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Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™.
Forensic Sci Int Genet. 2016 07; 23:178-189.FS

Abstract

The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing.

Authors+Show Affiliations

Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany.Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.Faculty of Life Sciences and Medicine, King's College, London, UK.Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.Department of Genetics, Faculty of Science, Eötvös Loránd University Budapest, Hungary.Department of Biology, University of Aveiro, Aveiro, Portugal.Fiji Police Forensic Biology and DNA Laboratory, Nasova, Suva, Fiji.Faculty of Life Sciences and Medicine, King's College, London, UK.Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain; Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany.Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA.Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain. Electronic address: c.phillips@mac.com.No affiliation info availableInstitute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA.Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain. Electronic address: c.phillips@mac.com.

Pub Type(s)

Evaluation Study
Journal Article

Language

eng

PubMed ID

27208666

Citation

Eduardoff, M, et al. "Inter-laboratory Evaluation of the EUROFORGEN Global Ancestry-informative SNP Panel By Massively Parallel Sequencing Using the Ion PGM™." Forensic Science International. Genetics, vol. 23, 2016, pp. 178-189.
Eduardoff M, Gross TE, Santos C, et al. Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™. Forensic Sci Int Genet. 2016;23:178-189.
Eduardoff, M., Gross, T. E., Santos, C., de la Puente, M., Ballard, D., Strobl, C., Børsting, C., Morling, N., Fusco, L., Hussing, C., Egyed, B., Souto, L., Uacyisrael, J., Syndercombe Court, D., Carracedo, Á., Lareu, M. V., Schneider, P. M., Parson, W., Phillips, C., ... Phillips, C. (2016). Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™. Forensic Science International. Genetics, 23, 178-189. https://doi.org/10.1016/j.fsigen.2016.04.008
Eduardoff M, et al. Inter-laboratory Evaluation of the EUROFORGEN Global Ancestry-informative SNP Panel By Massively Parallel Sequencing Using the Ion PGM™. Forensic Sci Int Genet. 2016;23:178-189. PubMed PMID: 27208666.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™. AU - Eduardoff,M, AU - Gross,T E, AU - Santos,C, AU - de la Puente,M, AU - Ballard,D, AU - Strobl,C, AU - Børsting,C, AU - Morling,N, AU - Fusco,L, AU - Hussing,C, AU - Egyed,B, AU - Souto,L, AU - Uacyisrael,J, AU - Syndercombe Court,D, AU - Carracedo,Á, AU - Lareu,M V, AU - Schneider,P M, AU - Parson,W, AU - Phillips,C, AU - ,, AU - Parson,W, AU - Phillips,C, Y1 - 2016/04/21/ PY - 2015/12/08/received PY - 2016/04/14/revised PY - 2016/04/15/accepted PY - 2016/5/22/entrez PY - 2016/5/22/pubmed PY - 2017/6/15/medline KW - Ancestry-informative SNPs KW - Forensic ancestry analysis KW - Ion PGM™ KW - Massively parallel sequencing (MPS) SP - 178 EP - 189 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 23 N2 - The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/27208666/Inter_laboratory_evaluation_of_the_EUROFORGEN_Global_ancestry_informative_SNP_panel_by_massively_parallel_sequencing_using_the_Ion_PGM™_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(16)30064-3 DB - PRIME DP - Unbound Medicine ER -