How to download sequences of one gene from all individuals from 1000 genome (phase III)

Question

[martinsindelar0077]

Hi,

I'm kind of new in this.... could you advice me if there is any tutorial or how can I do that to download sequences from all individuals from 1000 genome project of one gene? I want to study SNPs a bit and I need all sequencies of one specific gene... and also is there any option to download directly amino acid sequence? Is it possible to do it with Biomart or I need some programming with R? Thanks.

[GenoMax]

Data slicer may be one option (as there are bound to be others).

BioMart from GRCh37 Ensembl site is also recommended by 1000 genomes project.

Answer 1

[caggtaagtat]

Hi,

the 1000 genomes project was integrated in Ensembl, which gives you various informations about human genes, among others. To navigate to the different informations, use the menu bar at the left, once you are on the site of a certain gene (e.g. BRCA2)

You can now access all SNPs, which were found in the 1000 genome project, by looking at the so called "Variant table", which also gives you the respective frequency. You can see what nucleotide variations there are for different genomic positions, including non-coding sequences.

Another way would be the using the dbSNP, also founded on the 1000 genomes project.

From ensembl you can than download the sequence of a certain transcript and than compare the sequence with the SNP tables. Since, as far as I know, SNPs often occure in groups, its difficult to define, which sequence you want to download for a single SNP. Maybe there is a way to download the sequence of a gene with specific allels, which I'm not aware of.

Answer 2

[Emily]

If you're just looking for protein or CDS sequences, these are available in Ensembl. Search for your gene of interest, pick a transcript, then go to Haplotypes in the menu on the left. Here you'll see a list of all the variants that coincide in a single copy of the gene in all the 1000 genomes individuals (haplotypes), and their frequencies. You can expand a haplotype to see the protein or CDS sequence and the individual identifiers who have that haplotype.

Here's an example page.

You can also click on the button "Export data as JSON" to activate this REST API endpoint. You could also use the REST API endpoint directly and add things like individual identifiers to your output.

[mrals89]

This is a simpler approach to study the SNPs than just slicing the gene from the BAM files or assemblies, OP.

[bnorris823]

Is there a way to get to the haplotype data, including the frequency data, programmatically by searching for a transcript id instead of searching through the website? maybe the rest API?

[Emily]

Yes, as referred to in the second paragraph of my post.