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Massively parallel sequencing of 12 autosomal STRs in Cannabis sativa.
Electrophoresis. 2018 11; 39(22):2906-2911.E

Abstract

Massively parallel sequencing (MPS) is an emerging technology in the field of forensic genetics that provides distinct advantages compared to capillary electrophoresis. This study offers a proof of concept that MPS technologies can be applied to genotype autosomal STRs in Cannabis sativa. A custom panel for MPS was designed to interrogate 12 cannabis-specific STR loci by sequence rather than size. A simple workflow was implemented to integrate the custom PCR multiplex into a workflow compatible with the Ion Plus Fragment Library Kit, Ion™ Chef, and Ion™ S5 System. For data sorting and sequence analysis, a custom configuration file was designed for STRait Razor v3 to parse and extract STR sequence data. This study represents a preliminary investigation of sequence variation for 12 autosomal STR loci in 16 cannabis samples. Full concordance was observed between the MPS and CE data. Results revealed intra-repeat variation in eight loci where the nominal or size-based allele was identical, but variances were discovered in the sequence of the flanking region. Although only a small number of cannabis samples were evaluated, this study demonstrates that more informative STR data can be obtained via MPS.

Authors+Show Affiliations

Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, TX, USA.Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, TX, USA.Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA.Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, TX, USA. School of Biomedical Sciences, University of Queensland, Brisbane, Queensland, Australia.Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, TX, USA.

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

30221375

Citation

Houston, Rachel, et al. "Massively Parallel Sequencing of 12 Autosomal STRs in Cannabis Sativa." Electrophoresis, vol. 39, no. 22, 2018, pp. 2906-2911.
Houston R, Mayes C, King JL, et al. Massively parallel sequencing of 12 autosomal STRs in Cannabis sativa. Electrophoresis. 2018;39(22):2906-2911.
Houston, R., Mayes, C., King, J. L., Hughes-Stamm, S., & Gangitano, D. (2018). Massively parallel sequencing of 12 autosomal STRs in Cannabis sativa. Electrophoresis, 39(22), 2906-2911. https://doi.org/10.1002/elps.201800152
Houston R, et al. Massively Parallel Sequencing of 12 Autosomal STRs in Cannabis Sativa. Electrophoresis. 2018;39(22):2906-2911. PubMed PMID: 30221375.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Massively parallel sequencing of 12 autosomal STRs in Cannabis sativa. AU - Houston,Rachel, AU - Mayes,Carrie, AU - King,Jonathan L, AU - Hughes-Stamm,Sheree, AU - Gangitano,David, Y1 - 2018/09/25/ PY - 2018/03/31/received PY - 2018/09/06/revised PY - 2018/09/07/accepted PY - 2018/9/18/pubmed PY - 2019/10/8/medline PY - 2018/9/18/entrez KW - Cannabis sativa KW - Forensic plant science KW - Ion™ S5 KW - Massively parallel sequencing KW - STR SP - 2906 EP - 2911 JF - Electrophoresis JO - Electrophoresis VL - 39 IS - 22 N2 - Massively parallel sequencing (MPS) is an emerging technology in the field of forensic genetics that provides distinct advantages compared to capillary electrophoresis. This study offers a proof of concept that MPS technologies can be applied to genotype autosomal STRs in Cannabis sativa. A custom panel for MPS was designed to interrogate 12 cannabis-specific STR loci by sequence rather than size. A simple workflow was implemented to integrate the custom PCR multiplex into a workflow compatible with the Ion Plus Fragment Library Kit, Ion™ Chef, and Ion™ S5 System. For data sorting and sequence analysis, a custom configuration file was designed for STRait Razor v3 to parse and extract STR sequence data. This study represents a preliminary investigation of sequence variation for 12 autosomal STR loci in 16 cannabis samples. Full concordance was observed between the MPS and CE data. Results revealed intra-repeat variation in eight loci where the nominal or size-based allele was identical, but variances were discovered in the sequence of the flanking region. Although only a small number of cannabis samples were evaluated, this study demonstrates that more informative STR data can be obtained via MPS. SN - 1522-2683 UR - https://www.unboundmedicine.com/medline/citation/30221375/Massively_parallel_sequencing_of_12_autosomal_STRs_in_Cannabis_sativa_ L2 - https://doi.org/10.1002/elps.201800152 DB - PRIME DP - Unbound Medicine ER -