Question: Finding cancer gene sequences
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gravatar for banerjeeshayantan
22 months ago by
banerjeeshayantan150 wrote:

Where do I find gene sequences of cancer genes? I know cancer datasets are restrictive, but can we find the nucleotide sequences of the genes that cause cancer? I would explain a bit more what I am trying to do
Say I have a mutation in BRCA1 at location x. Now how do I find the sequence of BRCA1 gene such that I can look at the neighborhood of location x instead of downloading the whole genome?

sequencing next-gen • 480 views
ADD COMMENTlink modified 22 months ago by genomax78k • written 22 months ago by banerjeeshayantan150

use ensembl or UCSC or NCBI genome browsers for gene of interest (here BRCA1)

ADD REPLYlink modified 22 months ago • written 22 months ago by cpad011212k
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gravatar for Nicolas Rosewick
22 months ago by
Belgium, Brussels
Nicolas Rosewick8.7k wrote:

You can use ENSEMBL genome viewer . Example with BRCA1 : http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000012048;r=17:43044295-43170245

You can search for gene or genomic region/position

ADD COMMENTlink written 22 months ago by Nicolas Rosewick8.7k

Thanks! How can I download the gene sequence?

ADD REPLYlink written 22 months ago by banerjeeshayantan150

Got it. You can do export data to get the fasta sequence. Thanks for your help

ADD REPLYlink written 22 months ago by banerjeeshayantan150

One follow up question. So the link that you shared has the BRCA1 gene in chr17 from location 43,044,295-43,170,245 but in the cancer gene census as suggested by @genomax has BRCA1 gene from location 43045678..43124096 (link: https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=BRCA1).
Why does this difer?

ADD REPLYlink written 22 months ago by banerjeeshayantan150
1

It looks like the region shown by COSMIC is just the coding region of the transcript ENST00000357654, whereas the Ensembl region of the gene includes multiple transcripts and their UTRs.

ADD REPLYlink written 22 months ago by Emily_Ensembl20k
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gravatar for genomax
22 months ago by
genomax78k
United States
genomax78k wrote:

How about COSMIC census?

ADD COMMENTlink written 22 months ago by genomax78k

But I thought gene census has the mutation information for a particular driver gene. I want the gene sequence.

ADD REPLYlink modified 22 months ago • written 22 months ago by banerjeeshayantan150
1

If you export the table you will get the coordinates. That will allow you to get the sequence via many different ways (samtools faidx, BioMart or biomaRt in R).

ADD REPLYlink modified 22 months ago • written 22 months ago by genomax78k
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