Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™

M Eduardoff; T E Gross; C Santos; M de la Puente; D Ballard; C Strobl; C Børsting; N Morling; L Fusco; C Hussing; B Egyed; L Souto; J Uacyisrael; D Syndercombe Court; Á Carracedo; M V Lareu; P M Schneider; W Parson; C Phillips; EUROFORGEN-NoE Consortium; W Parson; C Phillips

doi:10.1016/j.fsigen.2016.04.008

Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™

Forensic Sci Int Genet. 2016 Jul:23:178-189. doi: 10.1016/j.fsigen.2016.04.008. Epub 2016 Apr 21.

Authors

M Eduardoff¹, T E Gross², C Santos³, M de la Puente³, D Ballard⁴, C Strobl¹, C Børsting⁵, N Morling⁵, L Fusco⁵, C Hussing⁵, B Egyed⁶, L Souto⁷, J Uacyisrael⁸, D Syndercombe Court⁴, Á Carracedo⁹, M V Lareu³, P M Schneider², W Parson¹⁰, C Phillips¹¹; EUROFORGEN-NoE Consortium; W Parson¹⁰, C Phillips¹¹

Affiliations

¹ Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
² Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany.
³ Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
⁴ Faculty of Life Sciences and Medicine, King's College, London, UK.
⁵ Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
⁶ Department of Genetics, Faculty of Science, Eötvös Loránd University Budapest, Hungary.
⁷ Department of Biology, University of Aveiro, Aveiro, Portugal.
⁸ Fiji Police Forensic Biology and DNA Laboratory, Nasova, Suva, Fiji.
⁹ 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.
¹⁰ Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA.
¹¹ Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain. Electronic address: [email protected].

PMID: 27208666
DOI: 10.1016/j.fsigen.2016.04.008

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.

Keywords: Ancestry-informative SNPs; Forensic ancestry analysis; Ion PGM™; Massively parallel sequencing (MPS).

Publication types

Evaluation Study

MeSH terms

DNA Degradation, Necrotic
DNA Fingerprinting
DNA Primers
Databases, Genetic
Gene Frequency
Genetic Markers
Genetics, Population*
Genotype
High-Throughput Nucleotide Sequencing / instrumentation*
Humans
Polymerase Chain Reaction
Polymorphism, Single Nucleotide*
Racial Groups / genetics*

Substances

DNA Primers
Genetic Markers