Question: Finding cancer gene sequences
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gravatar for banerjeeshayantan
2.4 years ago by
banerjeeshayantan170 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 • 553 views
ADD COMMENTlink modified 2.4 years ago by genomax89k • written 2.4 years ago by banerjeeshayantan170

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

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by cpad011214k
0
gravatar for Nicolas Rosewick
2.4 years ago by
Belgium, Brussels
Nicolas Rosewick9.0k 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 2.4 years ago by Nicolas Rosewick9.0k

Thanks! How can I download the gene sequence?

ADD REPLYlink written 2.4 years ago by banerjeeshayantan170

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

ADD REPLYlink written 2.4 years ago by banerjeeshayantan170

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 2.4 years ago by banerjeeshayantan170
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 2.4 years ago by Emily_Ensembl21k
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gravatar for genomax
2.4 years ago by
genomax89k
United States
genomax89k wrote:

How about COSMIC census?

ADD COMMENTlink written 2.4 years ago by genomax89k

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

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by banerjeeshayantan170
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 2.4 years ago • written 2.4 years ago by genomax89k
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