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

Allocco, 2007, Geography and genography: prediction of continental origin using randomly selected single nucleotide polymorphisms, BMC Genomics, 8, 68, 10.1186/1471-2164-8-68 Enoch, 2006, Using ancestry-informative markers to define populations and detect population stratification, J. Psychopharmacol., 20, 19, 10.1177/1359786806066041 Li, 2008, Worldwide human relationships inferred from genome-wide patterns of variation, Science, 319, 1100, 10.1126/science.1153717 Rosenberg, 2002, Genetic structure of human populations, Science, 298, 2381, 10.1126/science.1078311 Manica, 2005, Geography is a better determinant of human genetic differentiation than ethnicity, Hum. Genet., 118, 366, 10.1007/s00439-005-0039-3 Rosenberg, 2005, Clines, clusters, and the effect of study design on the inference of human population structure, PLoS Genet., 1, e70, 10.1371/journal.pgen.0010070 Serre, 2004, Evidence for gradients of human genetic diversity within and among continents, Genome Res., 14, 1679, 10.1101/gr.2529604 Phillips, 2015, Forensic genetic analysis of bio-geographical ancestry, Forensic Sci. Int. Genet., 18, 49, 10.1016/j.fsigen.2015.05.012 Rosenberg, 2003, Informativeness of genetic markers for inference of ancestry, Am. J. Hum. Genet., 73, 1402, 10.1086/380416 Shriver, 1997, Ethnic-affiliation estimation by use of population-specific DNA markers, Am. J. Hum. Genet., 60, 957 Børsting, 2014, Evaluation of the Ion Torrent™ HID SNP 169-plex: a SNP typing assay developed for human identification by second generation sequencing, Forensic Sci. Int. Genet., 12, 144, 10.1016/j.fsigen.2014.06.004 Daniel, 2014, A SNaPshot of next generation sequencing, Forensic Sci. Int. Genet., 14, 50, 10.1016/j.fsigen.2014.08.013 Eduardoff, 2015, Inter-laboratory evaluation of SNP-based forensic identification by massively parallel sequencing using the Ion PGM™, Forensic Sci. Int. Genet., 17, 110, 10.1016/j.fsigen.2015.04.007 Fordyce, 2015, Second-generation sequencing of forensic STRs using the Ion Torrent HID STR 10-plex and the Ion PGM, Forensic Sci. Int. Genet., 14, 132, 10.1016/j.fsigen.2014.09.020 Seo, 2013, Single base polymorphism typing with massively parallel sequencing for human identification, Int. J. Legal Med., 127, 1079, 10.1007/s00414-013-0879-7 Børsting, 2015, Next generation sequencing and its applications in forensic genetics, Forensic Sci. Int. Genet., 18, 78, 10.1016/j.fsigen.2015.02.002 Phillips, 2014, Building a forensic ancestry panel from the ground up: the EUROFORGEN Global AIM-SNP set, Forensic Sci. Int. Genet., 11, 13, 10.1016/j.fsigen.2014.02.012 Merriman, 2012, Progress in Ion Torrent 650 semiconductor chip based sequencing, Electrophoresis, 33, 3397, 10.1002/elps.201200424 Kayser, 2015, Forensic DNA Phenotyping: predicting human appearance from crime scene material for investigative purposes, Forensic Sci. Int. Genet., 18, 33, 10.1016/j.fsigen.2015.02.003 Phillips, 2013, Eurasiaplex: a forensic SNP assay for differentiating European and South Asian ancestries, Forensic Sci. Int. Genet., 7, 359, 10.1016/j.fsigen.2013.02.010 Santos, 2016, Pacifiplex: an ancestry-informative SNP panel centred on Australia and the Pacific region, Forensic Sci. Int. Genet., 20, 50, 10.1016/j.fsigen.2015.10.003 The 1000 Genomes Project Consortium, 2012, An integrated map of genetic variation from 1092 human genomes, Nature, 491, 56, 10.1038/nature11632 Drmanac, 2009, Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays, Science, 327, 78, 10.1126/science.1181498 1000 Genomes Project Consortium, 2015, A global reference for human genetic variation, Nature, 526, 68, 10.1038/nature15393 Amigo, 2008, SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access, BMC Bioinf., 9, 428, 10.1186/1471-2105-9-428 Onogi, 2011, Characterization of a Bayesian genetic clustering algorithm based on a Dirichlet process prior and comparison among Bayesian clustering methods, BMC Bioinf., 12, 263, 10.1186/1471-2105-12-263 Egyed, 2007, Mitochondrial control region sequence variations in the Hungarian population: analysis of populations samples from Hungary and from Transylvania (Romania), Forensic Sci. Int. Genet., 1, 158, 10.1016/j.fsigen.2007.03.001 Thermo Fisher Scientific, Life Technologies: Ion AmpliSeq™ library preparation user guide. April (2014). Thermo Fisher Scientific, Life Technologies: Ion OneTouch™ 200 Template Kit v2 user guide (2014). Thermo Fisher Scientific, Life Technologies: Ion PGM™ 200 Sequencing Kit user guide (2014). Thermo Fisher Scientific, Life Technologies: Torrent Suite™ software 4.2 user guide (2015). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria ISBN 3-900051-07-0, Available from: http://www.R-project.org. Robinson, 2011, Integrative genomics viewer, Nat. Biotechnol., 29, 24, 10.1038/nbt.1754 Thorvaldsdóttir, 2012, Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration, Brief. Bioinf., 14, 178, 10.1093/bib/bbs017 Nassir, 2009, An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels, BMC Genet., 10, 39, 10.1186/1471-2156-10-39 http://mathgene.usc.es/snipper/analysispopfile2_new.html. Pritchard, 2000, Inference of population structure using multilocus genotype data, Genetics, 155, 945, 10.1093/genetics/155.2.945 Porras-Hurtado, 2013, An overview of STRUCTURE: applications, parameter settings, and supporting software, Front. Genet., 4, 98, 10.3389/fgene.2013.00098 Earl, 2012, STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method, Conserv. Genet. Resour., 4, 359, 10.1007/s12686-011-9548-7 Evanno, 2005, Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study, Mol. Ecol., 14, 2611, 10.1111/j.1365-294X.2005.02553.x Jakobsson, 2007, CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure, Bioinformatics, 23, 1801, 10.1093/bioinformatics/btm233 Rosenberg, 2004, Distruct: a program for the graphical display of population structure, Mol. Ecol. Notes, 4, 137, 10.1046/j.1471-8286.2003.00566.x Excoffier, 2010, Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Mol. Ecol. Resour., 10, 564, 10.1111/j.1755-0998.2010.02847.x http://browser.1000genomes.org/index.html, data for rs6875659 (accessed July 2015). http://browser.1000genomes.org/index.html, data for rs146348214 (accessed July 2015). Sims, 2014, Sequencing depth and coverage: key considerations in genomic analyses, Nat. Rev. Genet., 15, 121, 10.1038/nrg3642 Nielsen, 2011, Genotype and SNP calling from next-generation sequencing data, Nat. Rev. Genet., 12, 443, 10.1038/nrg2986 Quail, 2012, A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers, BMC Genomics, 24, 341, 10.1186/1471-2164-13-341 Bentley, 2008, Accurate whole human genome sequencing using reversible terminator chemistry, Nature, 456, 53, 10.1038/nature07517 Bragg, 2013, Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data, PLoS Comput. Biol., 9, e1003031, 10.1371/journal.pcbi.1003031 Colonna, 2011, A world in a grain of sand: human history from genetic data, Genome Biol., 12, 234, 10.1186/gb-2011-12-11-234