Inference of biogeographical ancestry across central regions of Eurasia

Abstract

The inference of biogeographical ancestry (BGA) can provide useful information for forensic investigators when there are no suspects to be compared with DNA collected at the crime scene or when no DNA database matches exist. Although public databases are increasing in size and population scope, there is a lack of information regarding genetic variation in Eurasian populations, especially in central regions such as the Middle East. Inhabitants of these regions show a high degree of genetic admixture, characterized by an allele frequency cline running from NW Europe to East Asia. Although a proper differentiation has been established between the cline extremes of western Europe and South Asia, populations geographically located in between, i.e, Middle East and Mediterranean populations, require more detailed study in order to characterize their genetic background as well as to further understand their demographic histories. To initiate these studies, three ancestry informative SNP (AI-SNP) multiplex panels: the SNPforID 34-plex, Eurasiaplex and a novel 33-plex assay were used to describe the ancestry patterns of a total of 24 populations ranging across the longitudinal axis from NW Europe to East Asia. Different ancestry inference approaches, including STRUCTURE, PCA, DAPC and Snipper Bayes analysis, were applied to determine relationships among populations. The structure results show differentiation between continental groups and a NW to SE allele frequency cline running across Eurasian populations. This study adds useful population data that could be used as reference genotypes for future ancestry investigations in forensic cases. The 33-plex assay also includes pigmentation predictive SNPs, but this study primarily focused on Eurasian population differentiation using 33-plex and its combination with the other two AI-SNP sets.

A genome-wide association study in individuals of African ancestry reveals the importance of the Duffy-null genotype in the assessment of clozapine-related neutropenia

“…In order to select a cohort of individuals with African genetic ancestry, we stratified the CLOZUK2 individuals using Ancestry Informative Markers (AIMs), routinely employed in the field of forensic genetics 32 . The use of AIMs has been shown to be an efficient way of inferring biogeographical ancestry 33,34 , which reflects the genetic association of an individual to a particular continental or sub-continental population group. As these groups are broadly defined and show relatively large genetic differentiation 35 , this approach circumvents the problems associated with several other approximations to genetic ancestry 36 , such as self-reported ethnicity 37 or country-of-origin 38 .…”

Revisión sobre los marcadores del origen biogeográfico y su aplicación en la investigación forense

“…Bulbul et al [4] llevaron a cabo un estudio combinado de varios paneles de aim-snp: el 34-plex, el Eurasiaplex y un nuevo panel denominado 33-plex para obtener una mayor resolución genética de las poblaciones del Oriente Medio, del este de Europa y de población mediterránea. El análisis de componentes principales muestra una diferenciación creciente entre la población de estudio y la de referencia cuando al 34-plex se le añaden paneles adicionales.…”

“…Por lo tanto, la mejor separación de los cinco grupos (África, Europa, Oriente Medio, Asia centro-meridional y Asia del este) es obtenida utilizando los tres paneles de snp juntos, dado que cada uno contribuye a la diferenciación global. El análisis de la estructura genética mostró que la división óptima por grupos fue obtenida en K:5, en el que los grupos poblacionales están casi completamente diferenciados (figura 1) [4]. Figura 1.…”

“…Figura 1. En la imagen se muestra la división realizada a través de structure en cuatro grupos, siendo el K:5 el que muestra la mayor diferenciacion entre los grupos poblacionales analizados [4].…”

“…De esta manera, la mejor estrategia para estimar la ancestralidad consiste en, además de la utilización de estos genomas uniparentales, analizar marcadores informativos de ancestralidad conocidos como aim (Ancestry Informative Markers). Entre estos, los más utilizados son los aim-snp (Ancestry Informative Markers-snps) [3,4]. El empleo de nuevas herramientas de genotipado, como la secuenciación de nueva generación (Next Generation Sequencing, ngs), posibilita el análisis de miles de marcadores y permite el análi-sis simultáneo de marcadores aim y marcadores de linaje [5].…”