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Is It Possible To Get Rs Numbers For Indels?

I am currently designing an Illumina custom GoldenGate platform (for the first time, so with lack of experience..). I have finished the selection of SNPs and I'm ready to submit the list for validation. However, I have one question/problem. We also would like to look at 2 deletions in 2 genes. Is it possible to get rs numbers for indels? And if so, where could I obtain them? If not, is there any other possible way to include these indels on the platform? Many thanks in advance!

indel
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updated by Michael Dondrup Michael Dondrup • written by Braemmgm • Braemmgm

I'm not sure of a couple of things: 1) when you say get them--are you asking to obtain existing indel IDs, or are you saying you have novel ones that you need to generate and ID for? and 2) if it's existing indels, which species?

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written by Mary Mary

did you ask your question to the GoldenGate support ?

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks for your comments.

Hi Mary,

1) I am asking for existing indel ID's 2) human

Hi Pierre,

No I haven't yet. Good tip!

Many thanks

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written by Braemmgm • Braemmgm

Dear Mary, I was asking about existing indels (human).

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written by Braemmgm • Braemmgm

I have found the solution. You can specify the sequence of the indels in another file format and then combine the rs-numbers-file with the sequence-file.

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written by Braemmgm • Braemmgm

1 answer

Yes, you can get rsID-annotations if they exist, using e.g. Ensembl biomart. Use the Ensembl variation database, and select all or some "COMPLEX_INDEL*" filter values in Gene-based variation filters. Find below all the parameters I used in XML format. In the result, there is further documentation linked to rsIDs: like this one: http://www.ensembl.org/Homo_sapiens/Variation/Summary?r=11:70053008-70054010;v=rs3832730;vdb=variation;vf=147167 just in case you want to look up something.

I guess it could be possible to do a similar a search in dbSNP too, but it is maybe not as easy to do.

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >

    <Dataset name = "hsapiens_snp" interface = "default" >
        <Filter name = "consequence_type" value = "COMPLEX_INDEL&3PRIME_UTR,COMPLEX_INDEL&5PRIME_UTR,COMPLEX_INDEL&CODING_UNKNOWN,COMPLEX_INDEL&CODING_UNKNOWN&3PRIME_UTR,COMPLEX_INDEL&CODING_UNKNOWN&3PRIME_UTR&SPLICE_SITE,COMPLEX_INDEL&CODING_UNKNOWN&5PRIME_UTR,COMPLEX_INDEL&CODING_UNKNOWN&5PRIME_UTR&3PRIME_UTR,COMPLEX_INDEL&CODING_UNKNOWN&5PRIME_UTR&SPLICE_SITE,COMPLEX_INDEL&CODING_UNKNOWN&NMD_TRANSCRIPT&3PRIME_UTR,COMPLEX_INDEL&CODING_UNKNOWN&NMD_TRANSCRIPT&5PRIME_UTR,COMPLEX_INDEL&CODING_UNKNOWN&NMD_TRANSCRIPT&5PRIME_UTR&SPLICE_SITE,COMPLEX_INDEL&NMD_TRANSCRIPT&3PRIME_UTR,COMPLEX_INDEL&NMD_TRANSCRIPT&5PRIME_UTR"/>
        <Attribute name = "refsnp_id" />
        <Attribute name = "chr_name" />
        <Attribute name = "chrom_start" />
        <Attribute name = "phenotype_description" />
        <Attribute name = "associated_gene" />
        <Attribute name = "associated_variant_risk_allele" />
        <Attribute name = "p_value" />
        <Attribute name = "allele" />
    </Dataset>
</Query>
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updated by Ram Ram • written by Michael Dondrup Michael Dondrup

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