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Genetics Knowledge Provider (KP)

General Description

We developed the Genetics Knowledge Provider (KP), a knowledge-centric data provider for computation based genetic association results, as part of the NCATS Biomedical Data Translator (“Translator”). The Genetics KP aims to * integrate Genome Wide Association Studies (GWAS) data sources in an unbiased way. * provide a curated, unified framework for genetic associations to deepen our understanding of gene/disease biology.

The Genetics KP takes advantage of broad access to disease specific GWAS datasets, portals, and computational tools, to integrate information available for diseases and their associated genes, including similarity-based connections. We follow a stringent procedure to avoid expert bias, including data scouting and recording data provenance, to create a unified framework for gene/disease associations.

We bring to the Translator project computational genetics expertise, and using signal aggregating algorithms and tools to combine genetic signals across GWAS studies.

Team Members

  • Jason Flannick - Principal Investigator and Team Lead
  • Noel Burt - Director, Operations and Development, Knowledge Portals
  • Marc Duby (mduby@broadinstitute.org) - Principal Software Engineer - (contact with questions)
  • Ryan Koesterer - Senior Computational Analyst
  • Maria Costanzo - Manager, Knowledge Portals

Genetics KP Translator Reasoner API

  • https://genetics-kp.transltr.io/genetics_provider/trapi/v1.4/

Description of Genetics KP’s data resources

  • Genebass
  • Downloaded loss of function (LoF) gene/disease association data
  • https://app.genebass.org/
  • GenCC
  • Curated gene/disease association statistics
  • https://thegencc.org/
  • ClinVar
  • https://www.ncbi.nlm.nih.gov/clinvar/
  • ClinGen
  • https://clinicalgenome.org/
  • GWAS Dataset List
  • Downloaded and harmonized 200+ GWAS studies; data is used with Magma gene aggregation method
  • Studies mostly pertaining to metabolic and musculoskeletal diseases
  • https://hugeamp.org:8000/datasets.html

Computational Tools

  • Magma - for Gene/Disease variant pvalue aggregation using GWAS
  • https://ctg.cncr.nl/software/magma
  • HuGE Calculator - For calculating the probability a gene is associated to a disease using common and rare variants
  • https://hugeamp.org:8000/hugecalculator.html
  • PIGEAN - A framework for gene prioritization
  • https://www.kp4cd.org/index.php/node/1516

Source Code

  • GeneticsKP https://github.com/broadinstitute/genetics-kp-dev

External Documentation

  • Additional Genetics KP documentation in GitHub https://github.com/broadinstitute/genetics-kp-dev
  • Gene Level Meta Analysis Method https://hugeamp.org:8000/help.html?page=955
  • Calculating Gene/Disease Probability Method https://hugeamp.org:8000/help.html?page=961
  • Selecting and Processing of GWAS Datasets https://hugeamp.org:8000/help.html?page=935