Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans

Elena A. Vidal, Tomás C. Moyano, Bernabé I. Bustos, Eduardo Pérez-Palma, Carol Moraga, Eleodoro Riveras, Alejandro Montecinos, Lorena Azócar, Daniela C. Soto, Mabel Vidal, Alex Di Genova, Klaus Puschel, Peter Nürnberg, Stephan Buch, Jochen Hampe, Miguel L. Allende, Verónica Cambiazo, Mauricio González, Christian Hodar, Martín MontecinoClaudia Muñoz-Espinoza, Ariel Orellana, Angélica Reyes-Jara, Dante Travisany, Paula Vizoso, Mauricio Moraga, Susana Eyheramendy, Alejandro Maass, Giancarlo V. De Ferrari*, Juan Francisco Miquel, Rodrigo A. Gutiérrez

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

13 Scopus citations


Whole human genome sequencing initiatives help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations, and the information of the genomic structure of Native Americans, especially those from the Southern Cone is scant. Here we present annotation and variant discovery from high-quality complete genome sequences of a cohort of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile. We found approximately 3.1 × 10 6 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs events. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a sample from a marginally admixed population from the Southern Cone, whose main genetic component derives from Native American ancestors. Additionally, we found that HUI genomes contain variants in genes associated with 5 of the 6 leading causes of noncommunicable diseases in Chile, which may have an impact on the risk of prevalent diseases in Chilean and Amerindian populations. Our data represents a useful resource that can contribute to population-based studies and for the design of early diagnostics or prevention tools for Native and admixed Latin American populations.

Original languageEnglish
Article number2132
JournalScientific Reports
Issue number1
StatePublished - 1 Dec 2019
Externally publishedYes

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© 2019, The Author(s).


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