Journal Article

Admixture mapping of end stage kidney disease genetic susceptibility using estimated mutual information ancestry informative markers

Templeton, Alan, Yudkovsky, Guennady, Skorecki, Karl, Bercovici, Sivan, Shlush, Liran I, Wasser, Walter G, Geiger, Dan

2010

Overview

Background The question of a genetic contribution to the higher prevalence and incidence of end stage kidney disease (ESKD) among African Americans (AA) remained unresolved, until recent findings using admixture mapping pointed to the association of a genomic locus on chromosome 22 with this disease phenotype. In the current study we utilize this example to demonstrate the utility of applying a multi-step admixture mapping approach. Methods A multi-step case only admixture mapping study, consisted of the following steps was designed: 1) Assembly of the sample dataset (ESKD AA); 2) Design of the estimated mutual information ancestry informative markers (n = 2016) screening panel 3); Genotyping the sample set whose size was determined by a power analysis (n = 576) appropriate for the initial screening panel; 4) Inference of local ancestry for each individual and identification of regions with increased AA ancestry using two different ancestry inference statistical approaches; 5) Enrichment of the initial screening panel; 6) Power analysis of the enriched panel 7) Genotyping of additional samples. 8) Re-analysis of the genotyping results to identify a genetic risk locus. Results The initial screening phase yielded a significant peak using the ADMIXMAP ancestry inference program applying case only statistics. Subgroup analysis of 299 ESKD patients with no history of diabetes yielded peaks using both the ANCESTRYMAP and ADMIXMAP ancestry inference programs. The significant peak was found on chromosome 22. Genotyping of additional ancestry informative markers on chromosome 22 that took into account linkage disequilibrium in the ancestral populations, and the addition of samples increased the statistical significance of the finding. Conclusions A multi-step admixture mapping analysis of AA ESKD patients replicated the finding of a candidate risk locus on chromosome 22, contributing to the heightened susceptibility of African Americans to develop non-diabetic ESKD, and underscores the importance of using mutual information and multiple ancestry inference approaches to achieve a robust analysis, using relatively small datasets of \"affected\" only individuals. The current study suggests solutions to some limitations of existing admixture mapping methodologies, such as considerations regarding the distribution of ancestry information along the genome and its effects on power calculations and sample size.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: African Americans / Analysis / Biological markers / Biomedical and Life Sciences / Biomedicine / Chromosome Mapping - methods / Chromosomes / Chronic kidney failure / Computer science / Design / Disease susceptibility / Female / Gene Expression / Genealogy / Genetic aspects / Genetic Loci - genetics / Genetic Markers - genetics / Genetic Predisposition to Disease / Genetics / Genomes / Genotype & phenotype / Hispanic Americans / Human Genetics / Humans / Hypertension / Hypothesis testing / Kidney Failure, Chronic - epidemiology / Kidney Failure, Chronic - genetics / Male / Microarrays / Middle Aged / Physiological aspects / Reproducibility of Results / Research Article / Sample Size / Studies