Cancer based pharmacogenomics network supported with scientific evidences: from the view of drug repurposing

BioData Mining
Liwei WangQian Zhu

Abstract

Pharmacogenomics (PGx) as an emerging field, is poised to change the way we practice medicine and deliver health care by customizing drug therapies on the basis of each patient's genetic makeup. A large volume of PGx data including information among drugs, genes, and single nucleotide polymorphisms (SNPs) has been accumulated. Normalized and integrated PGx information could facilitate revelation of hidden relationships among drug treatments, genomic variations, and phenotype traits to better support drug discovery and next generation of treatment. In this study, we generated a normalized and scientific evidence supported cancer based PGx network (CPN) by integrating cancer related PGx information from multiple well-known PGx resources including the Pharmacogenomics Knowledge Base (PharmGKB), the FDA PGx Biomarkers in Drug Labeling, and the Catalog of Published Genome-Wide Association Studies (GWAS). We successfully demonstrated the capability of the CPN for drug repurposing by conducting two case studies. The CPN established in this study offers comprehensive cancer based PGx information to support cancer orientated research, especially for drug repurposing.

References

Jun 1, 1995·Current Opinion in Genetics & Development·K Gardiner
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Jun 22, 2001·Journal of the American Medical Informatics Association : JAMIA·M H Coletti, H L Bleich
Dec 26, 2001·Nucleic Acids Research·Micheal HewettTeri E Klein
Dec 19, 2003·Nucleic Acids Research·Olivier Bodenreider
Dec 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·Bin ZhangJohn Q Trojanowski
Mar 10, 2005·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Jitka StankovaRima Rozen
Jul 21, 2005·International Journal of Radiation Oncology, Biology, Physics·Bhaumik PatelUlka Vaishampayan
Dec 31, 2005·Nucleic Acids Research·David S WishartJennifer Woolsey
Feb 26, 2009·Briefings in Bioinformatics·Michel Dumontier, Natalia Villanueva-Rosales
Apr 7, 2010·Canadian Urological Association Journal = Journal De L'Association Des Urologues Du Canada·Jorg MichelsKim N Chi
Nov 26, 2010·Nucleic Acids Research·Eric W SayersJian Ye
Apr 26, 2011·Journal of the American Medical Informatics Association : JAMIA·Stuart J NelsonRobin Moore
Feb 14, 2012·Nature Medicine·Doron LipsonPhilip J Stephens
Oct 10, 2012·Bioinformatics·Halil KilicogluThomas C Rindflesch
Nov 8, 2012·Nature Methods·Rintaro SaitoTrey Ideker
May 11, 2013·Clinical Neurology and Neurosurgery·Leila MansouriRidha Mrissa
Jun 4, 2013·Journal of Biomedical Informatics·Qian ZhuChristopher G Chute
Jun 6, 2013·Journal of Biomedical Semantics·Patricia L Whetzel, UNKNOWN NCBO Team
Dec 4, 2013·Journal of Medicinal Chemistry·Thomas G Gant
Dec 1, 2010·Journal of the American Society for Information Science and Technology : JASIST·Alla KeselmanThomas C Rindflesch
Dec 21, 2013·PloS One·Vasilis P AndroutsopoulosAristidis M Tsatsakis
Sep 10, 2014·European Journal of Clinical Pharmacology·I DanésX Bonafont
Dec 10, 2014·Drug Metabolism and Disposition : the Biological Fate of Chemicals·Ellen ScheersGeert Mannens

❮ Previous
Next ❯

Citations

May 19, 2016·Oncotarget·Ekaterina A KotelnikovaDmitriy Vinogradov
May 23, 2018·BMC Cancer·Michael T ZimmermannJean-Pierre A Kocher

❮ Previous
Next ❯

Software Mentioned

NCBO Bioportal REST service
NCBO
Systematized ( SNOMED CT )
PGx
RxNorm
NCBO REST service
SemRep
Metamap
Cytoscape
PO

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.