title: Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas.
abstract: Most individuals throughout the Americas are admixed descendants of Native American, European, and African ancestors. Complex historical factors have resulted in varying proportions of ancestral contributions between individuals within and among ethnic groups. We developed a panel of 446 ancestry informative markers (AIMs) optimized to estimate ancestral proportions in individuals and populations throughout Latin America. We used genome-wide data from 953 individuals from diverse African, European, and Native American populations to select AIMs optimized for each of the three main continental populations that form the basis of modern Latin American populations. We selected markers on the basis of locus-specific branch length to be informative, well distributed throughout the genome, capable of being genotyped on widely available commercial platforms, and applicable throughout the Americas by minimizing within-continent heterogeneity. We then validated the panel in samples from four admixed populations by comparing ancestry estimates based on the AIMs panel to estimates based on genome-wide association study (GWAS) data. The panel provided balanced discriminatory power among the three ancestral populations and accurate estimates of individual ancestry proportions (R² > 0.9 for ancestral components with significant between-subject variance). Finally, we genotyped samples from 18 populations from Latin America using the AIMs panel and estimated variability in ancestry within and between these populations. This panel and its reference genotype information will be useful resources to explore population history of admixture in Latin America and to correct for the potential effects of population stratification in admixed samples in the region.
authors.affiliation: University of California San Francisco, San Francisco, California, United States of America. joshua.galanter@ucsf.edu
authors.forename: Joshua Mark
authors.initials: JM
authors.lastname: Galanter
authors.forename: Juan Carlos
authors.initials: JC
authors.lastname: Fernandez-Lopez
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Gignoux
authors.forename: Jill
authors.initials: J
authors.lastname: Barnholtz-Sloan
authors.forename: Ceres
authors.initials: C
authors.lastname: Fernandez-Rozadilla
authors.forename: Marc
authors.initials: M
authors.lastname: Via
authors.forename: Alfredo
authors.initials: A
authors.lastname: Hidalgo-Miranda
authors.forename: Alejandra V
authors.initials: AV
authors.lastname: Contreras
authors.forename: Laura Uribe
authors.initials: LU
authors.lastname: Figueroa
authors.forename: Paola
authors.initials: P
authors.lastname: Raska
authors.forename: Gerardo
authors.initials: G
authors.lastname: Jimenez-Sanchez
authors.forename: Irma Silva
authors.initials: IS
authors.lastname: Zolezzi
authors.forename: Maria
authors.initials: M
authors.lastname: Torres
authors.forename: Clara Ruiz
authors.initials: CR
authors.lastname: Ponte
authors.forename: Yarimar
authors.initials: Y
authors.lastname: Ruiz
authors.forename: Antonio
authors.initials: A
authors.lastname: Salas
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Nguyen
authors.forename: Celeste
authors.initials: C
authors.lastname: Eng
authors.forename: Lisbeth
authors.initials: L
authors.lastname: Borjas
authors.forename: William
authors.initials: W
authors.lastname: Zabala
authors.forename: Guillermo
authors.initials: G
authors.lastname: Barreto
authors.forename: Fernando Rondón
authors.initials: FR
authors.lastname: González
authors.forename: Adriana
authors.initials: A
authors.lastname: Ibarra
authors.forename: Patricia
authors.initials: P
authors.lastname: Taboada
authors.forename: Liliana
authors.initials: L
authors.lastname: Porras
authors.forename: Fabián
authors.initials: F
authors.lastname: Moreno
authors.forename: Abigail
authors.initials: A
authors.lastname: Bigham
authors.forename: Gerardo
authors.initials: G
authors.lastname: Gutierrez
authors.forename: Tom
authors.initials: T
authors.lastname: Brutsaert
authors.forename: Fabiola
authors.initials: F
authors.lastname: León-Velarde
authors.forename: Lorna G
authors.initials: LG
authors.lastname: Moore
authors.forename: Enrique
authors.initials: E
authors.lastname: Vargas
authors.forename: Miguel
authors.initials: M
authors.lastname: Cruz
authors.forename: Jorge
authors.initials: J
authors.lastname: Escobedo
authors.forename: José
authors.initials: J
authors.lastname: Rodriguez-Santana
authors.forename: William
authors.initials: W
authors.lastname: Rodriguez-Cintrón
authors.forename: Rocio
authors.initials: R
authors.lastname: Chapela
authors.forename: Jean G
authors.initials: JG
authors.lastname: Ford
authors.forename: Carlos
authors.initials: C
authors.lastname: Bustamante
authors.forename: Daniela
authors.initials: D
authors.lastname: Seminara
authors.forename: Mark
authors.initials: M
authors.lastname: Shriver
authors.forename: Elad
authors.initials: E
authors.lastname: Ziv
authors.forename: Esteban Gonzalez
authors.initials: EG
authors.lastname: Burchard
authors.forename: Robert
authors.initials: R
authors.lastname: Haile
authors.forename: Esteban
authors.initials: E
authors.lastname: Parra
authors.forename: Angel
authors.initials: A
authors.lastname: Carracedo
mesh_terms: D044467:American Indian or Alaska Native / Q000235:genetics*; D044383:Black People / Q000235:genetics*; D005819:Genetic Markers; D015894:Genome, Human; D006801:Humans; D007843:Latin America; D011157:Population Dynamics; D044465:White People / Q000235:genetics*
chemical_list: D005819:Genetic Markers