The Components of GP2’s 8th Data Release
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The Components of GP2’s 8th Data Release

By Hampton Leonard, Mike A. Nalls, Dan Vitale, Mathew Koretsky, Kristin Levine, Mary B. Makarious, Lietsel Jones, Zih-Hua Fang, and J Solle | , , , |
Author(s)
  • Co-lead, Complex Disease Data Analysis

    Hampton Leonard, MS

    Data Tecnica International / National Institutes of Health | USA

    Hampton has a background in data science and machine learning, which she applies to large multi-omic datasets in the neurodegenerative disease space. She is passionate about investigating differences on both clinical and omic levels and how these differences can affect clinical trial outcomes.

  • Lead, Complex Disease Data Analysis

    Mike A. Nalls, PhD

    Data Tecnica International | USA

    Mike founded Data Tecnica in early 2017 after over a decade of experience in large dataset analytics and methods research in healthcare and other scientific fields. 400+ peer-reviewed publications in the field of applied statistics in large datasets, brain diseases, and genomics. He is a strong advocate of open science, collaboration, and transparency in science.

  • Working Group Participant

    Dan Vitale, MS

    Data Tecnica International | USA

    Dan is a data science consultant for Data Tecnica, consulting primarily for the Laboratory of Neurogenetics and CARD at the National Institute on Aging of the National Institutes of Health. His work is focused on open science, automation and development of genetic analytic pipelines and software, and machine learning.

  • Working Group Participant

    Mathew Koretsky, BSc

    National Institutes of Health | USA

    Mat is a post-baccalaureate student at the National Institutes of Health. He is passionate about pipeline development and meaningful applications of computer science in the biomedical research space.

  • Working Group Participant

    Kristin Levine, MS

    Data Tecnica International | USA

    Kristin works with the Data Tecnica and National Institute on Aging (NIA) teams on data and code sharing plus real-world data analysis of biobanks and healthcare systems. She is also an accomplished writer, now applying her communication skills to scientific domains.

  • Co-lead, Data and Code Dissemination

    Mary B. Makarious, BSc

    National Institutes of Health | USA

    Mary is a graduate student participating in the NIH graduate partnership program in collaboration with the University College London. She is a rising star in biomedical data science, with a background in genomics, machine learning, and open science platforms. She is also passionate about increasing representation in research and empowering scientists to analyze their own data.

  • Lietsel Jones

    DataTecnica/National Institutes of Health | USA

    Lietsel is an analyst with Data Tecnica with a keen interest in the intersection between epidemiology and genetics. She is also a clinical data manager with GP2 working to collect and harmonize large clinical datasets from worldwide contributors.

  • Lead, Monogenic Data Analysis

    Zih-Hua Fang, PhD

    German Center for Neurodegenerative Diseases | Germany

    The lead of the monogenic data analysis efforts in GP2, they are making significant contributions to GP2’s efforts to study monogenic and familial Parkinson’s disease.

  • Justin Solle
    Co-lead, Operations and Compliance

    J Solle, MBA

    The Michael J. Fox Foundation | USA

    J is the implementation Program Lead for GP2, co-lead for the Operations & Compliance Working Group, and a member of the Operations Committee. J joined the Michael J. Fox Foundation in March 2021 and is the Director of Clinical Research, leading the implementation of GP2.

Overview

In September 2024, GP2 announced the eighth data release on the Terra and the Verily® Workbench platforms in collaboration with AMP® PD. This release includes 5,481 additional whole genome sequences and 10,454 clinical exome sequences. Additional genotyping will be provided in the following release.

  • 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).
    • Of note, cases recruited via the Monogenic Network are coded as ‘Other’
  • 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.

What’s New In This Release?

  • Additional GP2 whole genome sequencing samples and the joint-called variant sets including the samples from two AMP® PD cohorts (BioFind and PPMI) 
  • Clinical exome data from Parkinson’s Foundation
  • Additional clinical data for individuals, bringing our total to 62,087 individuals who have core clinical data available 

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 8 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 8 samples can be found on Workbench. Meanwhile, all release 8 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 62,087 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 and the Montreal Cognitive Assessment
  • Movement Disorder Society-Sponsored Revision of the Unified Parkinson’s Disease Rating Scale
  • Detailed “other” phenotypes, such as Lewy body Dementia
  • Cases recruited via the Monogenic network are coded as ‘Other’

Clinical Exome Sequences

Clinical exome sequencing provided by the Parkinson’s Foundation is available for 10,454 Parkinson’s Foundation samples in this release, offering analysis of the coding regions and splice junctions of 4,717 genes. This targeted sequencing aims to identify and report variants of potential clinical significance, focusing on those that align with the patient’s clinical information and family history. For more detailed information, visit the Fulgent Genetics Clinical Exome page.

Whole Genome Sequences called by DeepVariant-GLnexus

We use Google’s DeepVariant pipeline coupled with GLnexus for cohort-level variant calling. DeepVariant is a deep learning-based variant caller that outperforms existing state-of-the-art tools by accurately calling individual-level genetic variants. It also simplifies the process, enhancing accuracy and reliability. 

Genetically-determined ancestry of array genotyped GP2 participants is 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 include samples from previous releases that have been reclustered using the new cluster file and gone through quality control along with the newly genotyped and shared samples unique to this current release.

Future data releases will continue to grow the diversity of participants available. You can check out our Cohort 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!

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