Saturday, March 8, 2014

human MSH2 using the UCSC genome browser

Go to UCSC genome browser:
Click "genomes"

Input "MSH2" to the "search term" and press "submit".

You will see 6 entries of human MSH2. You can tell which one is the longest form based on their coordinates. Click any one of them will take you to the genomic regions of hMSH2

The region of MSH2 in the human genome looks like: 

Scroll down, and we can see options for adjustment. 
For "Genes and Gene Predictions",  we can 'hide' UCSC genes and 'pack' RefSeq Genes'. Hit 'refresh' and we should see the updated genome view. 

For 'Phenotype and Literature', we can 'hide' Publications and show 'full' 'pack'ed ClinVar Variants. 

After hitting 'refresh', we can see many 'mutations' in the human MSH2 region. 

Go to 'Tools' on the menu toolbar, and select 'Table Browser' 

Make sure that we are still at the MSH2 genomic region, chr2:47630206-47710367. 
We can set 'group' as 'Phenotype and Literature', 'track' as "clinVar Variants', and 'table' as "ClinVar Main(clivarmain)',  The 'region' should select 'position' in chr2:47630206-47710367,
the input output file as "human_msh2_clinvariant".  Then click "get output".

The downloaded file is a text file, and we can open it with any text editor. 

At the stage, we can run Excel and generate a new spread sheet. We can then copy-paste the downloaded clinic variants of human MSH2 into the Excel sheet. 

The file now looks like

In the column 'clinSign', we can see the clinic relevance of the mutations.  Let pick a 'pathogenic' variant start at 47702268.  From column 'hgvsProt', we can see this is a mutation Pro622Leu (or P622L). 

To double-check the SNP rs2303426, we can look at NCBI db-SNP database:

Now, we can design a mutagenic primer that can introduce this human mutation P622L into the cognant site in yeast.   The mutagenic primer should also consider the preferred codons in yeast. 

We shall also be able to design PCR primers that can amplify a fragment that cover this mutation in yeast MSH2 and identify a Restriction Enzyme that can distinguish the wildtype yeast MSH2 from the mutant MSH2. 

Yeast codon usage can be found at:


Human MSH2 protein: NP_000242

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