Forensic genetic analysis of bio-geographical ancestry.

With the great strides made in the last ten years in the understanding of human population variation and the detailed characterization of the genome, it is now possible to identify sets of ancestry informative markers suitable for relatively small-scale PCR-based assays and use them to analyze the ancestry of an individual from forensic DNA. This review outlines some of the current understanding of past human population structure and how it may have influenced the complex distribution of contemporary human diversity. A simplified description of human diversity can provide a suitable basis for choosing the best ancestry-informative markers, which is important given the constraints of multiplex sizes in forensic DNA tests. It is also important to decide the level of geographic resolution that is realistic to ensure the balance between informativeness and an over-simplification of complex human diversity patterns. A detailed comparison is made of the most informative ancestry markers suitable for forensic use and assessments are made of the data analysis regimes that can provide statistical inferences of a DNA donor's bio-geographical ancestry.

[1]  Á. Carracedo,et al.  “New turns from old STaRs”: Enhancing the capabilities of forensic short tandem repeat analysis , 2014, Electrophoresis.

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

[3]  M. Schanfield,et al.  A 50-SNP assay for biogeographic ancestry and phenotype prediction in the U.S. population. , 2014, Forensic science international. Genetics.

[4]  Ryan D. Hernandez,et al.  Classic Selective Sweeps Were Rare in Recent Human Evolution , 2011, Science.

[5]  Francisco M De La Vega,et al.  Analyses of a set of 128 ancestry informative single-nucleotide polymorphisms in a global set of 119 population samples , 2011, Investigative Genetics.

[6]  D. Reich,et al.  Principal components analysis corrects for stratification in genome-wide association studies , 2006, Nature Genetics.

[7]  Jun Zhang,et al.  Laplacian Eigenfunctions Learn Population Structure , 2009, PloS one.

[8]  N. Siva.  1000 Genomes project , 2008, Nature Biotechnology.

[9]  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.

[10]  S. Santos,et al.  Insertion–deletion polymorphisms—utilization on forensic analysis , 2012, International Journal of Legal Medicine.

[11]  Manfred Kayser,et al.  IrisPlex: a sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information. , 2011, Forensic science international. Genetics.

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

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

[14]  Kenneth K Kidd,et al.  Inference of human continental origin and admixture proportions using a highly discriminative ancestry informative 41-SNP panel , 2013, Investigative Genetics.

[15]  B. Malyarchuk,et al.  Simple and cost-effective 14-loci SNP assay designed for differentiation of European, East Asian and African samples. , 2015, Forensic science international. Genetics.

[16]  Mark Shriver,et al.  A panel of ancestry informative markers for estimating individual biogeographical ancestry and admixture from four continents: utility and applications , 2008, Human mutation.

[17]  L. Cavalli-Sforza,et al.  Demic expansions and human evolution , 1993, Science.

[18]  A 34-plex autosomal SNP single base extension assay for ancestry investigations. , 2012, Methods in molecular biology.

[19]  P. Schneider,et al.  A 21 marker insertion deletion polymorphism panel to study biogeographic ancestry. , 2013, Forensic science international. Genetics.

[20]  Á. Carracedo,et al.  Development of a novel forensic STR multiplex for ancestry analysis and extended identity testing , 2013, Electrophoresis.

[21]  Á. Carracedo,et al.  Exploring iris colour prediction and ancestry inference in admixed populations of South America. , 2014, Forensic science international. Genetics.

[22]  Laura Spinney.  Eyewitness identification: Line-ups on trial , 2008, Nature.

[23]  John Travis,et al.  Forensic science. Scientists decry isotope, DNA testing of 'nationality'. , 2009, Science.

[24]  Walther Parson,et al.  EMPOP--a forensic mtDNA database. , 2007, Forensic science international. Genetics.

[25]  Christopher R. Gignoux,et al.  Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas , 2012, PLoS genetics.

[26]  Christian Gieger,et al.  Correlation between Genetic and Geographic Structure in Europe , 2008, Current Biology.

[27]  Kenneth K. Kidd,et al.  ALFRED: an allele frequency resource for research and teaching , 2011, Nucleic Acids Res..

[28]  Fulvio Cruciani,et al.  Africans in Yorkshire? The deepest-rooting clade of the Y phylogeny within an English genealogy , 2007, European Journal of Human Genetics.

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

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

[31]  D. F. Roberts,et al.  The History and Geography of Human Genes , 1996 .

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

[33]  Nicholas J. Schork,et al.  A Method for Inferring an Individual’s Genetic Ancestry and Degree of Admixture Associated with Six Major Continental Populations , 2013, Front. Gene..

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

[35]  Holly M. Mortensen,et al.  Convergent adaptation of human lactase persistence in Africa and Europe , 2007, Nature Genetics.

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

[37]  Daniel Shriner,et al.  Moving toward System Genetics through Multiple Trait Analysis in Genome-Wide Association Studies , 2011, Front. Gene..

[38]  M. Pirinen,et al.  The fine-scale genetic structure of the British population , 2015, Nature.

[39]  Asan,et al.  Altitude adaptation in Tibet caused by introgression of Denisovan-like DNA , 2014, Nature.

[40]  C. Tyler-Smith,et al.  Human Evolutionary Genetics , 2004 .

[41]  John B. Shoven,et al.  I , Edinburgh Medical and Surgical Journal.

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

[43]  Mark D Shriver,et al.  The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs , 2004, Human Genomics.

[44]  Á. Carracedo,et al.  Completion of a worldwide reference panel of samples for an ancestry informative Indel assay. , 2015, Forensic science international. Genetics.

[45]  Brendan W. Vaughan,et al.  The 1000 Genomes Project: data management and community access , 2012, Nature Methods.

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

[47]  Á. Carracedo,et al.  The Genetic Legacy of the Pre-Colonial Period in Contemporary Bolivians , 2013, PloS one.

[48]  Mattias Jakobsson,et al.  Genetic Variation and Population Structure in Native Americans , 2007, PLoS genetics.

[49]  Joseph K. Pickrell,et al.  Toward a new history and geography of human genes informed by ancient DNA. , 2014, Trends in genetics : TIG.

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

[51]  A. Amorim,et al.  Assessing individual interethnic admixture and population substructure using a 48–insertion‐deletion (INSEL) ancestry‐informative marker (AIM) panel , 2010, Human mutation.

[52]  Ancestry Informative Markers , 2013 .

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

[54]  D. Falush,et al.  A Genetic Atlas of Human Admixture History , 2014, Science.

[55]  Scott M. Williams,et al.  A high-density admixture map for disease gene discovery in african americans. , 2004, American journal of human genetics.

[56]  Katsushi Tokunaga,et al.  A scan for genetic determinants of human hair morphology: EDAR is associated with Asian hair thickness. , 2008, Human molecular genetics.

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

[58]  C. Mckenzie,et al.  Phenotypic expression of melanocortin-1 receptor mutations in Black Jamaicans. , 2003, The Journal of investigative dermatology.

[59]  R. Lewontin.  The Apportionment of Human Diversity , 1972 .

[60]  S. Madore,et al.  CoAIMs: A Cost-Effective Panel of Ancestry Informative Markers for Determining Continental Origins , 2010, PloS one.

[61]  J. Stephenson.  1000 Genomes Project , 2008 .

[62]  Jonathan K. Pritchard,et al.  Adaptation – not by sweeps alone , 2010, Nature Reviews Genetics.

[63]  David Reich,et al.  Principal component analysis of genetic data , 2008, Nature Genetics.

[64]  L. Zhivotovsky,et al.  PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile , 2011, International Journal of Legal Medicine.

[65]  Manfred Kayser,et al.  Improving human forensics through advances in genetics, genomics and molecular biology , 2011, Nature Reviews Genetics.

[66]  M. Nalls,et al.  Reduced Neutrophil Count in People of African Descent Is Due To a Regulatory Variant in the Duffy Antigen Receptor for Chemokines Gene , 2009, PLoS genetics.

[67]  Manfred Kayser,et al.  Proportioning whole-genome single-nucleotide-polymorphism diversity for the identification of geographic population structure and genetic ancestry. , 2006, American journal of human genetics.

[68]  Haseena Rajeevan,et al.  Introducing the Forensic Research/Reference on Genetics knowledge base, FROG-kb , 2012, Investigative Genetics.

[69]  António Amorim,et al.  A new multiplex for human identification using insertion/deletion polymorphisms , 2009, Electrophoresis.

[70]  Chang-Heng Chang,et al.  Divergence and Shannon information in genomes. , 2004, Physical review letters.

[71]  Mark G. Thomas,et al.  Lactose digestion and the evolutionary genetics of lactase persistence , 2008, Human Genetics.

[72]  M W Feldman,et al.  An evaluation of genetic distances for use with microsatellite loci. , 1994, Genetics.

[73]  Gabriel Silva,et al.  Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America , 2009, Human mutation.

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

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

[76]  Joseph K. Pickrell,et al.  The Role of Geography in Human Adaptation , 2009, PLoS genetics.

[77]  M. Pirinen,et al.  Dissection of the genetics of Parkinson ’ s disease identifies an additional association 5 ′ of SNCA and multiple associated haplotypes at 17 q 21 The UK Parkinson ’ s Disease Consortium and The Wellcome Trust Case Control Consortium 2 , 2010 .

[78]  Yusuke Nakamura,et al.  A SNP in the ABCC11 gene is the determinant of human earwax type , 2006, Nature Genetics.

[79]  J C Murray,et al.  Pediatrics and , 1998 .

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

[81]  I W Evett,et al.  Inferring ethnic origin by means of an STR profile. , 2001, Forensic science international.

[82]  D. Reich,et al.  Population Structure and Eigenanalysis , 2006, PLoS genetics.

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

[84]  P. de Knijff,et al.  Developing a set of ancestry-sensitive DNA markers reflecting continental origins of humans , 2009, BMC Genetics.

[85]  C. Phillips,et al.  Differentiating European and South Asian individuals using SNPs and pyrosequencing technology , 2008 .

[86]  Alberto Piazza,et al.  The History and Geography of Human Genes: Abridged paperback Edition , 1996 .

[87]  Antonio Salas,et al.  Human genome-wide screen of haplotype-like blocks of reduced diversity. , 2005, Gene.

[88]  Á. Carracedo,et al.  Analysis of global variability in 15 established and 5 new European Standard Set (ESS) STRs using the CEPH human genome diversity panel. , 2011, Forensic science international. Genetics.

[89]  D. Reich,et al.  Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. , 2011, American journal of human genetics.

[90]  Michael W. Mahoney,et al.  PCA-Correlated SNPs for Structure Identification in Worldwide Human Populations , 2007, PLoS genetics.

[91]  B. Ludes,et al.  Pigment phenotype and biogeographical ancestry from ancient skeletal remains: inferences from multiplexed autosomal SNP analysis , 2009, International Journal of Legal Medicine.

[92]  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..

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

[94]  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.

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

[96]  Hongzhe Li,et al.  Examination of ancestry and ethnic affiliation using highly informative diallelic DNA markers: application to diverse and admixed populations and implications for clinical epidemiology and forensic medicine , 2005, Human Genetics.

[97]  Genetic genealogy goes global , 2006, EMBO reports.

[98]  T. Frudakis,et al.  A classifier for the SNP-based inference of ancestry. , 2003, Journal of forensic sciences.

[99]  M. Daly,et al.  A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms , 2001, Nature.

[100]  K. Kidd,et al.  Mini-haplotypes as lineage informative SNPs and ancestry inference SNPs , 2012, European Journal of Human Genetics.

[101]  Á. Carracedo,et al.  D9S1120, a simple STR with a common Native American-specific allele: forensic optimization, locus characterization and allele frequency studies. , 2008, Forensic science international. Genetics.

[102]  Jonathan Scott Friedlaender,et al.  The Genetic Structure of Pacific Islanders , 2008, PLoS genetics.

[103]  M. Stephens,et al.  Interpreting principal component analyses of spatial population genetic variation , 2008, Nature Genetics.

[104]  Amit R. Indap,et al.  Genes mirror geography within Europe , 2008, Nature.

[105]  Sascha Willuweit,et al.  Y chromosome haplotype reference database (YHRD): update. , 2007, Forensic science international. Genetics.

[106]  T. Sanders.  IMAGINING THE DARK CONTINENT: THE MET, THE MEDIA AND THE THAMES TORSQi , 2003 .

[107]  Keith C. Cheng,et al.  SLC24A5, a Putative Cation Exchanger, Affects Pigmentation in Zebrafish and Humans , 2005, Science.

[108]  Sreeurpa Ray,et al.  The Cell: A Molecular Approach , 1996 .

[109]  S. Fullerton,et al.  Familial Identification: Population Structure and Relationship Distinguishability , 2012, PLoS genetics.

[110]  Carlos D Bustamante,et al.  Ascertainment bias in studies of human genome-wide polymorphism. , 2005, Genome research.

[111]  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.

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

[113]  K. Kidd,et al.  Application of six IrisPlex SNPs and comparison of two eye color prediction systems in diverse Eurasia populations , 2014, International Journal of Legal Medicine.

[114]  K. Kidd,et al.  Current sequencing technology makes microhaplotypes a powerful new type of genetic marker for forensics. , 2014, Forensic science international. Genetics.

[115]  Titia Sijen,et al.  Tri-allelic SNP markers enable analysis of mixed and degraded DNA samples. , 2009, Forensic science international. Genetics.