TY - JOUR
T1 - Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans
AU - Vidal, Elena A.
AU - Moyano, Tomás C.
AU - Bustos, Bernabé I.
AU - Pérez-Palma, Eduardo
AU - Moraga, Carol
AU - Riveras, Eleodoro
AU - Montecinos, Alejandro
AU - Azócar, Lorena
AU - Soto, Daniela C.
AU - Vidal, Mabel
AU - Di Genova, Alex
AU - Puschel, Klaus
AU - Nürnberg, Peter
AU - Buch, Stephan
AU - Hampe, Jochen
AU - Allende, Miguel L.
AU - Cambiazo, Verónica
AU - González, Mauricio
AU - Hodar, Christian
AU - Montecino, Martín
AU - Muñoz-Espinoza, Claudia
AU - Orellana, Ariel
AU - Reyes-Jara, Angélica
AU - Travisany, Dante
AU - Vizoso, Paula
AU - Moraga, Mauricio
AU - Eyheramendy, Susana
AU - Maass, Alejandro
AU - De Ferrari, Giancarlo V.
AU - Miquel, Juan Francisco
AU - Gutiérrez, Rodrigo A.
N1 - Publisher Copyright:
© 2019, The Author(s).
PY - 2019/12/1
Y1 - 2019/12/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85061577433&partnerID=8YFLogxK
U2 - 10.1038/s41598-019-39391-z
DO - 10.1038/s41598-019-39391-z
M3 - Article
C2 - 30765821
AN - SCOPUS:85061577433
SN - 2045-2322
VL - 9
JO - Scientific Reports
JF - Scientific Reports
IS - 1
M1 - 2132
ER -
