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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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A figure comparing the speed of FAIS, FAIS-WY, BRUTE and BRUTE-WY as the length of the stream varies. Note that the axes are log-scaled (base 10)
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btv263-F4: A figure comparing the speed of FAIS, FAIS-WY, BRUTE and BRUTE-WY as the length of the stream varies. Note that the axes are log-scaled (base 10)

Mentions: Figure 4 compares the runtimes of FAIS, FAISWY, BRUTE and BRUTE-WY for parameters n = 100 and J = 100 (number of permutations) while varying the sequence length L. UFE is not included because it is simply linear in L. Note that the axes are log-scaled: for , FAIS-WY takes 26.56 s, while BRUTE takes 30 min and BRUTE-WY takes h. Further experiments were done for varying n and J (Supplementary Material), which shows that the WY methods are approximately linear in n and J. Extrapolating from these values, if J = 10000, then FAIS-WY would take min, while BRUTE-WY would take days. Other simulations in the Supplementary Material show that the runtime of FAIS and FAIS-WY scales approximately linearly in the number of cases and controls.Fig. 4.


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)

A figure comparing the speed of FAIS, FAIS-WY, BRUTE and BRUTE-WY as the length of the stream varies. Note that the axes are log-scaled (base 10)
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

btv263-F4: A figure comparing the speed of FAIS, FAIS-WY, BRUTE and BRUTE-WY as the length of the stream varies. Note that the axes are log-scaled (base 10)
Mentions: Figure 4 compares the runtimes of FAIS, FAISWY, BRUTE and BRUTE-WY for parameters n = 100 and J = 100 (number of permutations) while varying the sequence length L. UFE is not included because it is simply linear in L. Note that the axes are log-scaled: for , FAIS-WY takes 26.56 s, while BRUTE takes 30 min and BRUTE-WY takes h. Further experiments were done for varying n and J (Supplementary Material), which shows that the WY methods are approximately linear in n and J. Extrapolating from these values, if J = 10000, then FAIS-WY would take min, while BRUTE-WY would take days. Other simulations in the Supplementary Material show that the runtime of FAIS and FAIS-WY scales approximately linearly in the number of cases and controls.Fig. 4.

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