Inference of Ancestry in Forensic Analysis II: Analysis of Genetic Data.

Three approaches applicable to the analysis of forensic ancestry-informative marker data-STRUCTURE, principal component analysis, and the Snipper Bayesian classification system-are reviewed. Detailed step-by-step guidance is provided for adjusting parameter settings in STRUCTURE with particular regard to their effect when differentiating populations. Several enhancements to the Snipper online forensic classification portal are described, highlighting the added functionality they bring to particular aspects of ancestry-informative SNP analysis in a forensic context.

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

[2]  Christopher Phillips,et al.  ENGINES: exploring single nucleotide variation in entire human genomes , 2011, BMC Bioinformatics.

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

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

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

[6]  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..

[7]  Xavier Estivill,et al.  SNPassoc: an R package to perform whole genome association studies , 2007, Bioinform..

[8]  M. Stephens,et al.  Inferring weak population structure with the assistance of sample group information , 2009, Molecular ecology resources.

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

[10]  Jorge Amigo,et al.  The SNPforID browser: an online tool for query and display of frequency data from the SNPforID project , 2008, International Journal of Legal Medicine.

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

[12]  N. Rosenberg,et al.  Standardized Subsets of the HGDP‐CEPH Human Genome Diversity Cell Line Panel, Accounting for Atypical and Duplicated Samples and Pairs of Close Relatives , 2006, Annals of human genetics.

[13]  S. Kalinowski,et al.  The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure , 2011, Heredity.

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

[15]  Ángel Carracedo,et al.  Ancestry Analysis in the 11-M Madrid Bomb Attack Investigation , 2009, PloS one.

[16]  Jonathan Scott Friedlaender,et al.  A Human Genome Diversity Cell Line Panel , 2002, Science.

[17]  M V Lareu,et al.  Revision of the SNPforID 34-plex forensic ancestry test: Assay enhancements, standard reference sample genotypes and extended population studies. , 2013, Forensic science international. Genetics.

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

[19]  M. Stephens,et al.  Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. , 2003, Genetics.

[20]  António Amorim,et al.  Straightforward Inference of Ancestry and Admixture Proportions through Ancestry-Informative Insertion Deletion Multiplexing , 2012, PloS one.

[21]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

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

[23]  I. Jolliffe Principal Component Analysis , 2002 .

[24]  Á. Carracedo,et al.  pop.STR—An online population frequency browser for established and new forensic STRs , 2009 .

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

[26]  Á. Carracedo,et al.  Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. , 2007, Forensic science international. Genetics.