Massively parallel sequencing of 12 autosomal STRs in Cannabis sativa

Electrophoresis. 2018 Nov;39(22):2906-2911. doi: 10.1002/elps.201800152. Epub 2018 Sep 25.

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.

Keywords: Cannabis sativa; Forensic plant science; Ion™ S5; Massively parallel sequencing; STR.

Publication types

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

MeSH terms

  • Cannabis / genetics*
  • DNA, Plant / analysis
  • DNA, Plant / genetics*
  • Forensic Sciences / methods
  • High-Throughput Nucleotide Sequencing / methods*
  • Microsatellite Repeats / genetics*
  • Multiplex Polymerase Chain Reaction

Substances

  • DNA, Plant