Finding cancer gene sequences

Question

[Gene_MMP8]

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?

[cpad0112]

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

Answer 1

[Nicolas Rosewick]

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

[Gene_MMP8]

Thanks! How can I download the gene sequence?

[Gene_MMP8]

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

[Gene_MMP8]

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?

[Emily]

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.

Answer 2

[GenoMax]

How about COSMIC census?

[Gene_MMP8]

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

[GenoMax]

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).