Efficient inference of local ancestry. 2013

James J Yang, and Jia Li, and Anne Buu, and L K Williams
Public Health Sciences, Henry Ford Health System, Detroit, Department of Psychiatry, University of Michigan, Ann Arbor and Center for Health Services Research, Henry Ford Health System, Detroit, MI, USA.

BACKGROUND The inference of local ancestry of admixed individuals at every locus provides the basis for admixture mapping. Local ancestry information has been used to identify genetic susceptibility loci. RESULTS In this study, we developed a statistical method, efficient inference of local ancestry (EILA), which uses fused quantile regression and k-means classifier to infer the local ancestry for admixed individuals. We also conducted a simulation study using HapMap data to evaluate the performance of EILA in comparison with two competing methods, HAPMIX and LAMP. In general, the performance declined as the ancestral distance decreased and the time since admixture increased. EILA performed as well as the other two methods in terms of computational efficiency. In the case of closely related ancestral populations, all the three methods performed poorly. Most importantly, when the ancestral distance was large or moderate, EILA had higher accuracy and lower variation in comparison with the other two methods. METHODS EILA is implemented as an R package, which is freely available from the Comprehensive R Archive Network (http://cran.r-project.org/). BACKGROUND jyangstat@gmail.com.

UI MeSH Term Description Entries
D012044 Regression Analysis Procedures for finding the mathematical function which best describes the relationship between a dependent variable and one or more independent variables. In linear regression (see LINEAR MODELS) the relationship is constrained to be a straight line and LEAST-SQUARES ANALYSIS is used to determine the best fit. In logistic regression (see LOGISTIC MODELS) the dependent variable is qualitative rather than continuously variable and LIKELIHOOD FUNCTIONS are used to find the best relationship. In multiple regression, the dependent variable is considered to depend on more than a single independent variable. Regression Diagnostics,Statistical Regression,Analysis, Regression,Analyses, Regression,Diagnostics, Regression,Regression Analyses,Regression, Statistical,Regressions, Statistical,Statistical Regressions
D003627 Data Interpretation, Statistical Application of statistical procedures to analyze specific observed or assumed facts from a particular study. Data Analysis, Statistical,Data Interpretations, Statistical,Interpretation, Statistical Data,Statistical Data Analysis,Statistical Data Interpretation,Analyses, Statistical Data,Analysis, Statistical Data,Data Analyses, Statistical,Interpretations, Statistical Data,Statistical Data Analyses,Statistical Data Interpretations
D005828 Genetics, Population The discipline studying genetic composition of populations and effects of factors such as GENETIC SELECTION, population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES. Population Genetics
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D056426 Genetic Loci Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE. Genetic Locus,Loci, Genetic,Locus, Genetic
D060005 Genotyping Techniques Methods used to determine individuals' specific ALLELES or SNPS (single nucleotide polymorphisms). Genotype Assignment Methodology,Genotype Calling Methods,Genotype Determination Methods,Assignment Methodologies, Genotype,Assignment Methodology, Genotype,Calling Method, Genotype,Calling Methods, Genotype,Determination Method, Genotype,Determination Methods, Genotype,Genotype Assignment Methodologies,Genotype Calling Method,Genotype Determination Method,Genotyping Technique,Method, Genotype Calling,Method, Genotype Determination,Methodologies, Genotype Assignment,Methodology, Genotype Assignment,Methods, Genotype Calling,Methods, Genotype Determination,Technique, Genotyping,Techniques, Genotyping
D020641 Polymorphism, Single Nucleotide A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population. SNPs,Single Nucleotide Polymorphism,Nucleotide Polymorphism, Single,Nucleotide Polymorphisms, Single,Polymorphisms, Single Nucleotide,Single Nucleotide Polymorphisms

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