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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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Minimum attainable p-value Ψ(x) for n = 60, n1 = 15 (blue dots)
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btv263-F2: Minimum attainable p-value Ψ(x) for n = 60, n1 = 15 (blue dots)

Mentions: Let be the image of sorted in a monotonically decreasing sequence. Notice that there are only different values because is symmetric around (Fig. 2). Now, we define the testable region as the set such that . In other words, the interval is testable at level δ if and only if the margin of interval belongs to . Two important properties of the testable regions are:Property 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)

Minimum attainable p-value Ψ(x) for n = 60, n1 = 15 (blue dots)
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

btv263-F2: Minimum attainable p-value Ψ(x) for n = 60, n1 = 15 (blue dots)
Mentions: Let be the image of sorted in a monotonically decreasing sequence. Notice that there are only different values because is symmetric around (Fig. 2). Now, we define the testable region as the set such that . In other words, the interval is testable at level δ if and only if the margin of interval belongs to . Two important properties of the testable regions are:Property 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