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Identification of causal genes for complex traits.

Hormozdiari F, Kichaev G, Yang WY, Pasaniuc B, Eskin E - Bioinformatics (2015)

Bottom Line: As opposed to association studies that benefit from linkage disequilibrium (LD), the main challenge in identifying causal variants at associated loci lies in distinguishing among the many closely correlated variants due to LD.Through extensive simulations, we demonstrate that our method not only speeds up computation, but also have an average of 10% higher recall rate compared with the existing approaches.Software is freely available for download at genetics.cs.ucla.edu/caviar.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Inter-Departmental Program in Bioinformatics, Department of Human Genetics and Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA 90095, USA.

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CAVIAR-Gene provides better ranking of the causal genes for Outbred, F2, and HMDP datasets. Panels a and b illustrate the results for Outbred genotypes for case where we have one causal and two causal genes, respectively. Panels c and d illustrate the results for F2 genotypes for case where we have one causal and two causal genes, respectively. Panels e and f illustrate the results for Outbred genotypes for case where we have one causal and two causal genes, respectively
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btv240-F2: CAVIAR-Gene provides better ranking of the causal genes for Outbred, F2, and HMDP datasets. Panels a and b illustrate the results for Outbred genotypes for case where we have one causal and two causal genes, respectively. Panels c and d illustrate the results for F2 genotypes for case where we have one causal and two causal genes, respectively. Panels e and f illustrate the results for Outbred genotypes for case where we have one causal and two causal genes, respectively

Mentions: The results for all the methods across all three datasets are shown in Figure 2. In this figure, the X-axis is the number of genes selected by each method and the Y-axis is the recall rate for each method. Figure 2c and e indicates the recall rate for Outbred, F2, and HMDP datasets where we have implanted one causal gene. Although the difference between the TopK-Gene and CAVIAR-Gene in the case of one causal gene is negligible, we observe a 10% higher recall rate when there are multiple causal genes in a region (Fig. 2b, d, and f).Fig. 2.


Identification of causal genes for complex traits.

Hormozdiari F, Kichaev G, Yang WY, Pasaniuc B, Eskin E - Bioinformatics (2015)

CAVIAR-Gene provides better ranking of the causal genes for Outbred, F2, and HMDP datasets. Panels a and b illustrate the results for Outbred genotypes for case where we have one causal and two causal genes, respectively. Panels c and d illustrate the results for F2 genotypes for case where we have one causal and two causal genes, respectively. Panels e and f illustrate the results for Outbred genotypes for case where we have one causal and two causal genes, respectively
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4542778&req=5

btv240-F2: CAVIAR-Gene provides better ranking of the causal genes for Outbred, F2, and HMDP datasets. Panels a and b illustrate the results for Outbred genotypes for case where we have one causal and two causal genes, respectively. Panels c and d illustrate the results for F2 genotypes for case where we have one causal and two causal genes, respectively. Panels e and f illustrate the results for Outbred genotypes for case where we have one causal and two causal genes, respectively
Mentions: The results for all the methods across all three datasets are shown in Figure 2. In this figure, the X-axis is the number of genes selected by each method and the Y-axis is the recall rate for each method. Figure 2c and e indicates the recall rate for Outbred, F2, and HMDP datasets where we have implanted one causal gene. Although the difference between the TopK-Gene and CAVIAR-Gene in the case of one causal gene is negligible, we observe a 10% higher recall rate when there are multiple causal genes in a region (Fig. 2b, d, and f).Fig. 2.

Bottom Line: As opposed to association studies that benefit from linkage disequilibrium (LD), the main challenge in identifying causal variants at associated loci lies in distinguishing among the many closely correlated variants due to LD.Through extensive simulations, we demonstrate that our method not only speeds up computation, but also have an average of 10% higher recall rate compared with the existing approaches.Software is freely available for download at genetics.cs.ucla.edu/caviar.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Inter-Departmental Program in Bioinformatics, Department of Human Genetics and Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA 90095, USA.

Show MeSH
Related in: MedlinePlus