Advertisement

Species identification in forensic samples using the SPInDel approach: A GHEP-ISFG inter-laboratory collaborative exercise

      Highlights

      • GHEP-ISFG inter-laboratory collaborative exercise using the SPInDel approach.
      • The 24 participating laboratories identified the species in 11 forensic samples.
      • All samples were correctly identified by 22 of the 24 laboratories.
      • Correct species identifications were obtained in 98.8% of the reported SPInDel profiles.
      • The results indicate that the SPInDel can be used in forensic casework investigations.

      Abstract

      DNA is a powerful tool available for forensic investigations requiring identification of species. However, it is necessary to develop and validate methods able to produce results in degraded and or low quality DNA samples with the high standards obligatory in forensic research. Here, we describe a voluntary collaborative exercise to test the recently developed Species Identification by Insertions/Deletions (SPInDel) method. The SPInDel kit allows the identification of species by the generation of numeric profiles combining the lengths of six mitochondrial ribosomal RNA (rRNA) gene regions amplified in a single reaction followed by capillary electrophoresis. The exercise was organized during 2014 by a Working Commission of the Spanish and Portuguese-Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG), created in 2013. The 24 participating laboratories from 10 countries were asked to identify the species in 11 DNA samples from previous GHEP-ISFG proficiency tests using a SPInDel primer mix and control samples of the 10 target species. A computer software was also provided to the participants to assist the analyses of the results. All samples were correctly identified by 22 of the 24 laboratories, including samples with low amounts of DNA (hair shafts) and mixtures of saliva and blood. Correct species identifications were obtained in 238 of the 241 (98.8%) reported SPInDel profiles. Two laboratories were responsible for the three cases of misclassifications. The SPInDel was efficient in the identification of species in mixtures considering that only a single laboratory failed to detect a mixture in one sample. This result suggests that SPInDel is a valid method for mixture analyses without the need for DNA sequencing, with the advantage of identifying more than one species in a single reaction. The low frequency of wrong (5.0%) and missing (2.1%) alleles did not interfere with the correct species identification, which demonstrated the advantage of using a method based on the analysis of multiple loci. Overall, the SPInDel method was easily implemented by laboratories using different genotyping platforms, the interpretation of results was straightforward and the SPInDel software was used without any problems. The results of this collaborative exercise indicate that the SPInDel method can be applied successfully in forensic casework investigations.

      Keywords

      To read this article in full you will need to make a payment

      Purchase one-time access:

      Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online access
      One-time access price info
      • For academic or personal research use, select 'Academic and Personal'
      • For corporate R&D use, select 'Corporate R&D Professionals'

      Subscribe:

      Subscribe to Forensic Science International: Genetics
      Already a print subscriber? Claim online access
      Already an online subscriber? Sign in
      Institutional Access: Sign in to ScienceDirect

      References

        • Araújo R.
        • Pereira F.
        • Asch Bv.
        Applications of DNA-based methods in food forensics.
        Handbook of Forensic Genetics: Biodiversity and Heredity in Civil and Criminal Investigation. World Scientific, 2017: 493-517
        • Johnson R.N.
        • Wilson-Wilde L.
        • Linacre A.
        Current and future directions of DNA in wildlife forensic science.
        Forensic Science International: Genetics. 2014; 10: 1-11
        • Pereira F.
        • Carneiro J.
        • Amorim A.
        Identification of species with DNA-based technology: current progress and challenges.
        Recent Patents on DNA and Gene Sequences. 2008; 2: 187-200
        • Teletchea F.
        • Maudet C.
        • Hänni C.
        Food and forensic molecular identification: update and challenges.
        Trends in Biotechnology. 2005; 23: 359-366
        • Woolfe M.
        • Primrose S.
        Food forensics: using DNA technology to combat misdescription and fraud.
        TRENDS in Biotechnology. 2004; 22: 222-226
        • Dawnay N.
        • Ogden R.
        • McEwing R.
        • Carvalho G.R.
        • Thorpe R.S.
        Validation of the barcoding gene COI for use in forensic genetic species identification.
        Forensic Science International. 2007; 173: 1-6
        • Kitano T.
        • Umetsu K.
        • Tian W.
        • Osawa M.
        Two universal primer sets for species identification among vertebrates.
        International Journal of Legal Medicine. 2007; 121: 423-427
        • Pereira F.
        • Carneiro J.
        • Van Asch B.
        A guide for mitochondrial DNA analysis in non-human forensic investigations.
        Open Forensic Science Journal. 2010; 3: 33-44
        • Wilson-Wilde L.
        • Norman J.
        • Robertson J.
        • Sarre S.
        • Georges A.
        Current issues in species identification for forensic science and the validity of using the cytochrome oxidase I (COI) gene.
        Forensic Science, Medicine, and Pathology. 2010; 6: 233-241
        • Bandelt H.-J.
        • Salas A.
        Current next generation sequencing technology may not meet forensic standards.
        Forensic Science International: Genetics. 2012; 6: 143-145
        • Budowle B.
        • Connell N.D.
        • Bielecka-Oder A.
        • Colwell R.R.
        • Corbett C.R.
        • Fletcher J.
        • et al.
        Validation of high throughput sequencing and microbial forensics applications.
        Investigative Genetics. 2014; 5: 1
        • Pereira F.
        • Carneiro J.
        • Matthiesen R.
        • van Asch B.
        • Pinto N.
        • Gusmão L.
        • et al.
        Identification of species by multiplex analysis of variable-length sequences.
        Nucleic Acids Research. 2010; 38: e203
        • Gonçalves J.
        • Marks C.A.
        • Obendorf D.
        • Amorim A.
        • Pereira F.
        A multiplex PCR assay for identification of the red fox (Vulpes vulpes) using the mitochondrial ribosomal RNA genes.
        Conservation Genetics Resources. 2015; 7: 45-48
        • Carneiro J.
        • Pereira F.
        • Amorim A.
        SPInDel: a multifunctional workbench for species identification using insertion/deletion variants.
        Molecular Ecology Resources. 2012; 12: 1190-1195
        • Alves C.
        • Pereira R.
        • Prieto L.
        • Amorim A.
        • Pereira F.
        Results of the GHEP-ISFG collaborative exercise for the taxonomic identification of forensic samples using the SPInDel method.
        Forensic Science International: Genetics Supplement Series. 2015; 5: e184-e185
        • Butler J.M.
        Advanced Topics in Forensic DNA Typing: Methodology: Methodology.
        Academic Press, 2011
        • Crespillo M.
        • Barrio P.
        • Luque J.
        • Alves C.
        • Aler M.
        • Alessandrini F.
        • et al.
        GHEP-ISFG collaborative exercise on mixture profiles of autosomal STRs (GHEP-MIX01, GHEP-MIX02 and GHEP-MIX03): results and evaluation.
        Forensic Science International: Genetics. 2014; 10: 64-72
        • Montesino M.
        • Salas A.
        • Crespillo M.
        • Albarrán C.
        • Alonso A.
        • Alvarez-Iglesias V.
        • et al.
        Analysis of body fluid mixtures by mtDNA sequencing: an inter-laboratory study of the GEP-ISFG working group.
        Forensic Science International. 2007; 168: 42-56
        • Toscanini U.
        • Gusmão L.
        • Narváez MÁ
        • Álvarez J.
        • Baldassarri L.
        • Barbaro A.
        • et al.
        Analysis of uni and bi-parental markers in mixture samples: lessons from the 22nd GHEP-ISFG intercomparison exercise.
        Forensic Science International: Genetics. 2016; 25: 63-72
        • van Asch B.
        • Albarran C.
        • Alonso A.
        • Angulo R.
        • Alves C.
        • Betancor E.
        • et al.
        Forensic analysis of dog (Canis lupus familiaris) mitochondrial DNA sequences: an inter-laboratory study of the GEP-ISFG working group.
        Forensic Science International: Genetics. 2009; 4: 49-54
        • Vullo C.M.
        • Romero M.
        • Catelli L.
        • Šakić M.
        • Saragoni V.G.
        • Pleguezuelos M.J.J.
        • et al.
        GHEP-ISFG collaborative simulated exercise for DVI/MPI: lessons learned about large-scale profile database comparisons.
        Forensic Science International: Genetics. 2016; 21: 45-53