Question: whre we can get BRCA1 and 2 SNPs data for indian population?
1
gravatar for gskbioinfo143
5.1 years ago by
India
gskbioinfo14360 wrote:

Hi any one help me getting BRCA1 &2 SNP data of indian population.

any specific database other than dbSNP and BIC

Thanks

snp indian population brca2 brca1 • 1.5k views
ADD COMMENTlink modified 5.0 years ago • written 5.1 years ago by gskbioinfo14360
2
gravatar for Kamil
5.1 years ago by
Kamil2.0k
Boston
Kamil2.0k wrote:

You might consider 1000genomes.

Populations: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/20131219.populations.tsv

I'm using coordinates from GRCh37.p13:

Example commands:

f=http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr17.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
tabix $f 17:41196312-41277500 | gzip > BRCA1.vcf.gz
zcat BRCA1.vcf.gz | wc -l
2052

f=http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr13.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
tabix $f 13:32889617-32973809 | gzip > BRCA2.vcf.gz
zcat BRCA2.vcf.gz | wc -l
2286
ADD COMMENTlink written 5.1 years ago by Kamil2.0k
2
gravatar for kautilya
5.1 years ago by
kautilya410
United States
kautilya410 wrote:

I would recommend using the Indian Genome Variation Browser

You have the ability to search for a gene/region e.g incase of BRCA1. Once there you can select the SNPs from their phase1/2 data and get the frequency distribution amongst different Indian populations e.g for rs8176265

ADD COMMENTlink written 5.1 years ago by kautilya410
1
gravatar for Vivek
5.1 years ago by
Vivek2.4k
Denmark
Vivek2.4k wrote:

I'd also add ExAC which has a much larger cohort than 1000 Genomes and includes allele frequencies for south asian populations. You cannot sub divide that into Indians though.

http://exac.broadinstitute.org/gene/ENSG00000012048

http://exac.broadinstitute.org/gene/ENSG00000139618

ADD COMMENTlink written 5.1 years ago by Vivek2.4k
1
gravatar for Ozzie
5.1 years ago by
Ozzie10
Croatia/Zagreb
Ozzie10 wrote:

There was ReliBRCA database but it seems that it does not exist anymore!

http://www.rellife.com/pdf/mr_10oct2008.pdf

http://www.ncbi.nlm.nih.gov/pubmed/22752604

 

ADD COMMENTlink written 5.1 years ago by Ozzie10
0
gravatar for gskbioinfo143
5.0 years ago by
India
gskbioinfo14360 wrote:

Thanks every one

ADD COMMENTlink written 5.0 years ago by gskbioinfo14360
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