whre we can get BRCA1 and 2 SNPs data for indian population?

Question

[gskbioinfo143]

Hi anyone help me getting BRCA1 & 2 SNP data of Indian population. Any specific database other than dbSNP and BIC?

Thanks

[gskbioinfo143]

Thanks every one

Answer 1

[Kamil]

You might consider 1000genomes.

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

I'm using coordinates from GRCh37.p13:

• BRCA1
• BRCA2

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

Answer 2

[kautilya]

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

Answer 3

[Vivek]

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

Answer 4

[Ozzie]

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