Forum:Search for gene variants

Question

[Rm]

Biologists and clinicians are often faced with searching the literature for a set of given gene variants. There are a number of possible routes they could take, from using specialized databases (odd are they don't know about these) to simply using google. What are the common ways that you search for this kind of information and why do you prefer those ways? how you search for gene variants in google:

For example :

"MSH6" ( rs63750617 | "c.3226C>T" | "c.3226C->T" | "c.3226C-->T" | "c.3226C/T" | "p.Arg1076Cys" | "Arg1076Cys" | "R1076C" )

All possible ways variants are represented for easier searches

[Ram]

I don't. I use dbSNP or EnsEMBL. Not every variant report page is indexed by Google and I'm not interested in every Google-indexed page that mentions the variant.

[Rm]

Most of the novel variants are not YET reported in dbSNP or EnsEMBL etc. I believe Google is a good alternative to look for recent reports of publications

[Ram]

pubmed is a good alternative.

[Rm]

Pubmed is one of the best options, my intention was to alternate ways we often quickly search for variants reported (maybe by chromosome: position, by transcripts etc...

[Devon Ryan]

You might just update your post with that or a variant of what I wrote in a comment. The replies will probably be more useful then :)

[finswimmer]

What's your question/intention of this post?

[Rm]

alternate ways we fellow researchers search for variants

[GenoMax]

This post is lacking in detail (you are a moderator so you should be setting a good example). What is the link going to? What do you mean by this?

alternate ways we fellow researchers search for variants

[Rm]

it's a simple and straightforward: how we search for a variant : "MSH6" ( rs63750617 | "c.3226C>T" | "c.3226C->T" | "c.3226C-->T" | "c.3226C/T" | "p.Arg1076Cys" | "Arg1076Cys" | "R1076C" ) is the query and link will take you to the result in google (google is just one way). Where we can look for latest literature reporting the same, apart from that specialized DBs

[Ram]

Google is not great at searching journal articles, the least you'd need to do is switch to Google Scholar. Pubmed is better and has a lot more pertinent filters.

[Devon Ryan]

Can the post essentially be rephrased as the following?

Biologists and clinicians are often faced with searching the literature for a set of given gene variants. There are a number of possible routes they could take, from using specialized databases (odd are they don't know about these) to simply using google. What are the common ways that you search for this kind of information and why do you prefer those ways?

If that's not more or less what you're going after then please clarify :)

[Rm]

Well said @DevonRyan

[cpad0112]

search by dbSNP ID (first field within brackets) in dbSNP. That would get you rest of the HGVS notations you have posted or probe ENSEMBL API with rsIDs to fetch HGVS syntax for variants @ Rm

Answer 1

[jared.andrews07]

Probably the most comprehensive programmatic option I know is the MyVariant.info API, which is very easy to use in python, R, or javascript.

Queries can be gene symbols, chromosome positions, variant IDs, etc.

There is a kind of half-baked but fully-functional web interface somebody made for it here as well.