converting Illumina kgp SNP ids to rs ids

[Jeff Phillips]

Hi folks,

I'm working with ADNI GWAS data, and I've discovered that these files use Illumina's kgp* format for naming SNPs rather than the rs* format used by NCBI. I'd like to find the rs ids for these SNPs so that I can integrate the ADNI GWAS data with other data using rs ids. Illumina's website gives a number of reference files for their many different arrays (see http://support.illumina.com/array/downloads.html), but I'm not sure which pertains to ADNI's GWAS data. The most specific information I can find on the ADNI/LONI site is:

"Samples were sent to Illumina where non-CLIA WGS, as well as Illumina Omni 2.5M genome-wide association study (GWAS) single nucleotide polymorphism (SNP) arrays, were performed on each sample and completed in the spring of 2013."

Illumina has posted various support files for different versions of the human OMNI 2.5M array with dates from spring 2013 to early 2014, any of which seem like they may be relevant. Does anyone know which I should refer to, or has anyone used another method to convert kgp to rs ids?

Thanks,

Jeff Phillips

Postdoctoral Fellow

Penn FTD Center

Department of Neurology

University of Pennsylvania

[Danielle J Harvey]

Hi Jeff,

I don't work with the GWAS data, but if nobody else responds, you can also try submitting a question directed to the Genetics Core using the Ask the Experts tool on the ADNI website (http://adni.loni.usc.edu/support/experts-knowledge-base/ask-experts/) - someone from the Genetics Core might be able to help!

Danielle

---

From: adni...@googlegroups.com <adni...@googlegroups.com> on behalf of Jeff Phillips <jeffrey.s...@gmail.com>
Sent: Tuesday, January 03, 2017 3:56 PM
To: adni...@googlegroups.com
Subject: [adni-data] converting Illumina kgp SNP ids to rs ids

 

Hi folks,

I'm working with ADNI GWAS data, and I've discovered that these files use Illumina's kgp* format for naming SNPs rather than the rs* format used by NCBI. I'd like to find the rs ids for these SNPs so that I can integrate the ADNI GWAS data with other data using rs ids. Illumina's website gives a number of reference files for their many different arrays (see http://support.illumina.com/array/downloads.html), but I'm not sure which pertains to ADNI's GWAS data. The most specific information I can find on the ADNI/LONI site is:

Downloads - Array - Illumina support.illumina.com You can download current software and support files by clicking one of the links listed below. The description expands to show available downloads.

"Samples were sent to Illumina where non-CLIA WGS, as well as Illumina Omni 2.5M genome-wide association study (GWAS) single nucleotide polymorphism (SNP) arrays, were performed on each sample and completed in the spring of 2013."

Illumina has posted various support files for different versions of the human OMNI 2.5M array with dates from spring 2013 to early 2014, any of which seem like they may be relevant. Does anyone know which I should refer to, or has anyone used another method to convert kgp to rs ids?

Thanks,

Jeff Phillips

Postdoctoral Fellow

Penn FTD Center

Department of Neurology

University of Pennsylvania

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[Jeff Phillips]

Thanks, Danielle. I'll see if I can get a response there.

Jeff

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[Elena Conci]

Dear all, 

Was a response received? 

Same issue here. 

I would also like to confirm which reference genome was used for the WGS/SNP

Best wishes, 

Elena 

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[Gabriel Hoffmeister]

Dear all,

I came across this forum a while ago and tried the solution suggested above by Danielle of contacting the experts through the ADNI website. Unfortunately, I have not received any feedback yet.
I am currently working with the ADNI SNP/WGS datasets and had a similar question, especially regarding the reference genome/build used across the different ADNI phases (e.g., GRCh37/hg19 or GRCh38), as also previously mentioned by Elena.

I would greatly appreciate it if anyone could help or perhaps share any insights on how to obtain this information.

Best,
Gabriel

[Danielle J Harvey]

Hi Gabriel,

 

I reached out to the Genetics Core and received the following response -  hopefully it is helpful (since I don’t know GWAS!):

 

I think, GWAS data for ADNI-1 participants were mapped to GRCh36 (hg18) and GWAS data for ADNI-GO/2/3/4 participants were mapped to GRCh37 (hg19). In order to make sure this, please select several SNPs in GWAS data and then check their base positions.

 

Danielle

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[Gabriel Hoffmeister]

Hi Danielle,

thank you very much for sharing the feedback, I really appreciate it.
I will follow your suggestion and verify this by checking the genomic positions of a subset of SNPs across the datasets.

Just to clarify one additional point, if anyone has any insight: is there any official harmonized liftOver or re-annotation step applied to the ADNI distributed GWAS files, or do the differences in genome build simply reflect the original processing pipelines used in each study phase?

Best,
Gabriel