Local ancestry inference in a large US-based Hispanic/Latino study: Hispanic community health study/study of Latinos (HCHS/SOL)

Sharon R. Browning, Kelsey Grinde, Anna Plantinga, Stephanie M. Gogarten, Adrienne M. Stilp, Robert C. Kaplan, M. Larissa Avilés-Santa, Brian L. Browning, Cathy C. Laurie

Research output: Contribution to journalArticle

20 Citations (Scopus)

Abstract

We estimated local ancestry on the autosomes and X chromosome in a large US-based study of 12,793 Hispanic/Latino individuals using the RFMix method, and we compared different reference panels and approaches to local ancestry estimation on the X chromosome by means of Mendelian inconsistency rates as a proxy for accuracy. We developed a novel and straightforward approach to performing ancestryspecific PCA after finding artifactual behavior in the results from an existing approach. Using the ancestryspecific PCA, we found significant population structure within African, European, and Amerindian ancestries in the Hispanic/Latino individuals in our study. In the African ancestral component of the admixed individuals, individuals whose grandparents were from Central America clustered separately from individuals whose grandparents were from the Caribbean, and also from reference Yoruba and Mandenka West African individuals. In the European component, individuals whose grandparents were from Puerto Rico diverged partially from other background groups. In the Amerindian ancestral component, individuals clustered into multiple different groups depending on the grandparental country of origin. Therefore, local ancestry estimation provides further insight into the complex genetic structure of US Hispanic/Latino populations, which must be properly accounted for in genotype-phenotype association studies. It also provides a basis for admixture mapping and ancestry-specific allele frequency estimation, which are useful in the identification of risk factors for disease.

Original languageEnglish (US)
Pages (from-to)1525-1534
Number of pages10
JournalG3: Genes, Genomes, Genetics
Volume6
Issue number6
DOIs
StatePublished - 2016

Fingerprint

Hispanic Americans
Health
Passive Cutaneous Anaphylaxis
X Chromosome
Central America
Puerto Rico
Genetic Structures
Genetic Association Studies
Proxy
Gene Frequency
Population
Grandparents

Keywords

  • Hispanic/Latino
  • Local ancestry
  • Principal components analysis

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Genetics(clinical)

Cite this

Local ancestry inference in a large US-based Hispanic/Latino study : Hispanic community health study/study of Latinos (HCHS/SOL). / Browning, Sharon R.; Grinde, Kelsey; Plantinga, Anna; Gogarten, Stephanie M.; Stilp, Adrienne M.; Kaplan, Robert C.; Avilés-Santa, M. Larissa; Browning, Brian L.; Laurie, Cathy C.

In: G3: Genes, Genomes, Genetics, Vol. 6, No. 6, 2016, p. 1525-1534.

Research output: Contribution to journalArticle

Browning, SR, Grinde, K, Plantinga, A, Gogarten, SM, Stilp, AM, Kaplan, RC, Avilés-Santa, ML, Browning, BL & Laurie, CC 2016, 'Local ancestry inference in a large US-based Hispanic/Latino study: Hispanic community health study/study of Latinos (HCHS/SOL)', G3: Genes, Genomes, Genetics, vol. 6, no. 6, pp. 1525-1534. https://doi.org/10.1534/g3.116.028779
Browning, Sharon R. ; Grinde, Kelsey ; Plantinga, Anna ; Gogarten, Stephanie M. ; Stilp, Adrienne M. ; Kaplan, Robert C. ; Avilés-Santa, M. Larissa ; Browning, Brian L. ; Laurie, Cathy C. / Local ancestry inference in a large US-based Hispanic/Latino study : Hispanic community health study/study of Latinos (HCHS/SOL). In: G3: Genes, Genomes, Genetics. 2016 ; Vol. 6, No. 6. pp. 1525-1534.
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