Practiques Farmacogen*

Practiques Farmacogen*

Phamaceutical Biotecnology-Research Lab Classes: PHARMACOGENETICS AND PHARMACOGENOMICS
-In this lab class #3, you will get the basics on pharmacogenetics and pharmacogenomics that will serve to prepare your work.
The lab-class is divided in two main parts: i) Pharmacogenetics including the DNA sequences containing the SNPs, the structures of the affected proteins, human variability, information about diseases, drugs and recommendations as to how to implement pharmacogentics into therapeutic procedures; and ii) Pharmacogenomics, including the description of how to use the Gene Expression Omnibus (GEO) database with the software Geo2R, and how to construct gene-networks using STRING.
The characteristics of the work are specified at the end of this document. 

PHARMACOGENETICS
Polymorphism analyses
Look for CYP2C19
dbSNP
dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations

Variation Viewer
Variation Viewer allows you to view, search, and navigate variations in genomic context. You can review data from dbSNP, dbVar and ClinVar, or upload your own data.
You can search based on chromosomal location, gene, variant IDs from dbSNP and dbVar, or phenotype; and review results both as sequence annotation tracks and in a filterable table.

LitVar
LitVar allows the search and retrieval of variant relevant information from the biomedical literature and shows key biological relations between a variant and its close related entities (e.g. genes, diseases, and drugs). The LitVar results are automatically extracted (with regular updates) from over 30 million PubMed articles as well as applicable full-text articles in PubMed Central

GeneView (not available anymore)
Genome Aggregation Database (gnomAD)
GenomAD is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data

SNPs3D
SNPs3D is a website which assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis.

HumanVariability
GWAS Catalog (Catalog of published genome-wide association studies)
Search for: Blood pressure
PheWAS (Catalog of Phenome-wide association studies)
Search for Hyperbilirubinemia

Interrelacions Genes, Drugs, Diseases, Pathways
PharmGKB:
PharmGKB is a comprehensive resource that curates knowledge about the impact of genetic variation on drug response for clinicians and researchers.

CPIC
(Clinical Pharmacogenetics Implementation Consortium) is an international consortium interested in facilitating use of pharmacogenetic tests for patient care.
Go to Genes-Drugs, and look for: Azathioprine. Check for the Guideline and Genetic tested recommended action

MY RESULTS.
Go to DRUG Responses: The purpose of this site is to provide information about genetic test results, and what they can tell you about your risk of disease and the drugs you are taking. There are seven examples of common drugs including videos and detailed characteristics of the treatments and pharmacogenetic analyses.

FAERS (FDA Adverse Event Reporting System).
The FDA Adverse Event Reporting System (FAERS) is a database that contains adverse event reports, medication error reports and product quality complaints resulting in adverse events that were submitted to FDA. You can check there specific information for each drug.

Cytochrome P450 Drug Interaction Table.
This table contains the majority of drugs metabolized by CYP enzymes. Go to search to obtain detail information about each particular drug, including their drug-interactions, inhibitors and inducers.

PHARMACOGENOMICS
GEO (Gene Expression Omibus)
GEO is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles.

Go to Geo-Datasets (Use GSE9412, a comparative of gene expression between normal colon cancer cells HT29 and cells resistant to Methotrexate)
STRING (Functional Protein Association Networks)

-Treball a realitzar d'aquestes pràctiques:  
Escollir un gen diana, una malaltia, o un fàrmac del vostre interés particular.
Tot seguit i utilitzant les eines i webs visitades, generar un treball monogràfic
sobre el tema escollit d'interés farmacogenètic o/i farmacogenòmic.
Una vegada finalitzat, envieu-ho com a tasca al camp virtual.
La data límit per enviar el treball es 30-Desembre 2020