological evidence. The system employs a sequencing-by-synthesis chemistry on a semiconductor chip that measures a pH change due to the release of hydrogen ions as nucleotides are incorporated into the growing DNA strands. However, implementation of MPS into forensic laboratories requires a robust chemistry. Ion Torrent's Hi-Q™ Sequencing Chemistry was evaluated to determine if it could improve on the quality of the generated sequence data in association with selected genetic marker targets. The whole mitochondrial genome and the HID-Ion STR 10-plex panel were sequenced on the Ion PGM™ system with the Ion PGM™ Sequencing 400 Kit and the Ion PGM™ Hi-Q™ Sequencing Kit. Concordance, coverage, strand balance, noise, and deletion ratios were assessed in evaluating the performance of the Ion PGM™ Hi-Q™ Sequencing Kit. The results indicate that reliable, accurate data are generated and that sequencing through homopolymeric regions can be improved with the use of Ion Torrent's Hi-Q™ Sequencing Chemistry. Overall, the quality of the generated sequencing data supports the potential for use of the Ion PGM™ in forensic genetic laboratories.
authors.affiliation: Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., CBH-250, Fort Worth, TX, 76107, USA. Jennifer.Churchill@unthsc.edu.
authors.forename: Jennifer D
authors.initials: JD
authors.lastname: Churchill
authors.affiliation: Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., CBH-250, Fort Worth, TX, 76107, USA.
authors.forename: Jonathan L
authors.initials: JL
authors.lastname: King
authors.affiliation: Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., CBH-250, Fort Worth, TX, 76107, USA.
authors.forename: Ranajit
authors.initials: R
authors.lastname: Chakraborty
authors.affiliation: Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., CBH-250, Fort Worth, TX, 76107, USA.|Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Bruce
authors.initials: B
authors.lastname: Budowle
mesh_terms: D016172:DNA Fingerprinting; D000068598:Data Accuracy; D053803:Forensic Genetics; D005819:Genetic Markers; D054629:Genome, Mitochondrial; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation*; D006801:Humans; D018895:Microsatellite Repeats; D044469:Racial Groups / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers
keywords: Hi-Q™; Ion PGM™; Massively parallel sequencing (MPS); Mitochondrial DNA; STRs