title: Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort.
abstract: Using genome-wide genotypes, we characterized the genetic structure of 103,006 participants in the Kaiser Permanente Northern California multi-ethnic Genetic Epidemiology Research on Adult Health and Aging Cohort and analyzed the relationship to self-reported race/ethnicity. Participants endorsed any of 23 race/ethnicity/nationality categories, which were collapsed into seven major race/ethnicity groups. By self-report the cohort is 80.8% white and 19.2% minority; 93.8% endorsed a single race/ethnicity group, while 6.2% endorsed two or more. Principal component (PC) and admixture analyses were generally consistent with prior studies. Approximately 17% of subjects had genetic ancestry from more than one continent, and 12% were genetically admixed, considering only nonadjacent geographical origins. Self-reported whites were spread on a continuum along the first two PCs, indicating extensive mixing among European nationalities. Self-identified East Asian nationalities correlated with genetic clustering, consistent with extensive endogamy. Individuals of mixed East Asian-European genetic ancestry were easily identified; we also observed a modest amount of European genetic ancestry in individuals self-identified as Filipinos. Self-reported African Americans and Latinos showed extensive European and African genetic ancestry, and Native American genetic ancestry for the latter. Among 3741 genetically identified parent-child pairs, 93% were concordant for self-reported race/ethnicity; among 2018 genetically identified full-sib pairs, 96% were concordant; the lower rate for parent-child pairs was largely due to intermarriage. The parent-child pairs revealed a trend toward increasing exogamy over time; the presence in the cohort of individuals endorsing multiple race/ethnicity categories creates interesting challenges and future opportunities for genetic epidemiologic studies.
authors.affiliation: Institute for Human Genetics, University of California, San Francisco, California 94143-0794 banday@humgen.ucsf.edu rischn@humgen.ucsf.edu cathy.schaefer@kp.org.
authors.forename: Yambazi
authors.initials: Y
authors.lastname: Banda
authors.affiliation: Institute for Human Genetics, University of California, San Francisco, California 94143-0794.
authors.forename: Mark N
authors.initials: MN
authors.lastname: Kvale
authors.affiliation: Institute for Human Genetics, University of California, San Francisco, California 94143-0794 Department of Epidemiology and Biostatistics, University of California, San Francisco, California 94158-2549.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Hoffmann
authors.affiliation: Institute for Human Genetics, University of California, San Francisco, California 94143-0794.
authors.forename: Stephanie E
authors.initials: SE
authors.lastname: Hesselson
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: Dilrini
authors.initials: D
authors.lastname: Ranatunga
authors.affiliation: Department of Genetics, Stanford University, Stanford, California 94305-5120.
authors.forename: Hua
authors.initials: H
authors.lastname: Tang
authors.affiliation: Department of Health Research and Policy, Stanford University, Stanford, California 94305-5405.
authors.forename: Chiara
authors.initials: C
authors.lastname: Sabatti
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: Lisa A
authors.initials: LA
authors.lastname: Croen
authors.affiliation: Institute for Human Genetics, University of California, San Francisco, California 94143-0794.
authors.forename: Brad P
authors.initials: BP
authors.lastname: Dispensa
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: Mary
authors.initials: M
authors.lastname: Henderson
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: Carlos
authors.initials: C
authors.lastname: Iribarren
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: Eric
authors.initials: E
authors.lastname: Jorgenson
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: Lawrence H
authors.initials: LH
authors.lastname: Kushi
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: Dana
authors.initials: D
authors.lastname: Ludwig
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: Diane
authors.initials: D
authors.lastname: Olberg
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: Charles P
authors.initials: CP
authors.lastname: Quesenberry
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: Sarah
authors.initials: S
authors.lastname: Rowell
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: Marianne
authors.initials: M
authors.lastname: Sadler
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: Lori C
authors.initials: LC
authors.lastname: Sakoda
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: Stanley
authors.initials: S
authors.lastname: Sciortino
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: Ling
authors.initials: L
authors.lastname: Shen
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: David
authors.initials: D
authors.lastname: Smethurst
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: Carol P
authors.initials: CP
authors.lastname: Somkin
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: Stephen K
authors.initials: SK
authors.lastname: Van Den Eeden
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: Lawrence
authors.initials: L
authors.lastname: Walter
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304.
authors.forename: Rachel A
authors.initials: RA
authors.lastname: Whitmer
authors.affiliation: Institute for Human Genetics, University of California, San Francisco, California 94143-0794.
authors.forename: Pui-Yan
authors.initials: PY
authors.lastname: Kwok
authors.affiliation: Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304 banday@humgen.ucsf.edu rischn@humgen.ucsf.edu cathy.schaefer@kp.org.
authors.forename: Catherine
authors.initials: C
authors.lastname: Schaefer
authors.affiliation: Institute for Human Genetics, University of California, San Francisco, California 94143-0794 Department of Epidemiology and Biostatistics, University of California, San Francisco, California 94158-2549 Kaiser Permanente Northern California Division of Research, Oakland, California 94612-2304 banday@humgen.ucsf.edu rischn@humgen.ucsf.edu cathy.schaefer@kp.org.
authors.forename: Neil
authors.initials: N
authors.lastname: Risch
mesh_terms: D000328:Adult; D000375:Aging / Q000235:genetics*; D015331:Cohort Studies; D005006:Ethnicity / Q000235:genetics*; D005260:Female; D023281:Genomics; D006262:Health; D006801:Humans; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D010375:Pedigree; D025341:Principal Component Analysis; D044469:Racial Groups / Q000235:genetics*
keywords: RPGEH GERA; admixture; population structure; principal components; race/ethnicity