Question: Mutated Gene Sequence Database For Breast Cancer
3
gravatar for Elena
8.8 years ago by
Elena240
Elena240 wrote:

Is there any database to get the mutated gene sequence responsible for breast cancer or we have to generate our own mutated sequence using SNP database?

database sequence search snp cancer • 6.4k views
ADD COMMENTlink modified 8.8 years ago by jvijai1.1k • written 8.8 years ago by Elena240

What do you really mean ? You want a repository of known mutations that cause breast cancer ? Which genes are you interested in ? Precise and clarify your question so that people can try to help you.

ADD REPLYlink written 8.8 years ago by toni2.1k

i need mutated breast cancer genes for my analysis.. so i m bit confused whether there is an existing database which consists of sequences having mutations in it.

ADD REPLYlink written 8.8 years ago by Elena240
6
gravatar for Michael Kuhn
8.8 years ago by
Michael Kuhn5.0k
EMBL Heidelberg
Michael Kuhn5.0k wrote:

The COSMIC database may have what you're looking for.

ADD COMMENTlink written 8.8 years ago by Michael Kuhn5.0k

Ya... but the cosmic database is limited to only few genes, it doesn't contain information for many other genes like BCAR3, MAP3K1, BRMS1 and more.

ADD REPLYlink written 8.8 years ago by Elena240

Ya... but the cosmic database is limited to only few genes, it doesn't contain information for many other genes like BCAR3, MAP3K1, BRMS1, NCOA3 and many more..

ADD REPLYlink written 8.8 years ago by Elena240

There seems to be an enormous list of genes at that link, unless I'm reading it incorrectly. The top of the page just shows the "top 5".

ADD REPLYlink written 8.8 years ago by Neilfws48k

It has information on these genes, e.g. http://www.sanger.ac.uk/perl/genetics/CGP/cosmic?action=byhist&s=4&hn=carcinoma&sn=breast&ln=BCAR3 -- but it was not found to be mutated in the samples they have

ADD REPLYlink written 8.8 years ago by Michael Kuhn5.0k

ya the gene names are present, but the mutations on these genes are not present...

ADD REPLYlink written 8.8 years ago by Elena240
4
gravatar for Daniel Swan
8.8 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

You might however be interested in BIC "An Open Access On-Line Breast Cancer Mutation Data Base" although 'open' will still require you to register.

ADD COMMENTlink written 8.8 years ago by Daniel Swan13k
4
gravatar for Neilfws
8.8 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

As others have pointed out, there is no single "mutated gene sequence responsible for breast cancer".

If you're looking for SNPs that increase susceptibility to the disease, a good starting point is OMIM. You can search with a simple term (e.g. "breast cancer") to get started. Then, click on the tab that says "OMIM dbSNP" to limit results to those loci with a known SNP. View a gene from the list of results and you'll see a "SNP" link in the links box on the right of the page, which will take you to dbSNP entries - e.g. this page for BRCA1.

You can also do all of this programmatically, but I'd learn the basics of how the website works first.

ADD COMMENTlink written 8.8 years ago by Neilfws48k

I want to know the known mutations in the particular gene which influences the risk of cancer.

ADD REPLYlink written 8.8 years ago by Cynthia190
2
gravatar for Mary
8.8 years ago by
Mary11k
Boston MA area
Mary11k wrote:

Try the International Cancer Genome Consortium site. The data is new and still flowing in, but worth checking. The data portal is http://dcc.icgc.org/ , but for a grasp of the whole project see the main site: http://icgc.org/

ADD COMMENTlink written 8.8 years ago by Mary11k
1
gravatar for toni
8.8 years ago by
toni2.1k
Lyon
toni2.1k wrote:

'...mutated gene sequence responsible for breast cancer...'

that simply doesn't exist. So there is also no database.

ADD COMMENTlink written 8.8 years ago by toni2.1k

okay... so i need to do modify the normal sequence into mutated one..thank you.

ADD REPLYlink written 8.8 years ago by Elena240
0
gravatar for jvijai
7.5 years ago by
jvijai1.1k
United States
jvijai1.1k wrote:

Your HolyGrail is hosted by NHGRI here http://research.nhgri.nih.gov/projects/bic/

ADD COMMENTlink written 7.5 years ago by jvijai1.1k
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