Genomic Research Data, Networks & Collaborations

As more and more genomic sequencing is undertaken and the development of genomic medicine proceeds there is a growing need to connect health professionals and researchers and support the sharing of data, samples and clinical information to make links between genetic variants and clinical phenotypes. A number of networks and collaborations are actively supporting these efforts.



Project GENIE

A multi-phase, multi-year, national and international project that catalyzes precision oncology through the development of a regulatory-grade registry aggregating and linking clinical-grade cancer genomic data with clinical outcomes from tens of thousands of cancer patients.

Bravo

This variant browser shows chromosome locations, alleles, VEP functional annotations, and allele frequencies for variants observed in individuals sequenced in NHLBI's TOPMed program.

CIViC

An open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer. The goal is to enable precision medicine by providing an educational forum for dissemination of knowledge and active discussion of the clinical significance of cancer genome alterations.

ClinGen & ClinVar Partnership

A critical partnership to improve knowledge of clinically relevant genomic variation. This partnership includes significant efforts in data sharing, data archiving, and collaborative curation to characterize and disseminate the clinical relevance of genomic variation.

Cancer Dependency Map

A comprehensive preclinical reference map connecting tumor features with tumor dependencies.

European Genome-phenome Archive

The European Genome-phenome Archive (EGA) is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects.

Gene ATLAS

A large database of associations between hundreds of traits and millions of variants using the UK Biobank cohort.

Human Cancer Models Initiative

The Human Cancer Models Initiative (HCMI) is an international collaboration to provide a community resource of patient-derived next-generation cancer models with associated molecular sequencing and clinical data.

International Cancer Genome Consortium Data Portal

Cancer genomics data sets visualization, analysis and download.

Matchmaker Exchange

Helps find genetic causes for patients with rare disease through working towards a federated platform to facilitate the matching of cases with similar phenotypic and genotypic profiles using standardized application programming interfaces (APIs) and procedural conventions.

MyGene.info provides simple-to-use REST web services to query/retrieve gene annotation data.

National Institute on Aging Genetics of Alzheimer's Disease

NIAGADS is a national genetics repository created by NIA to facilitate access by qualified investigators to genotypic data for the study of genetics of late-onset Alzheimer's disease.

Pediatric Genomic Data Inventory

A resource that lists known ongoing and completed sequencing projects of pediatric cancer cohorts from the United States and other countries, along with some basic details and reference metadata.

Rare Disease Data Registry of Japan

RADDAR-J aims at providing a support system through the construction of a National Registry covering a wide variety of intractable diseases. hrough the secondary use of the integrated disease information on the platform, we will promote further research of intractable disease. English language version

SweGen Variant Frequency Dataset

Dataset contains whole-genome variant frequencies for 1000 Swedish individuals generated within the SweGen project.

Australian Functional Genomics Network

The Australian Functional Genomics Network has been formed to establish connections between clinical groups discovering gene variants in patients with rare diseases and cancers, and researchers who can analyse these gene variants in model systems.

BRCA Exchange

The BRCA Exchange aims to advance our understanding of the genetic basis of breast cancer, ovarian cancer and other diseases by pooling data on BRCA1/2 genetic variants and corresponding clinical data from around the world.

ClinGen

ClinGen is an authoritative central resource that defines the clinical relevance of genes and variants for use in precision medicine and research.

Color Data

Public database containing aggregated genetic and clinical information from 50,000 individuals who took a Color test.

DICE

DICE (Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics) provides details on how variations in DNA sequence impact gene activity in different types of immune cells.

A coalition of investigators seeking to aggregate and harmonize exome sequencing data from a wide variety of large-scale sequencing projects, and to make summary data available for the wider scientific community.

genomics4rd

genomics4rd is the first Canada-wide data lake for rare disease research, providing a centralized repository of structured and unstructured data from 5,000+ participants.

Human Gene Mutation Database

A database that collates all known (published) gene lesions responsible for human inherited disease.

LatinGen

Goal is to facilitate integration between public databases already established in Latin America centralizing the information.

The Medical Genome Initiative

A consortium of leading clinical laboratories in the U.S. and Canada with a mission to expand access to high-quality clinical whole genome sequencing (cWGS) for the diagnosis of genetic disease. The initial focus will be to publish recommended laboratory and clinical practices for cWGS, along with common clinical research frameworks for demonstrating its value.

MyVariant.info provides simple-to-use REST web services to query/retrieve variant annotation data, aggregated from many popular data resources.

Online Mendelian Inheritance in Man

An online catalog of human genes and disorders.

PopGen 2.0 Network

The PopGen 2.0 Network (P2N) is an association of nine research biobanks at Kiel University's Faculty of Medicine, at the UKSH's Campus Kiel and at the Research Center Borstel.

Repositive

The Repositive platform enables researchers to browse through multiple repositories for the human genomic data they need to power their research.

UK Biobank

A national and international health resource, open to all bona fide health researchers. UK Biobank is following the health and well-being of 500,000 volunteer participants and provides health information to approved researchers in the UK and overseas, from academia and industry.

viral-ngs

A set of scripts and tools for the analysis of viral NGS data.

Beacon Newtork

The Beacon Network is a search engine across the world's public beacons. It enables global discovery of genetic mutations, federated across a large and growing network of shared genetic datasets.

Canadian Open Genetics Repository

The Canadian Open Genetics Repository (COGR) is to design technologies that will help medical researchers and physicians diagnose, treat and cure both rare and common diseases.

ClinVar

ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence.

Decipher

DECIPHER is used by the clinical community to share and compare phenotypic and genotypic data.

Ensembl Genome Browser

A genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.

Fox Den

Fox DEN provides investigators with a tool to explore, download and apply statistical models on aggregated data collected for the Fox Insight online clinical study which collects patient-reported outcomes and genetic data from people with Parkinson's disease and their loved ones.

A resource developed with the goal of aggregating and harmonizing exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community.

IDseq

An unbiased global software platform that helps scientists identify pathogens in metagenomic sequencing data.

Leiden Open Variation Database

A flexible, freely available tool for Gene-centered collection and display of DNA variations. LOVD 3.0 extends this idea to also provide patient-centered data storage and storage of NGS data, even of variants outside of genes.

Monarch Initiative

This platform integrates biological information using semantics, and presents it in a novel way, leveraging phenotypes to bridge knowledge gaps. It's niche is the use of computational reasoning to enable phenotype comparison both within and across species, with the ultimate goal of improving biomedical research.

Nextstrain

An open-source project to harness the scientific and public health potential of pathogen genome data.

OncoKB

OncoKB is a precision oncology knowledge base and contains information about the effects and treatment implications of specific cancer gene alterations.

 

RD-Connect

RD-Connect is an integrated platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research.

Singapore Sequencing Malay Project

Deep whole-genome sequencing of 100 healthy Malays to comprehensively characterize the polymorphic variants in the population.

St Jude Cloud

A data-sharing resource for the global research community with whole genome sequencing (WGS), whole exome sequencing (WES) and RNA-Seq data and analysis tools for pediatric cancer cases.

Swiss Variant Interpretation Platform

The Swiss Variant Interpretation Platform for Oncology (SVIP-O) aims at providing a centralized, joint, and curated database for clinical somatic variants coming from Swiss hospitals and related institutions.

Vietnamese Genetic Variation Database

Sequence data of 305 genomes and exomes of healthy Kinh Vietnamese (KHV) people to characterize Vietnamese genetic variations.

Variant Interpretation for Cancer Consortium Meta-Knowledgebase

A knowledgebase that aggregates cancer variant interpretations from a number of key knowledgebases and resources that contain clinical information related to specific variants.