Wild-Type and database SNPs effect

Question

[fatma.mokhtar]

Hi all,

1-How to identify the wild-type of an SNP? for instance the SNP D19H rs11887534 of ABCG8 gene, you have the DD, DH, and HH. I know here that DD is the wild type. But is there a database where all of this is clear for different genes?

2- Is there a database that clarifies the effect of SNPs on the function of a gene (in vitro studies), or animal studies?

Many thanks, Fatma

[WouterDeCoster]

All humans are equally wild. There is no such thing as wild-type for human variants. You can have the reference allele, which is the one that arbitrarily ended up in the reference genome, or you could think about selecting the most common allele in the population (either global or local).

Answer 1

[Kevin Blighe]

1-How to identify the wild-type of an SNP? for instance the SNP D19H rs11887534 of ABCG8 gene, you have the DD, DH, and HH. I know here that DD is the wild type. But is there a database where all of this is clear for different genes?

The term 'wild-type' is not well defined when considered in the context of a population study looking at multiple diseases. A particular SNP may prove beneficial to some diseases / conditions, but detrimental in others. Keep in mind that most diseases are dictated by complex genetics. I elaborate on some terms here: A: Definition of minor and major allele and connection with risk, effect, wildtype

You may want to look at the ClinVar database and the NHGRI GWAS Catalog.

2- Is there a database that clarifies the effect of SNPs on the function of a gene (in vitro studies), or animal studies?

You may want to look through some of these: A: How to choose good tools for identifying functional SNPs?

Kevin

Answer 2

[ATpoint]

I would not make my life too difficult and simply take the nucleotide that is in the reference genome as wildtype. It is true that population-specific genotypes might not be well-represented with the current reference genomes but unless you are specifically interested in a certain ethnicity better stick with your reference genome. Simply look up the rs number at dbSNP.