Genetics
August 1, 2015, Volume 200, Number 4
pages 1285-1295
DOI: 10.1534/genetics.115.178616
Yambazi Banda
Mark N. Kvale
Thomas J. Hoffmann
Stephanie E. Hesselson
Dilrini Ranatunga
Hua Tang
Chiara Sabatti
Lisa A. Croen
Brad P. Dispensa
Mary Henderson
Carlos Iribarren
Eric Jorgenson
Lawrence H. Kushi
Dana Ludwig
Diane Olberg
Charles P. Quesenberry Jr.
Sarah Rowell
Marianne Sadler
Lori C. Sakoda
Stanley Sciortino
Ling Shen
David Smethurst
Carol P. Somkin
Stephen K. Van Den Eeden
Lawrence Walter
Rachel A. Whitmer
Pui-Yan Kwok
Catherine Schaefer
Neil Risch
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.
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