GenoGeographer – A tool for genogeographic inference

Abstract

Ancestry-informative markers (AIMs) are genetic markers that give information about the genogeographic ancestry of individuals. They are used for predicting the genogeographic origin of the investigated individual in crime and identification cases. When exploring the genogeographic origin of an AIMs profile, the likelihoods of the AIMs profile in various populations may be calculated. However, there might not be an apt population in the database of reference populations. The fact that the likelihood ratios (LR) of one population compared to other populations are large does not imply that any of the populations are relevant. This is because that even though the populations might be exclusive, they are not exhaustive in the sense that they cover all possible human populations.To handle this phenomena, we derive a likelihood ratio test (LRT), by which we can judge whether there is at least one population in our reference database that is "sufficiently close" to a profile's "true" genogeographic population. The LRT is a measure of absolute concordance between a profile and a population, rather than a relative measure of the profile's likelihood in two populations (the LR).The LRT is similar to a Fisher's exact test, which means that the varying sample sizes of the reference populations in the database is explicitly included in the calculations, and makes fewer assumptions than for LR calculations. The methodology has been implemented in an free open source interactive platform, GenoGeographer, that enables the forensic geneticist to make explorative analyses, produce various graphical outputs together with evidential weight computations.

Multivariate statistical approach and machine learning for the evaluation of biogeographical ancestry inference in the forensic field

“…Recently, the application of massively parallel sequencing technologies for BGA tool developments allowed the simultaneous analysis of a significant number of SNPs than the SNaPshot-based minisequencing technology as attested by the development for forensics of commercial and non-commercial panels 26 – 29 . To date, the statistical clustering methods most used for the inference of the biogeographical ancestry of a person or trace relies on are PCA, STRUCTURE 8 , 30 and GenoGeographer 31 , 32 . However, although they provide easy ways to visualize data clustering, these methods are empirical and not adequate for ancestry inference in the forensic field.…”

Comparative evaluation of the MAPlex, Precision ID Ancestry Panel, and VISAGE Basic Tool for biogeographical ancestry inference

“…For BGA inference based on genotype data, various prediction tools are currently available, including STRUCTURE, PCA, GenoGeographer [51], and Bayesian analysis tools such as Snipper [52]. In this study, analyses were conducted with STRUCTURE, the most widely used clustering tool in forensic genetic studies.…”

Review of the Forensic Applicability of Biostatistical Methods for Inferring Ancestry from Autosomal Genetic Markers

“… Boxplots of the Brier scores, , with in the STRUCTURE analysis and j running through the metapopulations of [ 58 ]. Reference: Samples constituting the metapopulations (and used to calculate ).…”