Location of RYR2 Associated CPVT Variants Dataset

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a rare inherited arrhythmia caused by pathogenic RYR2 variants. CPVT is characterized by exercise/stress-induced syncope and cardiac arrest in the absence of resting ECG and structural cardiac abnormalities.

Here, we present a database collected from 225 clinical papers, published from 2001-October 2020, about CPVT associated RYR2 variants. 1355 patients, both with and without CPVT, with RYR2 variants are in the database. There are a total of 968 CPVT patients or suspected CPVT patients in the database. The database includes information regarding genetic diagnosis, location of the RYR2 variant(s), clinical history and presentation, and treatment strategies for each patient. Patients will have a varying depth of information in each of the provided fields.

Database website: https://cpvtdb.port5000.com/

Dataset Information

This dataset includes:

1. all_patients.xlsx
   • Tabular version of the database
   • Most relevant tables in the PostgreSQL database regarding patient sex, conditions, treatments, family history, and variant information were joined to create this database
   • Views calculating the affected RYR2 exons, domains and subdomains have been joined to patient information
   • m-n tables for patient's conditions and treatments have been converted to pivot tables - every condition and treatment that has at least 1 person with that condition or treatment is a column.
   • NOTE: This was created using a LEFT JOIN of individuals and individual_variants tables. Individuals with more than 1 recorded variant will be listed on multiple rows.
     • There is only 1 patient in this database with multiple recorded variants (all intronic)
2. 20240716-dd040736b518.sql.gz
   
   • PostgreSQL database dump
   • Expands to about 4.1 GB after loading the database dump
   • The database includes two schemas:
     • public: Includes all information in patients and variants
       • Also includes all RYR2 variants in ClinVar
     • uta: Contains the biocommons/uta database required to make the hgvs Python package to work locally
       • See https://github.com/biocommons/uta for more information
   • NOTE: It is recommended to use this version of the database only for development or analysis purposes
3. database_tables.pdf
   • Contains information on most of the database tables in the public schema
4. 00_globals.sql
   • Required to load the PostgreSQL database dump
   • Creates a user named anonymous for the uta schema

How To Load Database Using Docker

First, download the 00_globals.sql and <DATE>_<ALEMBIC_REVISION>.gz.sql file and move it into a directory. The default postgres image will load files from the `/docker-entrypoint-initdb.d` directory if the database is empty. See Docker Hub for more information. Mount the directory with the files into the `/docker-entrypoint-initdb.d`.

Example using docker compose with pgadmin and a volume to persist the data.

# Use postgres/example user/password credentials
version: '3.9'

volumes:
  mydatabasevolume: null

services:

  db:
    image: postgres:16
    restart: always
    environment:
      POSTGRES_PASSWORD: mysecretpassword
      POSTGRES_USER: postgres
    volumes:
      - '<INSERT LOCATION OF DIRECTORY WITH DATABASE DUMP HERE>:/docker-entrypoint-initdb.d/'
      - 'mydatabasevolume:/var/lib/postgresql/data'
    ports:
      - 5432:5432

  pgadmin:
    image: dpage/pgadmin4
    environment:
      PGADMIN_DEFAULT_EMAIL: user@domain.com
      PGADMIN_DEFAULT_PASSWORD: SuperSecret
    ports:
      - 8080:80

Creating the Database from Scratch

See https://github.com/alexdaiii/cpvt-database-loader for source code to create the database from scratch.