Question: BRCA1 and BRCA2 database's for NGS diagnostics purposes
0
gravatar for dominik.saburo
3.0 years ago by
Poland/Lodz/ICZMP
dominik.saburo0 wrote:

Hi!

As I have mentioned in the topic we are trying to start a BRCA1 and BRCA2 genes diagnostics by Next Generation Sequencing. We are searching for good and reliable database's with gene variants.

Have some of you worked with the BRCA diagnostics and know such websites which could help us start with? It could be of course a paid database.

sequencing database ngs • 1.2k views
ADD COMMENTlink modified 3.0 years ago by Denise CS5.1k • written 3.0 years ago by dominik.saburo0
3

Hi you can have a look here : http://www.umd.be/ . The advantage is a manual curated database by biologist.

ADD REPLYlink written 3.0 years ago by Titus910
2

BRCA1 and BRCA2 to save you some time :)

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by genomax89k

Really thanks for that! :)

ADD REPLYlink written 3.0 years ago by dominik.saburo0
1

I would also contact my colleagues at Sheffield Children's Hospital, who have been doing BRCA testing for a few years: https://www.sheffieldchildrens.nhs.uk/sdgs/

ADD REPLYlink written 3.0 years ago by Kevin Blighe65k

We will try contact with them. Thanks for information!

ADD REPLYlink written 3.0 years ago by dominik.saburo0
1

In case you want an overview of all mutations (deletion, insertion, indel and SNV) from Ensembl Variation dataset and do some 3d analysis on the position of the mutations for BRCA1

ADD REPLYlink written 3.0 years ago by Ibrahim Tanyalcin1.1k

Thank you all for those informations! I think it will be very helpfull and we will have now an easier start in this field.

ADD REPLYlink written 3.0 years ago by dominik.saburo0
5
gravatar for Collin
3.0 years ago by
Collin850
United States
Collin850 wrote:

One option may be to look at the BRCA exchange (http://brcaexchange.org/ ) since it's curated by an expert panel. It's supported by the Global Alliance for Genomics and Health, and is a non-paid database. Although I'm not sure if it meets all of your needed criteria.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Collin850
0
gravatar for Denise CS
3.0 years ago by
Denise CS5.1k
UK, Hinxton, EMBL-EBI
Denise CS5.1k wrote:

I have not worked with BRCA diagnostics but Open Targets combines somatic and germline data from several resources (most if not all are manually curated variants for our genetic associations). We also have a variety of information in the profile page of the gene of interest e.g. BRCA1 from the variant information (mapped to the genomic sequence and linked to Ensembl) to the drugs targeting that gene.

The integrated data is ranked and scored for the disease associations (see the 18 diseases associated with BRCA1 based on genetic data only in our current release.

It's free and for all: our Open Targets Platform is designed and improved with experimental lab users in mind. This means it's easy, quick and intuitive for users in the diagnostic field or working in the lab who don't have much time for data wrangling plus rather cool visualisations.

ADD COMMENTlink written 3.0 years ago by Denise CS5.1k
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