Self-reported vs. genetic ancestry in a large US cohort

Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort (free full text; supplementary material)
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 (GERA) Cohort and analyzed the relationship to self-reported race/ethnicity. Participants endorsed any of 23 race/ethnicity/nationality categories, which were collapsed into 7 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. 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 non-adjacent 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 3,741 genetically-identified parent-child pairs, 93% were concordant for self-reported race/ethnicity; among 2,018 genetically-identified full-sib pairs, 96% were concordant; the lower rate for parent-child pairs was largely due to inter-marriage. The parent-child pairs revealed a trend towards 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. [. . .]

The initial analysis showed, as expected, a clear Ashkenazi cluster and a larger cluster depicting the northwest-southeast European cline (Price et al. 2008; Tian et al. 2008c).

In this Northern California sample, less than 1% of the self-identified "European/West Asian" group showed evidence of Amerindian ancestry, and less than half a percent showed evidence of black admixture.

As expected, all individuals who self-identified as European/West Asian had evidence of European/West Asian genetic ancestry. The next largest genetic ancestry component in this group was South Asian (4.3%), primarily attributable to individuals of West Asian ethnicity. Because there is a continuum of genetic ancestry from Europe to West Asia, Central/ South Asia to East Asia, genetic overlap exists for individuals whose national origins are geographically between these divisions (Li et al. 2008). Nearly 1% of this group also had evidence of Native American genetic ancestry, while a smaller fraction had evidence of African or East Asian genetic ancestry (0.3% and 0.4%, respectively). Nearly all individuals (99.7%) self-reporting African/African American race/ethnicity had evidence of African genetic ancestry; 91% also had evidence of European genetic ancestry, consistent with broad European admixture among African Americans. Native American and East Asian genetic ancestry occurred in this group at a similar low level as observed in the Europeans/West Asians (1.3% and 0.5%, respectively). Among self-reported East Asians, all had evidence of East Asian genetic ancestry; a sizeable proportion (21.7%) also had evidence of Pacific Islander genetic ancestry, but this likely represents difficulty in differentiating East Asian and Pacific Islander genetic ancestry. A modest subgroup (3.4%) had evidence of European/West Asian genetic ancestry (majority are self-reported Filipinos), while small proportions had evidence of African or Native American genetic ancestry (0.1% and 0.5%, respectively). Among the Latinos, nearly all had evidence of European/West Asian genetic ancestry; a similar high proportion (94.2%) had evidence of Native American genetic ancestry, and an additional 27.7% had evidence of African ancestry. A substantial number of self-reported Pacific Islanders had evidence of East Asian genetic ancestry (91.3%) in addition to Pacific Islander genetic ancestry (66.3%); these results are again likely due to close genetic similarity between East Asians and Pacific Islanders. There is also evidence of substantial European/West Asian and South Asian genetic ancestry in this group (57.6% and 26.1%, respectively). The former reflects a high rate of European admixture among some self-reported Pacific Islander groups, while the latter likely reflects Fijians of Indian origin.

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