The Components of GP2’s 9th Data Release

By: Hampton Leonard, Mike Nalls, Dan Vitale, Mathew Koretsky, Kristin Levine, Mary B Makarious, Lietsel Jones, Zih-Hua Fang, and J Solle

Overview

In December 2024, GP2 announced the 9th data release on the Terra and the Verily? Workbench platforms in collaboration with AMP? PD. This release includes 17,690 additional genotyped participants.?

• The genotype array data, including locally-restricted samples, now consists of a total of 71,835 genotyped participants (31,985 PD cases, 18,249 Controls, and 21,601 ‘Other’ phenotypes). When removing the locally-restricted samples, these now consist of 55,305 samples (23,709 PD cases, 13,404 Controls, and 18,192 ‘Other’ phenotypes)
• Of those 71,835 samples with genotyped data, 16,800 individuals also have deep clinical phenotyping information (Release 8), 10,454 total individuals also have clinical exomes information (Release 8), and 7,732 total individuals also have WGS data (Release 8)

What’s New in This Release?

Regarding additional data:

• We have added 17,690 genotyped participants to Release 9.
• For researchers who would prefer their raw data to be flipped and aligned, we are providing raw_genotypes_flipped in addition to the raw_genotypes.?

Regarding sample identifiers:

• The ‘m-’ prefix used to denote cohorts originally recruited through the monogenic network has been deprecated.?
• The ‘_s*’ suffix for GP2 sample naming is being deprecated. Sample number is still available via the master key to enable matching with previous release IDs, but GP2 sample IDs in the genetic files will no longer include the ‘_s*’ suffix.
• PPMI GP2IDs in all files have been updated to include their PATNO ID to make it easier for researchers working across platforms.

Locality-restricted GDPR Samples via the Verily Viewpoint Workbench

We are continuing to pilot granting access to locally-restricted samples, otherwise known as samples governed by the General Data Protection Regulation (GDPR) policy, through our collaboration with the Verily Viewpoint Workbench.

At this time, as GP2 continues to roll out data sharing solutions for GDPR protected data, Release 9 data with regional restrictions will be available to only GP2 consortium members and partners. As testing and implementation continues in 2024, this solution will be available to the broader research community. All Release 9 samples can be found on Workbench, meanwhile all Release 9 samples not governed by GDPR requirements can be found on the community workbench on Terra (like all previous releases). To gain access to the full release on VWB you must:

1. Have approved GP2 Tier 2 access
2. Fill out the GDPR-governed sample request form?
3. Be a GP2 consortium member (contributing cohort, GP2 partner, or project analyses team member)

Clinical Data

This release contains clinical data for a total of 71,835 individuals who have genetic and core clinical data available. There is deep clinical phenotyping data and genetic data for 16,800 individuals in this release. This information consists of:?

• Age at diagnosis and onset
• Primary, current, and latest diagnoses
• Cognitive exams such as the Mini-Mental State Examination (MMSE) and the Montreal Cognitive Assessment (MoCA)
• Movement Disorder Society-Sponsored Revision of the Unified Parkinson's Disease Rating Scale (MDS-UPDRS)
• Detailed “other” phenotypes, such as Lewy body Dementia (LBD)
• Cases recruited via the Monogenic network are coded as ‘Other’

Individual-level Data

We now capture the data from a total of 104 cohorts. Please refer to the GP2 Cohort Dashboard for more information on the cohorts that have been shared.?

Genetically-determined ancestry of array genotyped GP2 participants are broken into 11 ancestry groups; the table below details the genetically-determined ancestry of genotyped participants in this release that have passed quality control and been imputed. These numbers reflect samples from previous releases, reclustered using the updated cluster file and subjected to quality control, as well as newly genotyped samples exclusive to this release.

Future data releases will continue to grow the diversity of participants available. You can check out our dashboard to see our progress. For users with tier 2 access already, you can explore the data further on our cohort browser, expanded on in a previous blog post.?

As always, please refer to the README that accompanies each GP2 release for further details regarding recommendations for quality control, pipelines, data, and analyses!