Species identification in forensic samples using the SPInDel approach: A GHEP-ISFG inter-laboratory collaborative exercise.
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.
Instituto de Investigação e Inovação em Saúde, I3S, Universidade do Porto, Portugal; Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal. Electronic address: calves@ipatimup.pt.
Cíntia
C
Alves
Instituto de Investigação e Inovação em Saúde, I3S, Universidade do Porto, Portugal; Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal.
Rui
R
Pereira
Grupo de Medicina Xenómica. Instituto de Ciencias Forenses. Universidade de Santiago de Compostela, Spain.
Lourdes
L
Prieto
Sección de genética forense y criminalistica, Instituto de Medicina Legal y Ciencias Forenses de Valencia, Valencia, Spain.
Mercedes
M
Aler
Laboratório de Diagnóstico por DNA, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.
Cesar R L
CRL
Amaral
Laboratorio Biología-ADN, Comisaría General de Policía Científica, Instituto Universitario de Investigación en Ciencias Policiales (Universidad de Alcalá de Henares), Spain.
Cristina
C
Arévalo
PRICAI-Fundación Favaloro, CABA, Argentina.
Gabriela
G
Berardi
Laboratorio de Genética Molecular, Instituto Multidisciplinario de Biología Celular, CIC-CONICET-UNLP,La Plata, Argentina.
Florencia
F
Di Rocco
Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Junín 956 & CONICET - Consejo Nacional de Investigaciones Científicas y Tecnológicas, C1033AAJ, Buenos Aires, Argentina.
Mariela
M
Caputo
Sección de Bioquímica, Departamento de Ciencias Forenses Poder Judicial de Costa Rica, Costa Rica.
Cristian Hernandez
CH
Carmona
Laboratorio del Equipo Argentino de Antropología Forense (EAAF) y Laboratorio de Inmunogenética y Diagnóstico Molecular (LIDMO), Córdoba, Argentina.
Laura
L
Catelli
Serviço de Genética e Biologia Forense, Delegação do Sul, Instituto Nacional de Medicina Legal e Ciências Forenses, I.P., Lisboa, Portugal.
Heloísa Afonso
HA
Costa
Institute of Criminalistics Prague, Prague, Czech Republic.
Pavla
P
Coufalova
Laboratorio de Análisis de ADN, Facultad de Ciencias Médicas - UNCuyo, Mendoza, Argentina.
Sandra
S
Furfuro
Forensic Science Unit, Forensic Genetics Section, Basque Country Police-Ertzaintza, Erandio, Bizkaia, Spain.
Óscar
Ó
García
Laboratorio de Genética Molecular, Cruz Roja Ecuatoriana - Cruz Vital, Quito, Ecuador.
Anibal
A
Gaviria
Instituto de Investigação e Inovação em Saúde, I3S, Universidade do Porto, Portugal; Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal.
Ana
A
Goios
Laboratorio Genes SAS, Medellín, Colombia and Instituto de Biología, Universidad de Antioquia, Medellín, Colombia.
Juan José Builes
JJB
Gómez
INTCF - Instituto Nacional de Toxicología y Ciencias Forenses, Delegación de Canarias, Santa Cruz de Tenerife, Spain.
Alexis
A
Hernández
Instituto de Medicina Legal de Las Palmas, Laboratorio Genética Forense, Spain.
Eva Del Carmen Betancor
EDCB
Hernández
Laboratório de Genética Aplicada, Universidade de Aveiro, Portugal.
Luís
L
Miranda
Servicio de Criminalística de la Guardia Civil, Departamento de Química y Medio Ambiente, Madrid, Spain.
David
D
Parra
Unidad de Laboratorio de Navarra de Servicios y Tecnologías, Villava, Spain.
Susana
S
Pedrosa
Serviço de Genética e Biologia Forenses, Delegação do Centro, Instituto Nacional de Medicina Legal e Ciências Forenses, I.P., Coimbra, Portugal.
Maria João Anjos
MJA
Porto
Delegação do Norte, Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. Porto, Portugal.
Maria de Lurdes
ML
Rebelo
Istituto di Sanità Pubblica Sezione di Medicina Legale Università Cattolica del Sacro Cuore, Roma, Italy.
Matteo
M
Spirito
Unidad de Diagnóstico Molecular, Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, México.
María Del Carmen Villalobos
MDCV
Torres
Instituto de Investigação e Inovação em Saúde, I3S, Universidade do Porto, Portugal; Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal; Faculty of Sciences, University of Porto, Porto, Portugal.
António
A
Amorim
Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Porto, Portugal. Electronic address: fpereirapt@gmail.com.
Filipe
F
Pereira
D000818:Animals; D003299:Cooperative Behavior; D019075:Electrophoresis, Capillary; D005260:Female; D006801:Humans; D007753:Laboratories; D008297:Male; D060885:Multiplex Polymerase Chain Reaction; D012335:RNA, Ribosomal / Q000235:genetics*; D013045:Species Specificity
D012335:RNA, Ribosomal
Collaborative exercise; Forensic investigations; SPInDel; Species identification; mtDNA