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We show that the CASM approach improves VAAST's variant prioritization accuracy compared to its previous implementation, and compared to SIFT, PolyPhen-2, and MutationTaster.
These results clearly demonstrate the vast improvement of pgFusion over individual genomic data sources in the prioritization accuracy and suggest the power of data fusion.
Accordingly, pathway ontology annotations can serve to fill in this knowledge gap, helping to decide whether a gene is truly relevant to the query phenotype and improving prioritization accuracy by removing noise.
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Our benchmark analyses presented here demonstrate that CASM approach results in the highest variant prioritization accuracies yet achieved.
The variant prioritization accuracies of VAAST 1.0 and 2.0 on the HGMD/1KGP dataset (Fig. 1A and Table 1) are very similar.
Two more recently published algorithms, PolyPhen-2 Adzhubei et al., 2010 and MutationTaster Schwarz et al., 2010, improve upon this basic approach, integrating other information (e.g., protein structural changes) into the calculation, and thus significantly improving their variation prioritization accuracies compared to SIFT Ng and Henikoff, 2006.
Consequently, it is often assumed that more demanding tasks are likely to result in prioritization of fluency over accuracy and complexity and that tasks based on familiar or concrete information favor a concern for accuracy.
Integrating information concerning the time of origin of genes can serve as an important tool to further improve the accuracy of gene prioritization.
As the resultant rank-ordering of carrier frequencies impacts the design and prioritization of screening programs, the accuracy of this ranking is a public health concern.
That is, the ranking order of betweenness scores was almost completely uncorrelated with the results of differential expression test, and the differentially expressed tests only provide a low accuracy for the prioritization of genes.
To evaluate the accuracy of our gene prioritization score, we estimated the performance of ContrastRank using an increasing subset of high scoring genes.
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