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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: Although genome-wide association studies (GWAS) have identified thousands of variants associated with common diseases and complex traits, only a handful of these variants are validated to be causal.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: Although genome-wide association studies (GWAS) have identified thousands of variants associated with common diseases and complex traits, only a handful of these variants are validated to be causal.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