Generalized admixture mapping for complex traits.
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.
Type
Journal articleSubject
generalized linear modellocal ancestry
mapping by admixture linkage disequilibrium
quadratic normal moment prior
quantitative traits
African Americans
Case-Control Studies
Chromosome Mapping
Female
Genetic Association Studies
Genetics, Population
Genome, Human
Humans
Linkage Disequilibrium
Models, Theoretical
Pregnancy
Quantitative Trait Loci
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https://hdl.handle.net/10161/15601Published Version (Please cite this version)
10.1534/g3.113.006478Publication Info
Zhu, Bin; Ashley-Koch, Allison E; & Dunson, David B (2013). Generalized admixture mapping for complex traits. G3 (Bethesda), 3(7). pp. 1165-1175. 10.1534/g3.113.006478. Retrieved from https://hdl.handle.net/10161/15601.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Show full item recordScholars@Duke
Allison Elizabeth Ashley-Koch
Professor in Medicine
One of my major research foci is in the genetic basis of psychiatric and neurological
disorders. I am currently involved in studies to dissect the genetic etiology of
attention deficit hyperactivity disorder (ADHD), autism, chiari type I malformations,
essential tremor, and neural tube defects. Additional research foci include genetic
modifiers of sickle cell disease, and genetic contributions to birth outcomes, particularly
among African American women.
David B. Dunson
Arts and Sciences Distinguished Professor of Statistical Science
My research focuses on developing new tools for probabilistic learning from complex
data - methods development is directly motivated by challenging applications in ecology/biodiversity,
neuroscience, environmental health, criminal justice/fairness, and more. We seek
to develop new modeling frameworks, algorithms and corresponding code that can be
used routinely by scientists and decision makers. We are also interested in new inference
framework and in studying theoretical properties
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