Our 10-step guide to enabling your PGx study to be curated

At PharmGKB we manually curate pharmacogenetic (PGx) associations found in published articles and add them to our database. However, lack of information or clarity is unfortunately common in publications and these hurdles make it difficult or impossible to curate a particular association.

We have published a guideline in Clinical Pharmacology & Therapeutics of 10 simple rules to help your publication be curated:

Enabling the curation of your pharmacogenetic study

1. Use standard gene nomenclature. 

2. Provide dbSNP rsIDs, a reference sequence and mapping information for genetic variants. 

3. Clearly state which allele/genotype of the variant is associated with the phenotype and the direction of the association.  

4. Clearly state population size, ethnicity, gender and drug regimen. 

5. State the minor allele for the variant in the given population/cohort.

6. Clearly state on which chromosomal strand the alleles are reported. 

7. State all genetic variants that were screened (including SNPs, indels, copy number variations and structural variations). 

8. Specify how * alleles or haplotypes were defined. 

9. Report which genotypes/diplotypes were found in the study population and map them to phenotype groups. 

10. State the statistical tests used for each association analysis. Include methods used for multiple hypothesis correction. 

Why follow these steps? 

Here are some benefits to you for enabling us to add your study findings to our public database:

• Be part of the largest collection of curated PGx literatures, which is often used for identifying clinically relevant variants, interpreting genomes and used as a standard for evaluating methods and models for mining scientific literatures as well as drug discovery.

• Your results and a link to your publication on PubMed become accessible to a broad audience, including students, bioinformaticians, researchers and clinicians.

• By becoming part of our data set, your results may contribute to further research studies.

• Your findings can aid in the clinical interpretation of a PGx association (whether the association you found was negative or positive) by contributing evidence to a Clinical Annotation.

• These in turn may aid towards establishing a PGx-based dosing guideline for a particular drug.