A Random Forests Framework for Modeling Haplotypes as Mosaics of Reference Haplotypes
نویسندگان
چکیده
منابع مشابه
Identification of genes and haplotypes that predict rheumatoid arthritis using random forests
Random forest (RF) analysis of genetic data does not require specification of the mode of inheritance, and provides measures of variable importance that incorporate interaction effects. In this paper we describe RF-based approaches for assessment of gene and haplotype importance, and apply these approaches to a subset of the North American Rheumatoid Arthritis Consortium case-control data provi...
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Some pygmy chimpanzees (also called Bonobos) give much simpler patterns of hybridization on Southern blotting with killer cell immunoglobulin-like receptor (KIR) cDNA probes than do either humans or common chimpanzees. Characterization of KIRs from pygmy chimpanzees having simple and complex banding patterns identified nine different KIRs, representing seven genes. Five of these genes have orth...
متن کاملAlgorithms for inferring haplotypes.
Haplotype phase information in diploid organisms provides valuable information on human evolutionary history and may lead to the development of more efficient strategies to identify genetic variants that increase susceptibility to human diseases. Molecular haplotyping methods are labor-intensive, low-throughput, and very costly. Therefore, algorithms based on formal statistical theories were sh...
متن کاملHaplotypes histories as pathways of recombinations
MOTIVATION The diversity of a haplotype, represented as a string of polymorphic sites along a DNA sequence, increases exponentially with the number of sites if recombinations are taking place. Reconstructing the history of recombinations compared with that of the polymorphic sites is thus extremely difficult. However, in the human genome, because of the relatively simple pattern of haplotype di...
متن کاملModelling haplotypes with respect to reference cohort variation graphs
Motivation Current statistical models of haplotypes are limited to panels of haplotypes whose genetic variation can be represented by arrays of values at linearly ordered bi- or multiallelic loci. These methods cannot model structural variants or variants that nest or overlap. Results A variation graph is a mathematical structure that can encode arbitrarily complex genetic variation. We prese...
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ژورنال
عنوان ژورنال: Frontiers in Genetics
سال: 2019
ISSN: 1664-8021
DOI: 10.3389/fgene.2019.00562