Other ways to get allele frequencies for specific chromosome positions apart from 1000 genomes

Question

[python_fan]

Hi there,

In my project I am analysing SNPs in cancer datasets. I want to compare the allele frequencies occurring in "my" datasets with those in other populations. For this, I am using 1000 genomes, which works fine in a lot of cases.

However, in some cases, I will find a SNP at a position, where there is no frequency data available from 1000 genomes. Quite often, these SNPs do though appear in dbSNP.

Is there some way how I can estimate the frequency of such alleles in other populations? Maybe by using a "panel of normals", as suggested in GATK? But which dataset would be used for such kind of a panel?

Thank you for any suggestions and help :-)

Answer 1

[Kachibunny]

Hi Ben, I just posted something similar to your problem. In my case I am studying SNP's present in a subset of cancer using TCGA database, I want to search for the significance of the SNP's found on TCGA to the healthy population (frequency of occurrence). To do that I've searched NCBI using their SNP portal without finding any data for most of my chromosome positions. Where you able to find a solution to this problem? Thanks for mentioning the 1000 genome project I would check that out as well.

Answer 2

[Denise CS]

Have you looked at ExAC? Or the NHLBI Exome Sequencing Project (ESP) project?

Answer 3

[igor]

There is a new database gnomAD that includes 126,216 exome sequences and 15,136 whole-genome sequences from unrelated individuals sequenced as part of various disease-specific and population genetic studies: http://gnomad.broadinstitute.org/

[Denise CS]

ExAC is the precursor of the GnomAD containing only exome data.