TY - JOUR
T1 - Characterizing race/ethnicity and genetic ancestry for 100,000 subjects in the genetic epidemiology research on adult health and aging (GERA) cohort
AU - Banda, Yambazi
AU - Kvale, Mark N.
AU - Hoffmann, Thomas J.
AU - Hesselson, Stephanie E.
AU - Ranatunga, Dilrini
AU - Tang, Hua
AU - Sabatti, Chiara
AU - Croen, Lisa A.
AU - Dispensa, Brad P.
AU - Henderson, Mary
AU - Iribarren, Carlos
AU - Jorgenson, Eric
AU - Kushi, Lawrence H.
AU - Ludwig, Dana
AU - Olberg, Diane
AU - Quesenberry, Charles P.
AU - Rowell, Sarah
AU - Sadler, Marianne
AU - Sakoda, Lori C.
AU - Sciortino, Stanley
AU - Shen, Ling
AU - Smethurst, David
AU - Somkin, Carol P.
AU - Van Den Eeden, Stephen K.
AU - Walter, Lawrence
AU - Whitmer, Rachel
AU - Kwok, Pui Yan
AU - Schaefer, Catherine
AU - Risch1, Neil
PY - 2015/8/1
Y1 - 2015/8/1
N2 - 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 selfreported 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 selfidentified 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.
AB - 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 selfreported 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 selfidentified 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.
KW - Admixture
KW - Population structure
KW - Principal components
KW - Race/ethnicity
KW - RPGEH GERA
UR - http://www.scopus.com/inward/record.url?scp=84939422197&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84939422197&partnerID=8YFLogxK
U2 - 10.1534/genetics.115.178616
DO - 10.1534/genetics.115.178616
M3 - Article
C2 - 26092716
AN - SCOPUS:84939422197
VL - 200
SP - 1285
EP - 1295
JO - Genetics
JF - Genetics
SN - 0016-6731
IS - 4
ER -