PHAR5350: The PharmGKB Database for Pharmacogenetics - Report Writing Pharmacology Assignment Help

Assignment Task:

Task 1 – Dr Webb (50 marks) 

1. Halothane is an inhaled anaesthetic used for general anaesthesia. 

a. Interrogate the PharmGKB database for pharmacogenes associated with Halothane. List the genes you identify and the first variation for each gene. 

b. Use the GWAS catalog to determine if the gene /s you listed in 1a have been associated with a phenotypic response in genome wide association studies. Present your results and then identify any variations relevant to Halothane or its adverse effects. 

c. Produce a summary table for each of the SNPs you have identified in 1a and 1b from their dbSNP entries, (this should include comment on any population diversity information that is available). 

2. Investigate the small nucleotide polymorphisms database (dbSNP) for variations in the gene /s you identified in question 1a. 

For each gene: 

How many variations are present in total? 

How many variations are located in the coding region? 

How many variations are nonsynonymous? 

How many variations are pathogenic? 

a. Create a table that catalogues the information you have collected to answer the above questions. 

For the first pathogenic variation / s you identified in 2a access the variation viewer view of ~ 1000 bases of it in the GRCh38.p12 assembly (annotation release 109). 

b. For each gene variation create a table that catalogues the variation type and the molecular consequences of the variations in this region. 

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