Online PD Risk Score Platform

Motivation

Generating risk scores is becoming more common, but what do they mean? Here, we are putting together a website with context around risk scores, the different types, how they translate into different populations, and publications. Also, we are creating a series of notebooks that can be deployed in a containerized Binder to calculate risk scores for your own data, linked on the website.

In the future, plans include incorporating a calculator directly into the website, but we saw merit in developing both these sections individually.

Website: https://ipdgc.github.io/Online-PD-Risk-Score/

Notebook Binder: Coming Soon!

General Information

• Contributors:

  • Mary B. Makarious, NIA, NIH
  • Anni Moore, NIA, NIH
  • Eric Yu, McGill University
  • Bernabe Bustos, Northwestern University
  • Ignacio Juan Keller Sarmiento, Northwestern University
  • Mohammad Dehestani, University of Tübingen
  • Hui Lui, University of Tübingen

• Website: https://ipdgc.github.io/Online-PD-Risk-Score/

• Online README: https://demo.codimd.org/khJgourfSIKQDCaiv6OYzA

• Google Drive: https://drive.google.com/drive/folders/19KPc3c3Oh5FYGD66g8nhNeRNt2XKbWMs?usp=sharing

Hackathon

Responsibilities

• Website Team:
  • Updates and maintains the website
  • Helps updating the GitHub README to meet Hackthon deadlines
  • Helps with the other teams responsibilities
  • Help design IPDGC presentation
• Content Curating Team:
  • Look through papers/publications
  • Look through online resources
  • Consolidate statistics we can report
  • Think of interesting ways to visualize the data in a meaningful way
  • Help design IPDGC presentation
• Code Development Team:
  • Look through online resources that go through how to calculate these things
  • Start putting together a notebook in Jupyter
  • Calculate quartiles based on META5 data
  • Help design IPDGC presentation

Roles

• Website Team:
  • Mary
  • Bernabe
• Content Curating Team:
  • Mary
  • Eric
  • Bernabe
  • Ignacio
• Code Development Team:
  • Mo
  • Hui
  • Eric
  • Mary
  • Anni

Goals

Hackathon Goals (Mon-Tue)

• Publish draft website
• Running PRSice on French Canadian dataset
• Running PLINK on French Canadian dataset
• Adding R Script to GitHub repository
• Adding notebook to GitHub repository
• Cleaning up scripts and adding context
• Generating some visualization plots for PLINK PRS
• Generating binder for scripts
• Literature search to Anni's doc
• Clean up literature search for website
• ???

What's Next? (Next 2 months)

• Finish filling in website
• Polish up code
• Generate binder
• Add general PD section to website

Future Ideas (Beyond 2 months)

• Incorporating other features of the disease into calculations?
• Incorporating other diseases
• Making calculators for other types of PRS calculations
• Making it possible to generate PRS for single samples
• Generate tables reporting PRS for each disease
  • SampleID | PD_PRS | AD_PRS | PSP_PRS