title: Improved imputation accuracy in Hispanic/Latino populations with larger and more diverse reference panels: applications in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).
abstract: Imputation is commonly used in genome-wide association studies to expand the set of genetic variants available for analysis. Larger and more diverse reference panels, such as the final Phase 3 of the 1000 Genomes Project, hold promise for improving imputation accuracy in genetically diverse populations such as Hispanics/Latinos in the USA. Here, we sought to empirically evaluate imputation accuracy when imputing to a 1000 Genomes Phase 3 versus a Phase 1 reference, using participants from the Hispanic Community Health Study/Study of Latinos. Our assessments included calculating the correlation between imputed and observed allelic dosage in a subset of samples genotyped on a supplemental array. We observed that the Phase 3 reference yielded higher accuracy at rare variants, but that the two reference panels were comparable at common variants. At a sample level, the Phase 3 reference improved imputation accuracy in Hispanic/Latino samples from the Caribbean more than for Mainland samples, which we attribute primarily to the additional reference panel samples available in Phase 3. We conclude that a 1000 Genomes Project Phase 3 reference panel can yield improved imputation accuracy compared with Phase 1, particularly for rare variants and for samples of certain genetic ancestry compositions. Our findings can inform imputation design for other genome-wide association studies of participants with diverse ancestries, especially as larger and more diverse reference panels continue to become available.
authors.affiliation: Department of Biostatistics, University of Washington, Seattle, WA, USA sarahcn@uw.edu.
authors.forename: Sarah C
authors.initials: SC
authors.lastname: Nelson
authors.affiliation: Department of Biostatistics, University of Washington, Seattle, WA, USA.
authors.forename: Adrienne M
authors.initials: AM
authors.lastname: Stilp
authors.affiliation: Division of Cardiovascular Sciences, NHLBI, NIH, Bethesda, MD, USA.
authors.forename: George J
authors.initials: GJ
authors.lastname: Papanicolaou
authors.affiliation: Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research, Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA.
authors.forename: Kent D
authors.initials: KD
authors.lastname: Taylor
authors.affiliation: Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research, Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA.
authors.forename: Jerome I
authors.initials: JI
authors.lastname: Rotter
authors.affiliation: Department of Biostatistics, University of Washington, Seattle, WA, USA.
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Thornton
authors.affiliation: Department of Biostatistics, University of Washington, Seattle, WA, USA.
authors.forename: Cathy C
authors.initials: CC
authors.lastname: Laurie
mesh_terms: D005260:Female; D055106:Genome-Wide Association Study; D006630:Hispanic or Latino / Q000235:genetics*; D016045:Human Genome Project; D006801:Humans; D008297:Male; D014481:United States