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Genome-wide detection of intervals of genetic heterogeneity associated with complex traits.

Llinares-López F, Grimm DG, Bodenham DA, Gieraths U, Sugiyama M, Rowan B, Borgwardt K - Bioinformatics (2015)

Bottom Line: Here, we present an approach that overcomes both problems: it allows one to automatically find all contiguous sequences of single nucleotide polymorphisms in the genome that are jointly associated with the phenotype.We demonstrate on Arabidopsis thaliana genome-wide association study data that our approach can discover regions that exhibit genetic heterogeneity and would be missed by single-locus mapping.Our novel approach can contribute to the genome-wide discovery of intervals that are involved in the genetic heterogeneity underlying complex phenotypes.

View Article: PubMed Central - PubMed

Affiliation: Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan, JST, PRESTO, Japan and Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.

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Schematic illustration of the problem of detecting genomic intervals that may exhibit genetic heterogeneity
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btv263-F1: Schematic illustration of the problem of detecting genomic intervals that may exhibit genetic heterogeneity

Mentions: We are given a set of n individuals classified into two phenotypic groups, n1 cases and n2 controls (Fig. 1). Each individual is represented by an ordered sequence of L binary genotypes. The sequence of binary genotypes can represent binary SNPs in a homozygous setting or, more generally, a dominant/recessive encoding in a heterozygous setting.Fig. 1.


Genome-wide detection of intervals of genetic heterogeneity associated with complex traits.

Llinares-López F, Grimm DG, Bodenham DA, Gieraths U, Sugiyama M, Rowan B, Borgwardt K - Bioinformatics (2015)

Schematic illustration of the problem of detecting genomic intervals that may exhibit genetic heterogeneity
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4559912&req=5

btv263-F1: Schematic illustration of the problem of detecting genomic intervals that may exhibit genetic heterogeneity
Mentions: We are given a set of n individuals classified into two phenotypic groups, n1 cases and n2 controls (Fig. 1). Each individual is represented by an ordered sequence of L binary genotypes. The sequence of binary genotypes can represent binary SNPs in a homozygous setting or, more generally, a dominant/recessive encoding in a heterozygous setting.Fig. 1.

Bottom Line: Here, we present an approach that overcomes both problems: it allows one to automatically find all contiguous sequences of single nucleotide polymorphisms in the genome that are jointly associated with the phenotype.We demonstrate on Arabidopsis thaliana genome-wide association study data that our approach can discover regions that exhibit genetic heterogeneity and would be missed by single-locus mapping.Our novel approach can contribute to the genome-wide discovery of intervals that are involved in the genetic heterogeneity underlying complex phenotypes.

View Article: PubMed Central - PubMed

Affiliation: Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan, JST, PRESTO, Japan and Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.

Show MeSH
Related in: MedlinePlus