GP2 8th Data Release

Data Sharing and Publications
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Hi everyone, just wanted to highlight that a few weeks ago we announced GP2’s 8th data release: The Components of GP2’s 8th Data Release - GP2

A few of the highlights:

  • The whole genome sequencing (WGS) data now consists of a total of 7,734 sequenced participants (6,113 PD cases, 617 Controls, and 1,004 ‘Other’ phenotypes).

  • When removing the locally-restricted samples, these now consist of 4,713 participants (4,098 PD cases, 390 Controls, and 225 ‘Other’ phenotypes).

  • Additionally, included in this WGS release is a partial release of whole genome sequences from two AMP® PD cohorts (BioFind and PPMI) that have been joint-called with GP2 WGS. Released samples can be linked back to the original AMP® PD IDs through an ID crosswalk file included with the release.

  • This release also includes 10,454 joint-called clinical exome sequencing participants from the Parkinson’s Foundation.

  • This release includes a total of 62,087 individuals who have core clinical data available. Among these, 16,800 individuals have deep clinical phenotyping and genetic data available.

Release 8 focused on WGS data and additional clinical data, but we are prepping now for release 9 that will add more genotyping data. ETA for release 9 is mid-November! Hopefully many of you are already using the released data, please let me know if you ever have any questions (or just want to chat about the research you’re doing with GP2 :star_struck:)

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Hello,

Thank you for sharing the great news. I have a quick question about the GP2 WGS data. The AMP-PD WGS sample are independent from the GP2 WGS sample?

Thanks,
Jaeyoon

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Hi Jaeyoon! That’s a great question.

This release has been joint-called using all of the AMP PD WGS samples to improve quality, but many of the GP2 WGS samples are independent from the AMP PD WGS.

However, we did also re-release a few AMP PD cohorts as part of this GP2 release that we processed with the GP2 QC and joint calling pipeline (just to make them more comparable to the GP2 WGS). The AMP PD cohorts included in GP2 release 8 are BioFIND and PPMI. We have a sample ID crosswalk file included in this release to match GP2 IDs with the original AMP PD IDs as needed.

The choice is up to the researcher which set of overlapping data they would like to use, but if you want to use both AMP PD and GP2 for an analysis, just make sure to remove the overlapping PPMI and BioFIND samples from one of the cohorts.

I hope this answered your question, please let me know if you have any more!

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