Location of Ryanodine Receptor Type 2 Associated Catecholaminergic Polymorphic Ventricular Tachycardia Variants Dataset

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 221 clinical papers, published from 2001-October 2020, about CPVT associated RYR2 variants. 1342 patients, both with and without CPVT, with RYR2 variants are in the database. There are a total of 964 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:

all_data.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)

20241219-dd040736b518.sql.gz

PostgreSQL database dump

Expands to about 200MB 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 rows from biocommons/uta database required to make the hgvs Python package validate RYR2 variants

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

database_tables.pdf

Contains information on most of the database tables and columns in the public schema

00_globals.sql

Required to load the PostgreSQL database dump

How To Load Database Using Docker

First, download the `00_globals.sql` and `_.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

volumes:
mydatabasevolume: null

services:

db:
image: postgres:16
restart: always
environment:
POSTGRES_PASSWORD: mysecretpassword
POSTGRES_USER: postgres
volumes:
- ':/docker-entrypoint-initdb.d/'
- 'mydatabasevolume:/var/lib/postgresql/data' ports: - 5432:5432

pgadmin:
image: dpage/pgadmin4
environment:
PGADMIN_DEFAULT_EMAIL: [e-mail]
PGADMIN_DEFAULT_PASSWORD: SuperSecret ports: - 8080:80

Analysis Code

See https://github.com/alexdaiii/cpvt_database_analysis for source code to create the xlsx file and analysis of the data.

Changelist

v0.3.0

Removed inasscessable publications

Updated publications tgo include information on what type of publication it is (e.g. Original Article, Abstract, Review, etc)

 v0.2.1

Updated all_patients.xlsx -> all_data.xlsx

Corrected how the data from all the patient's conditions, diseases, treatments, and the patients' variants tables are joined