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G3 (Bethesda). 2013 Jul 8;3(7):1165-75. doi: 10.1534/g3.113.006478.

Generalized admixture mapping for complex traits.

Author information

1
Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland 20850, USA. bin.zhu@nih.gov

Abstract

Admixture mapping is a popular tool to identify regions of the genome associated with traits in a recently admixed population. Existing methods have been developed primarily for identification of a single locus influencing a dichotomous trait within a case-control study design. We propose a generalized admixture mapping (GLEAM) approach, a flexible and powerful regression method for both quantitative and qualitative traits, which is able to test for association between the trait and local ancestries in multiple loci simultaneously and adjust for covariates. The new method is based on the generalized linear model and uses a quadratic normal moment prior to incorporate admixture prior information. Through simulation, we demonstrate that GLEAM achieves lower type I error rate and higher power than ANCESTRYMAP both for qualitative traits and more significantly for quantitative traits. We applied GLEAM to genome-wide SNP data from the Illumina African American panel derived from a cohort of black women participating in the Healthy Pregnancy, Healthy Baby study and identified a locus on chromosome 2 associated with the averaged maternal mean arterial pressure during 24 to 28 weeks of pregnancy.

KEYWORDS:

generalized linear model; local ancestry; mapping by admixture linkage disequilibrium; quadratic normal moment prior; quantitative traits

PMID:
23665878
PMCID:
PMC3704244
DOI:
10.1534/g3.113.006478
[Indexed for MEDLINE]
Free PMC Article
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