Inference of ancestry: constructing hierarchical reference populations and assigning unknown individuals

Abstract

The ability to infer personal genetic ancestry is being increasingly utilised in certain medical and forensic situations. Herein, the unsupervised Bayesian clustering algorithms structure, is employed to analyse 377 autosomal short tandem repeats typed on 1,056 individuals from the Centre d'Etude du Polymorphisme Humain Human Diversity Panel. Individuals of known geographical origin were hierarchically classified into a framework of increasingly homogeneous clusters to serve as reference populations into which individuals of unknown ancestry can be assigned. The groupings were characterised by the geographical affinities of cluster members and the accuracy of these procedures was verified using several genetic indices. Fine-scale substructure was detectable beyond the broad population level classifications that previously have been explored in this dataset. Metrics indicated that within certain lines, the strongest structuring signals were detected at the leaves of the hierarchy where lineage-specific groupings were identified. The accuracy of unknown assignment was assessed at each level of the hierarchy using a 'leave one out' strategy in which each individual was stripped of cluster membership and then re-assigned using the supervised Bayesian clustering algorithm implemented in GeneClass2. Although most clusters at all levels of resolution experienced highly accurate assignment, a decline was observed in the finer levels due to the mixed membership characteristics of some individuals. The parameters defined by this study allowed for assignment of unknown individuals to genetically defined clusters with measured likelihood. Shared ancestry data can then be inferred for the unknown individual.

The geographic origin of old Douglas-fir stands growing in Central Europe

“…Similar effects in densely sampled areas have been reported in other studies (e.g. Ekins et al 2006) and may be seen as an effect of isolation by distance. We addressed this problem by introducing intermediate populations (0.4 < Q < 0.6) e.g.…”

Standardized Subsets of the HGDP‐CEPH Human Genome Diversity Cell Line Panel, Accounting for Atypical and Duplicated Samples and Pairs of Close Relatives

“…comm.). The hierarchical population structure analysis of Ekins et al (2006) further suggested the presence in the diversity panel of many additional groups of related individuals.…”

Expanded and mega-plex STR panels as a tool for presumptive population assignment

“…Inference of the ethnic origin of a suspect from their DNA recovered from a crime scene sample can act as 'investigative intelligence' and help enforcement agencies concentrate their resources in the absence of any other suspect specific information. This idea is not new and has been explored extensively in the literature through the development and application of assignment approaches that use genetic markers to identify unique genetic groups or populations [1][2][3]. The specific identification of Ancestry Informative Markers (AIMs) panels that are particularly powerful at inferring ethnic origin has also been the focus of much research and the assessment of different classes of molecular marker has slowly moved from mitochondrial DNA (mtDNA) sequence variation, through autosomal and Y linked Short Tandem Repeat (STRs) markers to Single Nucleotide Polymorphisms (SNPs) [4][5][6][7][8].…”