Efficacy of computational predictions of the functional effect of idiosyncratic pharmacogenetic variants

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Bioinformatics and Genomics

Main article text

 

Introduction

Materials & methods

Pharmacogenetic variant datasets

Classification of off-target pharmacogenetic variants

Validation of classification scheme

Functional effect prediction

Receiver operator curves (ROC)

Results

Distributions of pharmacogenetic variant functional inferences

Classification of variation in pharmacogenes to detect off-target effects

Discussion

Conclusions

Supplemental Information

Thirty PharmGKB variants with a known pharmacogenetic mechanism used for scoring classification scheme.

DOI: 10.7717/peerj.11774/supp-1

Functional inference prediction scores for all 561 PharmGKB missense mutations and 2155 randomly selected common dbSNP variants.

DOI: 10.7717/peerj.11774/supp-2

Candidate Type B PharmGKB variants.

Functional inference prediction scores from 11 algorithms for all 561 PharmGKB missense mutations and 2155 randomly selected common dbSNP variants.

DOI: 10.7717/peerj.11774/supp-3

Additional Information and Declarations

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Hannah McConnell performed the experiments, analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

T. Daniel Andrews conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Matt A. Field conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Data Availability

The following information was supplied regarding data availability:

The raw data is available in the Supplemental Files.

Funding

This work was supported by Australian government fellowship for Matt A Field: NHMRC APP5121190. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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