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Effects of the Ion PGM™ Hi-Q™ sequencing chemistry on sequence data quality.
Int J Legal Med. 2016 Sep; 130(5):1169-80.IJ

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+Show Affiliations

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.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.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.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.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

27025714

Citation

Churchill, Jennifer D., et al. "Effects of the Ion PGM™ Hi-Q™ Sequencing Chemistry On Sequence Data Quality." International Journal of Legal Medicine, vol. 130, no. 5, 2016, pp. 1169-80.
Churchill JD, King JL, Chakraborty R, et al. Effects of the Ion PGM™ Hi-Q™ sequencing chemistry on sequence data quality. Int J Legal Med. 2016;130(5):1169-80.
Churchill, J. D., King, J. L., Chakraborty, R., & Budowle, B. (2016). Effects of the Ion PGM™ Hi-Q™ sequencing chemistry on sequence data quality. International Journal of Legal Medicine, 130(5), 1169-80. https://doi.org/10.1007/s00414-016-1355-y
Churchill JD, et al. Effects of the Ion PGM™ Hi-Q™ Sequencing Chemistry On Sequence Data Quality. Int J Legal Med. 2016;130(5):1169-80. PubMed PMID: 27025714.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Effects of the Ion PGM™ Hi-Q™ sequencing chemistry on sequence data quality. AU - Churchill,Jennifer D, AU - King,Jonathan L, AU - Chakraborty,Ranajit, AU - Budowle,Bruce, Y1 - 2016/03/30/ PY - 2016/01/22/received PY - 2016/03/04/accepted PY - 2016/3/31/entrez PY - 2016/3/31/pubmed PY - 2017/9/7/medline KW - Hi-Q™ KW - Ion PGM™ KW - Massively parallel sequencing (MPS) KW - Mitochondrial DNA KW - STRs SP - 1169 EP - 80 JF - International journal of legal medicine JO - Int J Legal Med VL - 130 IS - 5 N2 - 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. SN - 1437-1596 UR - https://www.unboundmedicine.com/medline/citation/27025714/Effects_of_the_Ion_PGM™_Hi_Q™_sequencing_chemistry_on_sequence_data_quality_ L2 - https://dx.doi.org/10.1007/s00414-016-1355-y DB - PRIME DP - Unbound Medicine ER -