Straightforward Inference of Ancestry and Admixture Proportions through Ancestry-Informative Insertion Deletion Multiplexing

• Type: Article in International Scientific Journal
• Date: 2012

Authors

Rui Pereira (Author) Other; Christopher Phillips (Author) Other; Nadia Pinto (Author) Other; Carla Santos (Author) Other; Sidney Emanuel B Batista dos Santos (Author) Other; Antonio Amorim (Author) FCUP; Angel Carracedo (Author) Other; Leonor Gusmao (Author) Other

Journal

Title: PLoS ONE

Vol. 7 No. 4

Final page: e29684

ISSN: 1932-6203

Publisher: Public Library of Science

Indexing

ISI Web of Knowledge - 169 Citations

Scopus - 184 Citations

Other information

Authenticus ID: P-002-DVX

DOI: 10.1371/journal.pone.0029684

Abstract (EN): Ancestry-informative markers (AIMs) show high allele frequency divergence between different ancestral or geographically distant populations. These genetic markers are especially useful in inferring the likely ancestral origin of an individual or estimating the apportionment of ancestry components in admixed individuals or populations. The study of AIMs is of great interest in clinical genetics research, particularly to detect and correct for population substructure effects in case-control association studies, but also in population and forensic genetics studies. This work presents a set of 46 ancestry-informative insertion deletion polymorphisms selected to efficiently measure population admixture proportions of four different origins (African, European, East Asian and Native American). All markers are analyzed in short fragments (under 230 basepairs) through a single PCR followed by capillary electrophoresis (CE) allowing a very simple one tube PCR-to-CE approach. HGDP-CEPH diversity panel samples from the four groups, together with Oceanians, were genotyped to evaluate the efficiency of the assay in clustering populations from different continental origins and to establish reference databases. In addition, other populations from diverse geographic origins were tested using the HGDP-CEPH samples as reference data. The results revealed that the AIM-INDEL set developed is highly efficient at inferring the ancestry of individuals and provides good estimates of ancestry proportions at the population level. In conclusion, we have optimized the multiplexed genotyping of 46 AIM-INDELs in a simple and informative assay, enabling a more straightforward alternative to the commonly available AIM-SNP typing methods dependent on complex, multi-step protocols or implementation of large-scale genotyping technologies.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 10