ClinPGx Blog (Page 44)

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Considerations for automated functional comparisons

Congratulations on a great paper from Sean Mooney's lab and colleagues at the National Center for Biomedical Ontology at Stanford. It shows that when performing high throughput analysis of omics datasets such as microarrays, proteomics etc, combining manually curated GO terms with additional terms found by text mining

PharmGKB at the ASCPT 2013 Annual Meeting

The American Society for Clinical Pharmacology and Therapeutics (ASCPT) Annual Meeting is being held this week in Indianapolis. Michelle Whirl-Carrillo, Assistant Director of PharmGKB, will be presenting a talk entitled "PharmGKB: From Pharmacogenomics Knowledge to Clinical Interpretation and Implementation" in the "Putting Pharmacogenetics into Practice"

Curators' Favorite Papers

The current Curators' Favorite Papers' highlight an article describing a new method in identifying the genetic variation of gene expression using gene sets. To test their novel approach, Abo et al. used KEGG and PharmGKB pathways to define gene sets. In their method, SNPs and mRNA expression were

Congratulations, David Botstein!

We extend our hearty congratulations to Dr. David Botstein, winner of one of the initial Breakthrough Prizes in Life Sciences! Dr. Botstein, the former chairman of genetics at Stanford University, is now Professor of Genomics and molecular biology and Director of the Lewis-Sigler Institute for Integrative Genomics at Princeton

FDA to post black box warning on codeine

The FDA has announced they will add a black box warning to the codeine drug label to contraindicate the use of the drug in children after tonsillectomy and/or adenoidectomy (see link). Codeine is a pro-drug that is converted to morphine, a reaction that occurs more efficiently in CYP2D6

TPMT allele nomenclature update published

Nomenclature for alleles of the Thiopurine Methyltransferase (TPMT) gene has been updated by the TPMT Nomenclature Committee and has been published online in Pharmacogenetics & Genomics. The committee have addressed issues such as previously existing duplication in star allele names, and has provided dbSNP rsIDs when available. View the updated

How does methylene blue work in the treatment of methemoglobinemia?

Methylene blue is a drug with many clinical applications, including treatment of infectious diseases such as malaria, a cyanide antidote, a dye for diagnostics, and even has the potential as a therapy for Alzheimer Disease and septic shock. It is indicated for the treatment of drug-induced methemoglobinemia - an increase

SLCO1B1 Haplotypes updated on PharmGKB

The PharmGKB Haplotype table for SLCO1B1 has just been updated and now contains information for alleles *1-*36. The literature includes two different alleles which were both named *16 at the time of publication, and we are using the definition for the first *16 allele to be published. References are

Curators' Favorite Papers

Russ Altman’s recent commentary in Clinical Pharmacology & Therapeutics highlights the importance of integrating personal genomic information with traditional health information in order to use it for 'personalized medicine' [PMID: 23241835]. PharmGKB’s PI uses a hypothetical example to illustrate how general population-based data can be

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We have updated the pathway: Tamoxifen PK pathway. Tamoxifen is a selective estrogen receptor modulator. It is used to treat estrogen receptor positive breast cancer, and has been shown to decrease disease recurrence and mortality rates by 50% and 30%, respectively. PharmGKB's Tamoxifen PK pathway describes the metabolism