Measurement of admixture proportions and description of admixture structure in different U.S. populations

Indrani Halder, Bao Zhu Yang, Henry R. Kranzler, Murray B. Stein, Mark D. Shriver, Joel Gelernter

Research output: Contribution to journalArticlepeer-review

53 Scopus citations


Variation in individual admixture proportions leads to heterogeneity within populations. Though novel methods and marker panels have been developed to quantify individual admixture, empirical data describing individual admixture distributions are limited. We investigated variation in individual admixture in four U.S. populations (European American [EA], African American [AA], Hispanics from Connecticut [East Coast, or EC], and Hispanics from California [West Coast, or WC]) assuming three-way intermixture among Europeans, Africans, and Indigenous Americans. Admixture estimates were inferred using a panel of 36 microsatellites and one SNP, which have significant allele frequency differences between ancestral populations, and by using both a maximum likelihood (ML)-based method and a Bayesian method implemented in the program STRUCTURE. Simulation studies showed that estimates obtained with this marker panel are within 96% of expected values. EAs had the lowest non-European admixture with both methods, but showed greater homogeneity with STRUCTURE than with ML. All other samples showed a high degree of variation in admixture estimates with both methods, were highly concordant, and showed evidence of admixture stratification. With both methods, AA subjects had on average, 16% European and <10% Indigenous American admixture. EC Hispanics had higher mean African admixture and the WC Hispanics had higher mean Indigenous American admixture, possibly reflecting their different continental origins.

Original languageEnglish (US)
Pages (from-to)1299-1309
Number of pages11
JournalHuman mutation
Issue number9
StatePublished - Sep 2009

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)


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