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

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.

[1]  Mitsuo Morita,et al.  Characterization of a Bayesian genetic clustering algorithm based on a Dirichlet process prior and comparison among Bayesian clustering methods , 2011, BMC Bioinformatics.

[2]  R. Ward,et al.  Informativeness of genetic markers for inference of ancestry. , 2003, American journal of human genetics.

[3]  W Parson,et al.  Inter-laboratory evaluation of SNP-based forensic identification by massively parallel sequencing using the Ion PGM™. , 2015, Forensic science international. Genetics.

[4]  N. Rosenberg.  distruct: a program for the graphical display of population structure , 2003 .

[5]  Niels Morling,et al.  Next generation sequencing and its applications in forensic genetics. , 2015, Forensic science international. Genetics.

[6]  Chris Phillips,et al.  Forensic genetic analysis of bio-geographical ancestry. , 2015, Forensic science international. Genetics.

[7]  P. Donnelly,et al.  Inference of population structure using multilocus genotype data. , 2000, Genetics.

[8]  Kenny Q. Ye,et al.  An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.

[9]  Manfred Kayser,et al.  Forensic DNA Phenotyping: Predicting human appearance from crime scene material for investigative purposes. , 2015, Forensic science international. Genetics.

[10]  G. Evanno,et al.  Detecting the number of clusters of individuals using the software structure: a simulation study , 2005, Molecular ecology.

[11]  Christopher Phillips,et al.  An overview of STRUCTURE: applications, parameter settings, and supporting software , 2013, Front. Genet..

[12]  Roland A H van Oorschot,et al.  Pacifiplex: an ancestry-informative SNP panel centred on Australia and the Pacific region. , 2016, Forensic science international. Genetics.

[13]  H. S. Mogensen,et al.  Evaluation of the Ion Torrent™ HID SNP 169-plex: A SNP typing assay developed for human identification by second generation sequencing. , 2014, Forensic science international. Genetics.

[14]  Theunis Piersma,et al.  The interplay between habitat availability and population differentiation , 2012 .

[15]  T. Parsons,et al.  Mitochondrial control region sequence variations in the Hungarian population: analysis of population samples from Hungary and from Transylvania (Romania). , 2007, Forensic science international. Genetics.

[16]  Bridgett M. vonHoldt,et al.  STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method , 2011, Conservation Genetics Resources.

[17]  Nancy F. Hansen,et al.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.

[18]  M. Feldman,et al.  Clines, Clusters, and the Effect of Study Design on the Inference of Human Population Structure , 2005, PLoS genetics.

[19]  C. Tyler-Smith,et al.  A world in a grain of sand: human history from genetic data , 2011, Genome Biology.

[20]  F. Balloux,et al.  Geography is a better determinant of human genetic differentiation than ethnicity , 2005, Human Genetics.

[21]  David H. Warshauer,et al.  Single nucleotide polymorphism typing with massively parallel sequencing for human identification , 2013, International Journal of Legal Medicine.

[22]  S. Pääbo,et al.  Evidence for gradients of human genetic diversity within and among continents. , 2004, Genome research.

[23]  Gabor T. Marth,et al.  A global reference for human genetic variation , 2015, Nature.

[24]  Barry Merriman,et al.  Progress in Ion Torrent semiconductor chip based sequencing , 2012, Electrophoresis.

[25]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[26]  Robert B. Hartlage,et al.  This PDF file includes: Materials and Methods , 2009 .

[27]  C. Ponting,et al.  Sequencing depth and coverage: key considerations in genomic analyses , 2014, Nature Reviews Genetics.

[28]  M V Lareu,et al.  Eurasiaplex: a forensic SNP assay for differentiating European and South Asian ancestries. , 2013, Forensic science international. Genetics.

[29]  L. Excoffier,et al.  Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows , 2010, Molecular ecology resources.

[30]  Joshua S. Paul,et al.  Genotype and SNP calling from next-generation sequencing data , 2011, Nature Reviews Genetics.

[31]  Noah A. Rosenberg,et al.  CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure , 2007, Bioinform..

[32]  L. Jin,et al.  Ethnic-affiliation estimation by use of population-specific DNA markers. , 1997, American journal of human genetics.

[33]  M. Feldman,et al.  Genetic Structure of Human Populations , 2002, Science.

[34]  David Goldman,et al.  Using ancestry-informative markers to define populations and detect population stratification , 2006, Journal of psychopharmacology.

[35]  I. Kohane,et al.  Geography and genography: prediction of continental origin using randomly selected single nucleotide polymorphisms , 2007, BMC Genomics.

[36]  Christopher Phillips,et al.  SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access , 2008, BMC Bioinformatics.

[37]  H. Swerdlow,et al.  A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers , 2012, BMC Genomics.

[38]  M. Feldman,et al.  Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation , 2008 .

[39]  N. Morling,et al.  Building a forensic ancestry panel from the ground up: The EUROFORGEN Global AIM-SNP set. , 2014, Forensic science international. Genetics.

[40]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[41]  Niels Morling,et al.  Second-generation sequencing of forensic STRs using the Ion Torrent™ HID STR 10-plex and the Ion PGM™. , 2015, Forensic science international. Genetics.

[42]  Philip Hugenholtz,et al.  Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data , 2013, PLoS Comput. Biol..

[43]  Gabriel Silva,et al.  An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels , 2009, BMC Genetics.

[44]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[45]  Á. Carracedo,et al.  A SNaPshot of next generation sequencing for forensic SNP analysis. , 2015, Forensic science international. Genetics.