Overview of Admixture Mapping

Shriner, Daniel

doi:10.1002/0471142905.hg0123s76

Cited by 80 publications

(66 citation statements)

References 19 publications

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“…This approach uses admixture information to localize disease-associated polymorphisms that are divergent in frequency in the parental populations that have contributed to the population under study. MALD assumes that the genomic region containing disease-susceptibility alleles will be enriched for ancestry from the parental population in which disease risk is more prevalent [111]. Thus, MALD can be used to identify regions of the genome that potentially contain loci associated with differential disease susceptibility.…”

Section: Implications Of Genetic Structure and Admixture For Disease mentioning

confidence: 99%

The peopling of the African continent and the diaspora into the new world

Campbell

Hirbo

Townsend

et al. 2014

Current Opinion in Genetics & Development

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Africa is the birthplace of anatomically modern humans, and is the geographic origin of human migration across the globe within the last 100,000 years. The history of African populations has consisted of a number of demographic events that have influenced patterns of genetic and phenotypic variation across the continent. With the increasing amount of genomic data and corresponding developments in computational methods, researchers are able to explore long-standing evolutionary questions, expanding our understanding of human history within and outside of Africa. This review will summarize some of the recent findings regarding African demographic history, including the African Diaspora, and will briefly explore their implications for disease susceptibility in populations of African descent.

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Section: Implications Of Genetic Structure and Admixture For Disease mentioning

confidence: 99%

The peopling of the African continent and the diaspora into the new world

Campbell

Hirbo

Townsend

et al. 2014

Current Opinion in Genetics & Development

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“…There are several software programs available for ancestry estimation; however, it has been suggested that LAMP-LD is currently the most accurate software available to estimate local ancestry inference among unrelated individuals. 40,73 This provides higher resolution for ancestry switches and allows detection of smaller local ancestry regions. We acknowledge that despite the availability of a dense set of markers, we were limited by the use of a predefined set of GWAS SNPs and the subsequent loss during quality control.…”

Section: Discussionmentioning

confidence: 99%

Admixture Mapping of Subclinical Atherosclerosis and Subsequent Clinical Events Among African Americans in 2 Large Cohort Studies

Shendre¹,

Wiener²,

Irvin³

et al. 2017

Circ Cardiovasc Genet

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Background Local ancestry may contribute to the disproportionate burden of subclinical and clinical cardiovascular disease (CVD) among admixed African Americans (AAs) compared to other populations, suggesting a rationale for admixture mapping. Methods and Results We estimated local European ancestry (LEA) using Local Ancestry Inference in adMixed Populations using Linkage Disequilibrium (LAMP-LD) and evaluated the association with common carotid artery intima-media thickness (cCIMT) using multivariable linear regression analysis among 1,554 AAs from the Multi-Ethnic Study of Atherosclerosis (MESA). We conducted secondary analysis to examine the significant cCIMT-LEA associations with clinical CVD events. We observed genome-wide significance in relation to cCIMT association with the secretion regulating guanine nucleotide exchange factor (SERGEF) gene (β=0.0137, P=2.98×10−4), also associated with higher odds of stroke (odds ratio (OR)=1.71, P=0.02). Several regions, in particular Ca2+-dependent secretion activator 1 (CADPS) gene region identified in MESA were also replicated in the Atherosclerosis Risk in Communities (ARIC) cohort. We observed other cCIMT-LEA regions associated with other clinical events, most notably the regions harboring creatine kinase, mitochondrial 2 (CKMT2) and Ras protein specific guanine nucleotide releasing factor 2 (RASGRF2) genes with all clinical events except stroke, the leucine rich repeat containing 3B (LRRC3B) gene with myocardial infarction, the protein arginine methyltransferase 3 (PRMT3) gene with stroke, and the lipoma high mobility group protein I-C (HMGIC) fusion partner-like 2 (LHFPL2) gene with hard and all coronary heart disease. Conclusions We identified several novel LEA regions, in addition to previously identified genomic regions, associated with cCIMT and CVD events among African Americans.

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“…It is therefore impera ve to penalize SNPs that are correlated with popula on structure, as the lack of controlled experiments can generate spurious associa ons between gene c variants more common in some human ancestry groups with regional measurement errors or different cultural and nutri onal environments 56 . When a popula on includes mul ple ancestries with different disease suscep bili es, popula on structure correc on can obscure real signals, which has in turn led to the development of admixture mapping 57 . Similarly, in animal or plant breeding, SNPs conferring an advantageous trait but that are highly associated with a par cular group of breeds or varie es (the equivalent of geographic popula ons) are also avoided, as selec on of these SNPs can drag along undesirable traits from such parents 58 .…”

Section: V3 Important Notes On Popula On Structure Correc On In a Wimentioning

confidence: 99%

A map of climate change-driven natural selection in Arabidopsis thaliana

Expósito-Alonso

Burbano

Bossdorf

et al. 2018

Preprint

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Through the lens of evolution, climate change is an agent of natural selection that forces populations to change and adapt, or face extinction. Current assessments of the risk of biodiversity associated with climate change1, however, do not typically take into account the genetic makeup of populations and how natural selection impacts it2. We made use of the extensive genome information in Arabidopsis thaliana and measured how rainfall-manipulation affected the fitness of 517 natural lines grown in Spain and Germany. This allowed us to directly infer selection along the genome3. Natural selection was particularly strong in the hot-dry Spanish location, killing 63% of lines and significantly changing the frequency of ~5% of all genome-wide variants. A significant portion of this climate-driven natural selection over variants was predictable from signatures of local adaptation (R2=29-52%), as genetic variants found in geographic areas with climates more similar to the experimental sites were positively selected. Field-validated predictions across the species range indicated that Mediterranean and Western Siberian populations — at the edges of the species’ environmental limits — currently experience the strongest climate-driven selection. With more frequent droughts and rising temperatures in Europe4, we forecast an increase in directional natural selection moving northwards from the southern end, and putting many native A. thaliana populations at evolutionary risk.

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Overview of Admixture Mapping

Cited by 80 publications

References 19 publications

The peopling of the African continent and the diaspora into the new world

The peopling of the African continent and the diaspora into the new world

Admixture Mapping of Subclinical Atherosclerosis and Subsequent Clinical Events Among African Americans in 2 Large Cohort Studies

A map of climate change-driven natural selection in Arabidopsis thaliana

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