Catalogue of Genomic Data Initiatives


The purpose of the catalogue is to identify and aggregate global resources for sharing clinical and genomic data.

ResetFilters

Category
Initiative type
214  of   Initiatives
1000 Genomes

Category: eHealth

Initiative type: Database

The 1000 Genomes Project set out to catalogue common human genetic variation, publishing a set of variations based on sequencing of 2504 individuals from 26 populations. Additional work was done to investigate structural variations in the human genome. Variant calls, sequence data, high-density genotyping chip calls and cell lines from the Project are all available. Data from the 1000 Genomes Project is now housed in the International Genome Sample Resource (IGSR), which is realigning sequence data from the 1000 Genomes Project to the updated GRCh38 human genome assembly and also expanding the data resources produced by 1000 Genomes to include new samples with similarly open consent, new populations and a wider range of data types. Further information, access to data and user support are a

Contact: test1
100k Wellness Project

The Institute for Systems Biology (ISB) launched the 100K Wellness Project in 2014. The first phase was the Hundred Person Wellness Project (HPWP), a 10-month pilot study of 100 _well_ individuals where integrated data from whole-genome sequencing, gut microbiome, clinical laboratory tests and quantified self measures from each individual were used to provide actionable results for health coaching with the goal of optimizing wellness and minimizing disease. The HPWP pilot study was completed in 2015; ISB is now initiating the next phase, scaling up to 100,000 individuals (100K Wellness Project) in partnership with Arivale (a spin-out company created through the pilot study).

Product duration: Ongoing
Cohort size: 100000
Cohort description:

Unaffected individuals

Data type: Whole Genome,
23andMe

Initiative type: Industry

23andMe, Inc. is the leading personal genetics company. Founded in 2006, the mission of the company is to help people access, understand and benefit from the human genome. 23andMe has more than 1.2 million customers worldwide, and more than a million customers who have consented to participate in research on a broad range of topics, ranging from diseases to traits to ancestral origins.

Product duration: Ongoing
Cohort size: 1000000
Cohort description:

Customers (>80% consented to research)

Data type: Variants/Genotyping,
AACR Project Genomics, Evidence, Neoplasia, Information, Exchange (GENIE)

Initiative type: Research Network/Project

Disease area: Cancer

AACR Project Genomics, Evidence, Neoplasia, Information, Exchange (GENIE) is a multi-phase, multi-year, international data-sharing project that catalyzes precision oncology through the development of a regulatory-grade registry that aggregates and links clinical-grade cancer genomic data with clinical outcomes from tens of thousands of cancer patients treated at multiple international institutions. The data within GENIE will ultimately be shared with the global research community after defined periods of time; the initial genomic data set will be publicly available on Nov. 6, 2016.

Product duration: Ongoing
Scale International
Cohort size: 17000
Cohort description:

International cancer patients

Function role: Data sharing (Genomic Medicine),
ACMG Foundation for Genetic and Genomic Medicine

Category: eHealth

The American College of Medical Genetics (ACMG) was founded in 1991, at a time when medical genetics was focused on rare disorders and the major diagnostic tools were cytogenetics, single gene analysis, and biochemical assays. Despite relatively small numbers of members, ACMG has had a strong influence on the field, largely due to its activities funded by grants and contracts, and the broad reach of its policy statements, technical standards, and clinical practice guidelines. ACMG is the specialty society for diplomates certified by the American Board of Medical Genetics and Genomics (ABMGG) and other healthcare professionals committed to the practice of medical genetics. It provides educational resources and a voice for the medical genetics profession.

Product duration: Started 2018
Contact: 7101 Wisconsin Avenue, Suite 1101 | Bethesda, MD 20814
African Partnership for Chronic Disease Research (APCDR)

The African Partnership for Chronic Disease Research (APCDR) is an initiative that facilitates collaborative epidemiological and genomic research of non-communicable diseases across sub-Saharan Africa. Collaborative working by teams across the continent and world wide on large-scale projects that span the sub-Saharan region will allow patterns within, interactions between, and the causes of, non-infectious disease to be discovered. The large data sets generated by these studies will help to reveal the geographic, epidemiological and genomic factors at work, and will provide substantive guidance for health promotion and treatment strategies. This collaboration currently includes 18 partner centres spanning 10 sub-Saharan Africa countries, together with partner organizations from the UK and

Scale Regional
Americian College of Medical Genetics and Genomics (ACMG)

Category: eHealth

To Improve Health Through Medical Genetics.
The American College of Medical Genetics and Genomics will:
Define and promote excellence in the practice of medical genetics and genomics and the integration of translational research into practice;
Promote and provide medical genetics and genomics education;
Increase access to medical genetics and genomics services and integrate them into patient care;
Advocate for and represent providers of medical genetics and genomics services and their patients; and
Maintain structure and integrity of ACMG and its value to members and the public.

Ancestry.com

Initiative type: Industry

Ancestry provides family history and personal DNA testing, harnessing the information found in family trees, historical records, genetics and health history to help people gain a new level of understanding about their lives. Ancestry has more than 2 million paying subscribers across all its family history websites and approximately 1.4 million DNA samples in the AncestryDNA database. AncestryDNA is leading a population genetics research project (Ancestry Human Diversity Project) based on pedigrees, historical records, surveys, family health data, medical and health records, and genetic information, to analyze human evolution, migration, population genetics, population health issues, ethnographic diversity and boundaries, genealogy, etc.

Cohort size: 1400000
Cohort description:

Customer DNA samples

Data type: Variants/Genotyping,
Antigenic Variation Database (VarDB)

Category: eHealth

Initiative type: Database

Many phylogenetically diverse organisms use antigenic variation to avoid recognition by the immune system. varDB was developed to serve as a centralized database of antigenically variable protein families from a range of pathogenic organisms. Infectious diseases and their pathogens are often studied in isolation, but observations made in one species may be used to formulate hypotheses relevant to other taxa. VarDB is intended to facilitate large-scale examination of the evolution of antigenic gene families and help provide insight into how a conserved function can be maintained despite extreme sequence diversity.

Asian Cancer Research Group (ACRG)

Disease area: Cancer

Formed in 2010, ACRG is an independent, not-for-profit company established jointly by Eli Lilly and Company, Merck and Pfizer Inc. to accelerate research and improve treatment for patients affected with the most commonly-diagnosed cancers in Asia. ACRG seeks to increase and improve the knowledge of cancers prevalent in Asia by generating comprehensive genomic data sets and sharing them freely with the scientific community in order to accelerate drug discovery efforts. ACRG is focusing its initial efforts on Asian liver, gastric and lung cancers.
Mission statement: Generate a unique and best-in-class genomic data resource for the most prevalent cancers in Asia that is open to scientists and clinicians worldwide.

Product duration: Ongoing
Cohort size: 176
Cohort description:

HCC tumours and paired normal tissues

Data type: Whole Genome,
Function role: Data sharing (Genomic Research),
AstraZeneca

One of the world’s largest pharmaceutical companies has launched a massive effort to compile genome sequences and health records from two million people over the next decade. In doing so, AstraZeneca and its collaborators hope to unearth rare genetic sequences that are associated with disease and with responses to treatment. AstraZeneca will partner with research institutions including the Wellcome Trust Sanger Institute and Human Longevity. AstraZeneca also expects to draw on data from 500,000 participants in its own clinical trials, and medical samples that it has accrued over the past 15 years.

Product duration: Finished/finishing 2026
Cohort size: 2000000
Cohort description:

Individuals (includes 500,000 participants from AstraZeneca clinical trials)

Data type: Whole Genome,
Australian Genomics

The Australian Genomics Health Alliance (AGHA) is a national network of 47 partner organisations including research institutes, hospitals and universities. The Alliance envisages a whole system change built on existing state-based diagnostic services linked with existing genomic research centres of excellence. Such integration is proposed to facilitate continual improvement and rapid implementation of innovations and new discoveries into clinical practice.
A number of projects will be rolled out under the Rare Disease and Cancer Flagships: in the first tranche (2016 _ 2018) we will study neuromuscular disorders, mitochondrial disorders, neurodevelopmental disabilities (epileptic encephalopathy, malformations of cortical development and intellectual disability), genetic immune disorders an

Product duration: Finished/finishing 2020
Scale National
Cohort size: 1800
Cohort description:

Cases (approximately 900 cancer, 900 rare disease)

Data type: Whole Genome, Whole Exome, Gene Panel, RNAseq, mtDNA,
Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine), Standards,
BBMRI (Biobanking and Biomedical Research Infrastructure)

Category: eHealth

This is in EU and local EU country governmen-funded effort to harmonize and leverage data elements, access and output across large scale european epidemiological, clinical cohort and large clinical trial data sets.

Beacon Project

Initiative type: GA4GH Driver Project

Disease area: Cancer, Rare Disease

The Beacon Project is an open web service that tests the willingness of international sites to share genetic data. It is being implemented on the websites of the world’s top genomic research organizations. Each Beacon is a simple, web-based discovery tool that answers questions of the form, “Do you have a specific allele at a specified position?” It provides a response of “Yes” or “No_. Using a first-of-its-kind search engine called the Beacon Network (beacon-network.org), any user can search for the presence of specific alleles across international datasets. Future upgrades include varied access tiers, and incorporation of clinical metadata for more meaningful searches.

Product duration: Ongoing
Scale International
Cohort size: 100000
Cohort description:

Individuals

Function role: Ecosystem,
Beijing Genomics Institute (BGI)

Category: eHealth

BGI provides comprehensive sequencing and bioinformatics services for medical, agricultural and environmental applications. We help our customers achieve their research goals by delivering rapid, high-quality results using a broad array of cost-effective, cutting-edge technologies. Our customers also benefit from our scientific expertise and research experience that have generated over 900 publications, many in top-tier journals such as Nature and Science. BGI is recognized globally as an innovator for conducting international collaborative projects with leading research institutions to better mankind and our world.

BioBank Japan

Initiative type: Biobank/Repository

Disease area: Cancer

The BioBank Japan (BBJ) represents a large repository with human biospecimens, such as DNA and serum, and relevant medical record information established by the support of MEXT, Japanese government.
The BBJ’s “Tailor-Made Medical Treatment Program” is a research project aiming to enable the practical implementation of individually optimized medical treatment.
Many papers have been published as a result of the rich resources available at BioBank Japan, which target 51 diseases from over 260,000 patients.

Product duration: Ongoing
Scale National
Cohort size: 260000
Cohort description:

Patients only

Data type: Whole Genome, Variants/Genotyping,
Biobank UK

Category: eHealth

Initiative type: Biobank/Repository

Disease area: Complex Diseases

Collected data include demographics, medical history, family history, physical and laboratory measurements, physical findings, and free-form notes.

Biobanking and Biomolecular resources Research Infrastructure (BBMRI)

The Biobanking and BioMolecular resources Research Infrastructure – European Research Infrastructure Consortium (BBMRI-ERIC) aims to establish, operate and develop a pan-European distributed research infrastructure of biobanks and biomolecular resources in order to facilitate access to resources as well as facilities and to support high quality biomolecular and medical research. BBMRI-ERIC operates on a non-economic basis.

Product duration: Ongoing
Scale International
Function role: Data sharing (Genomic Research),
BioSHaRE Project

Category: eHealth

The mission of BioSHaRE is to ensure the development of harmonized measures and standardized computing infrastructures.

Product duration: Started 2018
Contact: Lisette Giepmans
BioVU

Category: eHealth

Initiative type: Biobank/Repository

In addition to data collection, PhenoTips automatically analyzes a wide range of measurements and plots live the corresponding growth curves. It also supports accurate diagnosis based on the entered data, and can suggest additional clinical investigations that can improve the diagnosis.

Data type: Pharmacogenomics, Genomics,
BRCA Challenge

Initiative type: GA4GH Driver Project

Disease area: Cancer

BRCA Challenge is an international effort to advance understanding of hereditary breast, ovarian, and other BRCA-associated cancers by pooling international BRCA1 and BRCA2 genetic data. The BRCA Exchange website (brcaexchange.org) allows users to access expert opinion on the predicted clinical impact of BRCA variants.

Product duration: Ongoing
Scale International
Cohort size: 13500
Cohort description:

BRCA1 and BRCA2 variants, assertions of disease risk, and evidence for pathogenicity classification

Data type: Variants/Genotyping,
Function role: Expert resource,
Broad Genomics Data Donation Platform

“The Broad Genomics Data Donation Platform (DDP) is a disease registry architecture that enables direct participant engagement, including consent and recontact, via intuitive web and mobile interfaces. The DDP will collect and store results of whole genome sequencing and patient and caregiver questionnaires. Future efforts will also include data abstracted from electronic medical records, and wearable and sensor applications. The cloud-based platform will allow qualified researchers to securely access the derived clinical and genomic data and provide a model for direct, bilateral participant engagement that can be used with a variety of disease studies and organizations to advance research and care.
The first study hosted by the broad Genomics Data Donation Platform launched in March 20

Product duration: Ongoing
Data type: Whole Genome,
Function role: Data sharing (Genomic Research),
Broad-Novartis Cancer Cell Line Encyclopedia (CCLE)

The Cancer Cell Line Encyclopedia (CCLE) project is a collaboration between the Broad Institute and the Novartis Institutes for Biomedical Research (including its Genomics Institute of the Novartis Research Foundation). This collaboration aims to conduct detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE has 30,765 registered users, and provides public access to genomic data, analysis and visualization for over 1000 cell lines.

Cohort size: 1074
Cohort description:

Cancer cell lines

Function role: Data sharing (Genomic Research),
Cafe Variome

Initiative type: Other

Data and sample collections in research and healthcare need to be made more easily to accurately discoverable, and then ethically, legally and efficiently sharable. Database, biobank and hospital IT systems do not emphasize these functionalities. Café Variome was therefore developed to sit alongside existing data systems to enable controlled or open discovery of resource entities, within public or restructed ecosystems structured as centralised or federated networks. For example, it enables consortia of diagnostic laboratories/disease labs to check each other’s databases for the presence of mutations and/or phenotypes they observe in their own patients. Other current uses extend across cohort selection, clinical trial setup, healthcare data mining, omics data scanning, national mutation da

Data type: Genotype, Phenotype, Omics, Biosamples, Data and Metadata,
Contact: Tony Brookes: ajb97@leicester.ac.uk
Cancer Core Europe

Disease area: Cancer

The Cancer Core Europe consortium will link cancer programmes on a huge scale to help the joint monitoring of patients and the development of next-generation clinical trials. The consortium sees 60,000 newly diagnosed patients, 300,000 cancer treatments, and ~1,000,000 outpatient visits annually.

Product duration: Ongoing
Scale International
Cohort size: 60000
Cohort description:

Newly diagnosed patients per year

Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine),
Cancer MoonShot 2020

Cancer MoonShot 2020 Program is one of the most comprehensive cancer collaborative initiatives launched to date, seeking to accelerate the potential of combination immunotherapy as the next generation standard of care in cancer patients. This initiative aims to explore a new paradigm in cancer care by initiating randomized Phase II trials in patients at all stages of disease in 20 tumor types in 20,000 patients within the next 36 months. These findings will inform Phase III trials and the aspirational moonshot to develop an effective vaccine-based immunotherapy to combat cancer by 2020. Additional work includes the QUILT program (Quantitative Integrative Lifelong Trial), studying cancer patients undergoing next generation panomic analysis (genome, proteome, immunome and metabolome). The Mo

Product duration: Finished/finishing 2020
Scale National
Cohort size: 20000
Cohort description:

Cancer patients (representing 20 tumour types)

Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine),
CARE for RARE (FORGE)

CARE for RARE is a collaborative team of clinicians, informaticians, scientists and researchers building upon the infrastructure and discoveries of the FORGE Canada (Finding of Rare Disease Genes) project which identified more than 67 novel disease genes using whole-exome sequencing (April 2011-March 2013). The goal of CARE for RARE is to improve clinical care for patients and families affected by rare diseases by expanding and improving diagnosis and treatment.

Contact: Taila Hartley: care4rare@cheo.on.ca
CDISC

Category: eHealth

CDISC is a global, open, multidisciplinary, non-profit organization that has established standards to support the acquisition, exchange, submission and archive of clinical research data and metadata. The CDISC mission is to develop and support global, platform-independent data standards that enable information system interoperability to improve medical research and related areas of healthcare. CDISC standards are vendor-neutral, platform-independent and freely available via the CDISC website.

Center for Disease Control (CDC LabHIT)

Category: eHealth

The Laboratory Health Information Technology (LabHIT) Team in the CDC’s Division of Laboratory Programs, Standards and Services was formed to facilitate the safe and effective integration of laboratory information in the electronic health record and health information technology for the benefit of patients and healthcare providers. The LabHIT Team focuses its efforts on the following three areas:
engaging laboratory professionals,
supporting interoperable health information standards, and
advancing usability of laboratory information.

The Centers for Mendelian Genomics (CMG) are co-funded by NHGRI, the National Heart, Lung, and Blood Institute, and the National Eye Institute of National Institutes of Health (NHLBI). The program aims to make major contributions to discovering most or all causal” genes for human Mendelian and monogenic disorders in two main ways. The first is to use genome-wide sequencing and other genomic approaches to discover causal genes during the funding period. The second is to accelerate the discovery by disseminating the obtained knowledge and effective approaches

Contact: http://mendelian.org
Centre for Proteomic & Genomic Research (CPGR)

Disease area: Cancer

The CPGR is a non-profit company based in Cape Town, South Africa. It originated from an initiative by the South African Department of Science and Technology (DST), and is financially supported by the Technology Innovation Agency (TIA), to boost the development of a bio-economy in South Africa. The CPGR combines state-of-the-art information rich genomic and proteomic (_omics_) technologies with bio-computational pipelines to create unique solutions in the human health and the agri-biotech sectors. The National Cancer Institute (NCI) provided $3M (USD) to CPGR and other South-African, pan-African and American scientists to perform a GWAS study on prostate cancer in African men (MADCaP Project)

Children's Hospital of Philadelphia Biorepository

Initiative type: Biobank/Repository

Disease area: Cancer, Rare Disease

The world’s largest pediatric biorepository connects DNA to the hospital’s health records for studies of childhood diseases. Associated with the Children’s Brain Tumour Tissue Consortium (CBTTC).

Cohort size: 8600000
Cohort description:

Pediatric biological samples

China Kadoorie Biobank

Initiative type: Biobank/Repository

Disease area: Cancer, Complex Diseases

The CKB is a collaboration between the CTSU (Oxford University), China CDC, and Chinese Academy of Medical Sciences. The China Kadoorie Biobank Study (CKB) is a prospective health study investigating the causes of major chronic diseases, such as stroke, heart disease, cancer, diabetes and chronic respiratory disease. Over 512,000 people aged 30-79 were recruited from 10 areas across China. During the baseline survey, each participant consented to take part, had a blood sample taken, underwent physical examination, and completed a questionnaire. Participants will be closely monitored over the coming decades for illnesses, hospital admissions and deaths. The CKB study group is committed to making the cohort data available to the international scientific community.

Product duration: Ongoing
Cohort size: 512000
Cohort description:

Unaffected individuals from China (genotyping data is available for ~100,000)

Function role: Data sharing (Genomic Research),
China Kadoorie Biobank

Category: eHealth

Initiative type: Biobank/Repository

Disease area: Complex Diseases

The CKB is a collaboration between the CTSU (Oxford University), China CDC, and Chinese Academy of Medical Sciences. The China Kadoorie Biobank Study (CKB) is a prospective health study investigating the causes of major chronic diseases, such as stroke, heart disease, cancer, diabetes and chronic respiratory disease. Over 512,000 people aged 30-79 were recruited from 10 areas across China. During the baseline survey, each participant consented to take part, had a blood sample taken, underwent physical examination, and completed a questionnaire. Participants will be closely monitored over the coming decades for illnesses, hospital admissions and deaths. The CKB study group is committed to making the cohort data available to the international scientific community.

Chinese Newborn Sequencing Project

Disease area: Rare Disease

A national newborn genome sequencing project has been jointly launched by the Chinese Board of Genetic Counseling and Children’s Hospital of Fudan University in Shanghai. The project will carry out genetic testing on 100,000 newborn babies over the coming five years. The findings will be gathered in a database and a genetic testing standard for hereditary diseases will be developed, which seeks to improve the identification and treatment of inherited diseases.

Product duration: Finished/finishing 2021
Scale National
Cohort size: 100000
Cohort description:

Newborn babies

Data type: Whole Genome,
ClinGen Data Modeling Working Group

Category: eHealth

Develop the data models required to inform ClinGen system development and promote robust system interoperability. The group also seeks to assist groups working to promote the development of healthcare information technology by addressing core clinical genetic data modeling challenges.

ClinGen EHR Working Group

Category: eHealth

Enhance the usability, dissemination and implementation of genomic information to improve healthcare by facilitating interfaces between ClinGen and clinical information systems.

Function role: Defines requirements,
Clinical Data Interchange Standards Consortium (CDISC)

Category: eHealth

Initiative type: Standards

The CDISC vision is to inform patient care and safety through higher quality medical research.
Mission Statement
CDISC is a global, open, multidisciplinary, non-profit organization that has established standards to support the acquisition, exchange, submission and archive of clinical research data and metadata. The CDISC mission is to develop and support global, platform-independent data standards that enable information system interoperability to improve medical research and related areas of healthcare. CDISC standards are vendor-neutral, platform-independent and freely available via the CDISC website.
Core Principles
Lead the development of standards that improve efficiency while supporting the scientific nature of clinical research.
Recognize the ultimate goal of creating regulat

Clinical Genome Resource (ClinGen)

ClinGen is a National Institutes of Health (NIH)-funded resource dedicated to building an authoritative central resource that defines the clinical relevance of genes and variants for use in precision medicine and research.

Data type: Genomics,
Contact: clingen@clinicalgenome.org
Clinical Laboratory Improvement Advisory Committee (CLIAC)

Category: eHealth

The Clinical Laboratory Improvement Advisory Committee (CLIAC), managed by the Centers for Disease Control and Prevention (CDC), provides scientific and technical advice and guidance to the Department of Health and Human Services (HHS). The Committee includes diverse membership across laboratory specialties, professional roles, (laboratory management, technical, physicians, nurses) and practice settings (academic, clinical, public health), and includes a consumer representative. The clinical and anatomic pathology laboratory specialties represented include microbiology, immunology, chemistry, hematology, immunohematology, cytopathology, histopathology, genetic testing, and informatics. The Committee also includes three ex officio members from the federal agencies that oversee the Clinical

Clinical Pharmacogenetics Implementation Consortium (CPIC)

Category: eHealth

The Clinical Pharmacogenetics Implementation Consortium (CPIC) was formed in late 2009, as a shared project between PharmGKB and the Pharmacogenomics Research Network. CPIC guidelines are peer-reviewed and published in a leading journal (in partnership with Clinical Pharmacology and Therapeutics) with simultaneous posting to PharmGKB with supplemental information/data and updates. Anyone with clinical interests in pharmacogenetics is eligible for membership. CPIC’s goal is to address some of the barriers to implementation of pharmacogenetic tests into clinical practice.

Clinical Sequencing Exploratory Research (CSER)

Medical uses of genome sequencing are being applied and adapted on a case-by-case basis, but research to study the optimal uses and implementation of these tests is needed. To rapidly address these questions, the National Human Genome Research Institute (NHGRI) and the National Cancer Institute (NCI) have initiated a Clinical Sequencing Exploratory Research (CSER) program to support multidimensional research in this area. CSER is a national consortium of projects that bring together clinicians, scientists, laboratories, bioinformaticians, economists, legal scholars, ethicists, and patients working together to develop and share innovations and best practices in the integration of genomic sequencing into clinical care. CSER includes 377 researchers and 21 institutions. Areas of research incl

Product duration: Finished/finishing 2017
Scale National
Cohort size: 6000
Cohort description:

Pediatric and adult patients with various phenotypes, healthy adults, and physicians. ~6,000 have already been enrolled through CSER. The projected enrollment (through May, 2017) is ~7,000.

Data type: Whole Genome, Whole Exome,
Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine), Standards,
Clinical Sequencing Exploratory Research (CSER)

Category: eHealth

National Human Genome Research Institute (NHGRI) and the National Cancer Institute (NCI) have initiated a Clinical Sequencing Exploratory Research (CSER) program to support multidimensional research in this area. CSER is a national consortium of projects that bring together clinicians, scientists, laboratories, bioinformaticians, economists, legal scholars, ethicists, and patients working together to develop and share innovations and best practices in the integration of genomic sequencing into clinical care.

Clinical Sequencing Exploratory Research (CSER) Electronic Health Records Working Group

Category: eHealth

Leverage the experiences of the CSER sites to understand what needs to be done to improve support for genetics in the EHR

Clinical Sequencing Exporatory Research (CSER) Consortium

The National Human Genome Research Institute (NHGRI) and the National Cancer Institute (NCI) have initiated a Clinical Sequencing Exploratory Research (CSER) program to support multidimensional research in this area. CSER is a national consortium of projects that bring together clinicians, scientists, laboratories, bioinformaticians, economists, legal scholars, ethicists, and patients working together to develop and share innovations and best practices in the integration of genomic sequencing into clinical care.

Data type: Genomics,
Contact: Lucia Hindorff: hindorffl@mail.nih.gov
ClinVar

Initiative type: Database

ClinVar is designed to provide a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. By so doing, ClinVar facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar collects reports of variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for interactive users as well as those wishing to use ClinVar in daily workflows and other local applications. ClinVar works

Data type: Genetic Variant, Phenotype,
ClinVar

Initiative type: Database

ClinVar is designed to provide a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. By so doing, ClinVar facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar collects reports of variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for interactive users as well as those wishing to use ClinVar in daily workflows and other local applications. ClinVar works

Data type: Genetic Variant, Phenotype,
Contact: Melissa Landrum: landrum@ncbi.nlm.nih.gov
ClinVar

ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. ClinVar is an active partner in the ClinGen project.

Product duration: Ongoing
Scale International
Data type: Variants/Genotyping,
Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine),
ClinVar

Category: eHealth

Initiative type: Database

ClinVar aggregates information about genomic variation and its relationship to human health.

Critical Assessment of Genome Interpretation (CAGI)

CAGI is a community experiment to objectively assess computational methods for predicting phenotypic impacts of genomic variation and to inform future research directions. Participants are provided genetic variants and make predictions of resulting phenotype; predictions are evaluated against experimental characterizations by independent assessors. The work culminates with a community workshop and publications to disseminate results. CAGI shares pre-publication datasets for evaluation and improvement of genomic variant interpretation methodologies. Includes an ethics forum to evaluate the sharing of “NOT human subjects” data that are derived from human research participants.

Product duration: Ongoing
Scale International
Data type: Whole Genome, Whole Exome, Single Gene, Variants/Genotyping,
Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine), Expert resource,
Database of Genomic Structural Variation (dbVar)

Initiative type: Database

Database of genetic structural variation.

Data type: Genomics,
DatabasE of genomiC varIants and Phenotype in Humans Using Ensembl Resources (DECIPHER)

Initiative type: Database

The overall aims of DECIPHER are to: 1. Aid in the interpretation of plausibly pathogenic variants from genome- wide analyses by placing them in the context of known pathogenic variants, other plausibly pathogenic variants and population variation 2. Annotate plausibly pathogenic variants with their likely functional impact using Ensembl tools to compare sequence and structural variants with the latest functional annotation of the current human reference genome e.g define which genes are involved in a specific copy number variant (microdeletion / microduplication) or for sequence variants, whether they are positioned within a gene or regulatory element. 3. Facilitate research into the study of genes that affect human health and development to improve diagnosis, management and therapy of

Data type: Genetic Variant, Phenotype,
Contact: Helen Firth: hvf21@cam.ac.uk Matt Hurles: meh@sanger.ac.uk
Database of Genotypes and Phenotypes (dbGaP)

Initiative type: Database

The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute the results of studies that have investigated the interaction of genotype and phenotype.

Data type: Genomics,
Database of Short Genetic Variations (dbSNP)

Initiative type: Database

Short genetic variations.

Data type: Genomics,
DataMed

Category: eHealth

Initiative type: Tool

DataMed is a Data Discovery Index prototype developed by bioCADDIE (biomedical and healthCAre Data Discovery Index Ecosystem) to provide a platform for users to find data distributed in multiple repositories and other sources. DataMed incorporates the DATS metadata model to unify and map metadata for indexing which is utilized by the search engine. Various enhancement modules such as publication, terminology and NLP-server are employed to provide an efficient search engine and intuitive user interface.

DECIPHER

Initiative type: Database

DECIPHER is used by the clinical & research community to share and compare phenotypic and genotypic data to enable diagnosis and gene discovery. The DECIPHER database contains data from 21,475 patients who have given consent for broad data-sharing; DECIPHER supports flexible and proportionate data sharing. Records can be private, shared with a consortium or open. DECIPHER has facilitated >1000 publications in the peer-reviewed scientific literature. DECIPHER is a leading participant in the GA4GH matchmaker exchange.

Product duration: Ongoing
Scale International
Cohort size: 21475
Cohort description:

International patients

Data type: Variants/Genotyping,
Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine),
Deciphering Developmental Disorders (DDD)

The Deciphering Developmental Disorders (DDD) study aims to find out if using new genetic technologies can help doctors understand why patients get developmental disorders. To do this we have brought together doctors in the 24 Regional Genetics Services, throughout the UK and Republic of Ireland, with scientists at the Wellcome Trust Sanger Institute, a charitably funded research institute which played a world-leading role in sequencing (reading) the human genome. The DDD study involves experts in clinical, molecular and statistical genetics, as well as ethics and social science. We have collected DNA and clinical information from 13,500 undiagnosed children in the UK with developmental disorders and their parents.

Contact: Helen Firth: hvf21@cam.ac.uk, Matt Hurles: meh@sanger.ac.uk
deCODE Genetics

Initiative type: Industry

Disease area: Cancer, Complex Diseases

deCODE (headquartered in Iceland) leads the world in the discovery of genetic risk factors for common diseases. Their gene discovery engine is driven by a unique approach and resources, including detailed genetic and medical information on some 500,000 individuals from around the globe taking part in the discovery work and proprietary statistical algorithms and informatics tools for gathering, analyzing, visualizing and storing large amounts of data. deCODE became a subsidiary of Amgen in 2012 (www.amgen.com).

Product duration: Ongoing
Cohort size: 500000
Cohort description:

International participants

Data type: Whole Genome, Variants/Genotyping,
DNAdigest

Category: eHealth

The objectives of DNAdigest are to educate, facilitate, and engage on issues regarding access to genomic data for research. We are a non-profit organisation founded in Cambridge, UK. We are a community of individuals from diverse backgrounds who all want to see data used to its full potential for the benefit of patients.

Data type: Genomics,
Drug-Gene Interaction Database (DGIdb)

Category: eHealth

Initiative type: Database

A database where users can search for drug-gene interactions by gene or drug name.

East London Genes & Health

Initiative type: Research Network/Project

Disease area: Complex Diseases

East London Genes & Health is one of the world_s largest community-based genetics studies, aiming to improve health among people of Pakistani and Bangladeshi heritage in East London by analysing the genes and health of 100,000 local people. The project does not include creation of a DNA database.

Cohort size: 100000
Cohort description:

Unaffected individuals from East London, of Pakistani or Bangladeshi heritage

Data type: Whole Exome,
East London Genes and Health

Category: eHealth

East London Genes & Health is one of the world’s largest community-based genetics studies, aiming to improve health among people of Pakistani and Bangladeshi heritage in East London by analysing the genes and health of 100,000 local people.

Electronic Health Records for Clinical Research (EHR4CR)

Category: eHealth

The EHRCR project is -to date- one of the largest public-private partnerships aiming at providing adaptable, reusable and scalable solutions (tools and services) for reusing data from Electronic Health Record systems for Clinical Research.

Electronic Medical Records and Genomics (eMERGE)

The Electronic Medical Records and Genomics (eMERGE) is a national network organized and funded by the National Human Genome Research Institute (NHGRI) since 2007 to conduct genomic medicine research on genomic variant discovery and clinical implementation by leveraging biorepositories linked to electrical medical records (EMRs). Currently, the network includes nine study sites, two sequencing centers, a coordinating center, and NHGRI program staff. Genome-wide genotyping and phenotyping data from over 55,000 participants in Phase I (2007-2011) and Phase II (2011-2015) is already available now through dbGaP, and data including some candidate gene sequencing, whole exome or whole genome sequencing data on over 65,000 more participants will be added in the current Phase III (2015-2019). Pha

Product duration: Ongoing
Scale National
Cohort size: 55028
Cohort description:

Patients

Data type: Variants/Genotyping,
Function role: Data sharing (Genomic Medicine), Standards,
Electronic Medical Records and Genomics (eMERGE) Network

Category: eHealth

The Electronic Medical Records and Genomics (eMERGE) Network is a national consortium organized by NHGRI to develop, disseminate, and apply approaches to research. It combines DNA biorepositories with electronic medical record (EMR) systems for large-scale, high-throughput genetic research with the ultimate goal of returning genomic testing results to patients in a clinical care setting. During Phases I and II, the Network deployed 37 electronic phenotype algorithms across more than 58,000 subjects with dense genomic data, and more than 40 new phenotypes are prioritized for genomic and targeted sequencing data during eMERGE III. Projects from the eMERGE Network have been cited over 14,000 times and 548 total projects have been published as of August 2016. Themes of bioinformatics, genomic

Electronic Medical Records and Genomics Network (eMERGE) Electronic Health Record Working Group

Category: eHealth

The EHR Integration workgroup entails developing methodologies and best practices for not only the incorporation of a patient’s genomic data into the EHR but also the usability of these data by physicians and patients. The workgroup will work to delineate common and distinct approaches and challenges for EMR integration, share best practices, address challenges and approaches for utilization of whole genome/exome sequence-associated information, establish a dialog with EMR vendors and support the use and evaluation of CDS tools. The eMERGE Network is actively working through all steps of this process to make select data available at all network sites.

Elements of Morphology

An international group of clinicians working in the field of dysmorphology has initiated the standardization of terms used to describe human morphology. The goals are to standardize these terms and reach consensus regarding their definitions. In this way, we will increase the utility of descriptions of the human phenotype and facilitate reliable comparisons of findings among patients. Discussions with other workers in dysmorphology and related fields, such as developmental biology and molecular genetics, will become more precise…

Data type: Phenotype Ontology,
Contact: John Carey: John.Carey@hsc.utah.edu
ELIXIR

ELIXIR unites Europe_s leading life science organizations in managing and safeguarding the massive amounts of data being generated every day by publicly funded research. It is a pan-European research infrastructure for biological information. ELIXIR provides the facilities necessary for life science researchers – from bench biologists to cheminformaticians – to make the most of our rapidly growing store of information about living systems, which is the foundation on which our understanding of life is built. Governments and ministries of countries are members of the ELIXIR consortium, and the scientific community in each member country develops their national Node.

Product duration: Ongoing
Scale International
Function role: Data sharing (Genomic Research), Standards, Ecosystem,
eMERGE

Category: eHealth

The eMERGE Network, originally founded in 2007 and funded by the National Human Genome Research Institute (NHGRI) is a national collaboration that combines DNA biorepositories with electronic medical record (EMR) systems for large scale, high-throughput genetic research in support of implementing genomic medicine. The Network is currently in its third phase and reaches across the United States consisting of nine sites, two sequencing centers, two coordinating centers, and several affiliates.

ENIGMA Consortium

Disease area: Cancer

ENIGMA is an international consortium of investigators focused on determining the clinical significance of sequence variants in BRCA1, BRCA2 and other known or suspected breast cancer genes, to provide this expert opinion to global database and classification initiatives, and to explore optimal avenues of communication of such information at the provider and patient level.

Product duration: Ongoing
Scale International
Cohort description:

Patients and relatives sequenced for genetic predisposition to breast/ovarian cancer; molecular resources and results used to improve variant classification methods and variant classification.

Data type: Variants/Genotyping, RNAseq,
Function role: Data sharing (Genomic Research), Expert resource,
EU-US eHealth Cooperative Initiative

Category: eHealth

Initiative type: Standards

To support an innovative collaborative community of public- and private-sector entities, including suppliers of eHealth solutions, working toward the shared objective of developing, deploying, and using eHealth science and technology to empower individuals, support care, improve clinical outcomes, enhance patient safety and improve the health of populations.

EuRenomics

Our Consortium is devoted to improving the lives of patients affected by rare kidney diseases. In line with the objectives of the International Rare Disease Research Consortium (IRDiRC), we aim to develop novel tools that will allow to make more accurate diagnoses, predict the disease course and the efficacy of available treatments, and help developing new and better therapies for rare kidney diseases.
This project is receiving funding as part of the European Community’s commitment to the IRDiRC initiative. In this quest we are joining forces with our FP7 partner project Neuromics (for neuromuscular disorders) and the RD-CONNECT infrastructure platform.

Contact: Franz Schaefer: franz.schaefer@med.uni-heidelberg.de
European Medical Information Framework (EMIF)

Category: eHealth

Initiative type: Standards

The EMIF project aims to develop a common information framework of patient-level data that will link up and facilitate access to diverse medical and research data sources, opening up new avenues of research for scientists. To provide a focus and guidance for the development of the framework, the project will focus initially on questions relating to obesity and Alzheimer’s disease.

European Network for Genetic and Genomic Epidemiology (ENGAGE)

ENGAGE aims to translate the wealth of data emerging from large-scale research in genetic and genomic epidemiology from European (and other) population cohorts into information relevant to future clinical applications. The concept of ENGAGE is to enable European researchers to identify large numbers of novel susceptibility genes that influence metabolic, behavioural and cardiovascular traits, and to study the interactions between genes and life style factors. The ENGAGE consortium will integrate and analyse one of the largest ever human genetics dataset. The ENGAGE Consortium has brought together 24 leading research organizations and two biotechnology and pharmaceutical companies across Europe and in Canada and Australia. ENGAGE is coordinated by the University of Helsinki.

Product duration: Finished/finishing 2013
Scale International
Cohort size: 600000
Cohort description:

Individuals who have provided plasma samples. GWAS scans are available for 80,000

Data type: Variants/Genotyping,
Function role: Data sharing (Genomic Research),
EUROREC Institute

Category: eHealth

The EUROREC Institute (EuroRec) is an independent not-for-profit organisation, promoting in Europe the use of high quality Electronic Health Record systems (EHRs). One of its main missions is to support, as the European certification body, EHRs quality labelling and defining functional and other criteria.
EuroRec is organised as a permanent network of National ProRec centres and provides services to industry (the developers and vendors), healthcare providers (the buyers), policy makers and patients.

Exome Aggregation Consortium (ExAC)

The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The database includes 60,706 unrelated individuals sequenced through various disease-specific and population genetic studies; individuals affected by severe pediatric disease have been removed, so this data set should serve as a useful reference set of allele frequencies for severe disease studies.

Product duration: Ongoing
Scale International
Cohort size: 60706
Cohort description:

Unrelated individuals sequenced through various disease-specific and population genetic studies (not including severe pediatric disease patients)

Data type: Whole Exome,
Function role: Data sharing (Genomic Research),
Farr Institute

Category: eHealth

The Farr Institute is a UK-wide research collaboration involving 21 academic institutions and health partners in England, Scotland and Wales. Publically funded by a consortium of ten organisations led by the Medical Research Council, the Institute is committed to delivering high-quality, cutting-edge research using ‘big data’ to advance the health and care of patients and the public.
The Farr Institute aims to position the UK as a world leader in health informatics research through scientific discovery and the enhancement of patient and public health. By analysing data from multiple sources and collaborating with the government, public sector, academia and industry, the Institute will unleash the value of vast sources of clinical, biological, population and environmental data for public b

Fast Healthcare Interoperability Resources (FHIR) (of HL7)

Category: eHealth

Initiative type: Standards

Fast Healthcare Interoperability Resources (FHIR, pronounced “Fire”) defines a set of “Resources” that represent granular clinical and administrative healthcare concepts. The resources can be managed in isolation, or aggregated into complex documents. Technically, FHIR is designed for the web; the resources are based on simple XML, JSON or RDF structures, with an http-based RESTful protocol where each resource has predictable URL. Where possible, open internet standards are used for data representation.

FINDbase

Initiative type: Database

Disease area: Rare Disease

Frequency of INherited Disorders database (FINDbase) is a relational database, derived from the ETHNOS software, recording frequencies of causative mutations leading to inherited disorders and pharmacogenomic markers worldwide. The initial information is derived from the published literature, locus-specific databases, genetic disease consortia and most importantly direct submissions from laboratories and individual researchers documented against their unique ResearcherIDs. FINDbase offers a user-friendly query interface, providing instant access to the list and frequencies of the different mutations, based on PivotViwer and Silverlight technology. Registered users from three different groups, namely administrator, national coordinator and curator, are responsible for database curation and/

Product duration: Ongoing
Cohort size: 100000
Cohort description:

Individuals from 92 populations worldwide, providing information on 3,800 disease-causing mutations across 26 genes

Data type: Variants/Genotyping,
Function role: Data sharing (Genomic Research),
Food and Drug Administration (FDA) Molecular and Clinical Genetics Panel

Category: eHealth

Molecular and Clinical Genetics Panel
Molecular and Clinical Genetics Panel reviews and evaluates data concerning the safety and effectiveness of marketed and investigational in vitro devices for use in clinical laboratory medicine including clinical and molecular genetics and makes appropriate recommendations to the Commissioner of Food and Drugs.

France Genomic Medicine 2025

The French government announced in June 2016 that it plans to invest _670 million in a genomics and personalized medicine program meant to improve the diagnosis and prevention of disease in the country. The effort is aiming for the establishment of 12 sequencing platforms throughout the country, and two national centers for genomic expertise and data analysis that will ensure the platforms are consistent and regularly updated. The government will establish an inter-ministerial strategic committee, presided over by French Prime Minister Manuel Valls, to monitor the implementation of the program. The efforts will concentrate initially on cancer, diabetes, and rare diseases. After 2020, the effort will be opened up to common diseases as well. Of the _670 million being invested in the first fi

Product duration: Finished/finishing 2025
Scale National
Data type: Whole Genome,
Geisinger Health System

Category: eHealth

Geisinger is an integrated health care system in central Pennsylvania and southern New Jersey with >1.5 million active patients. It operates one of the largest research projects in the world matching patient genomic sequencing data with electronic health record (EHR) data. Geisinger’s EHR goes back 20 years and data have been normalized and modeled to facilitate research studies. The MyCode Community Health Initiative population research program is open to all patients. Currently more than 140,000 are consented and exome sequence data are available on most of them. MyCode is returning medically actionable exome results and actively engages participants in research. Both the Genomic Medicine Institute and the Autism & Developmental Medicine Institute are engaged with patient advocacy groups

Product duration: Started 2018
Data type: Pharmacogenomics,
Gen2Phen

The GEN2PHEN project aims to unify human and model organism genetic variation databases towards increasingly holistic views into Genotype-To-Phenotype (G2P) data, and to link this system into other biomedical knowledge sources via genome browser functionality. After its EU FP7 funding expired, it has continued at the GEN2PHEN-Alliance.

Data type: Genetic Variant, Phenotype,
Contact: Tony Brookes: ajb97@leicester.ac.uk
GeneMatcher

Initiative type: Database

GeneMatcher is a freely accessible web site designed to enable connections between clinicians, researchers, and patients/families from around the world who share an interest in the same gene or genes. The principle goal for making GeneMatcher available is to help solve unsolved” exomes. This may be done with cases from research or clinical sources. No identifiable data are collected. GeneMatcher was developed with support from the Baylor-Hopkins Center for Mendelian Genomics as part of the Centers for Mendelian Genomics network.”

Data type: Genetic Variant, Phenotype,
Contact: Ada Hamosh: ahamosh@jhmi.edu
Generation Scotland

Category: eHealth

Initiative type: Biobank/Repository

Generation Scotland aims to create more effective treatments based on gene knowledge to the medical, social and economic benefit of Scotland and its people. It is a unique partnership between the Scottish University Medical Schools and NHS Scotland and the people of Scotland. GS is a bioresource of human biological samples and data available for medical research, along with targeted recruitment to new studies. Longitudinal data is available by consented linkage to routine medical records.

GENESIS (formerly known as GEM.app)

Initiative type: Other

GENESIS (aka GEM.app) is a software tool to annotate, manage, visualize, analyze and SHARE large genomic datasets. Currently, ~900 registered users from 45 countries are building dynamic communities centered around phenotypic interests, with full control remaining with the PI of a study. GENESIS currently contains >7,000 whole exomes and genomes from 100 different phenotypes. The focus of GENESIS is on user-friendly analysis for nonbioinformaticians to make next-generation sequencing data directly accessible. Yet, GENESIS provides powerful and flexible filter options, including single family filtering, across family/phenotype queries, and evaluation of segregation in families. GENESIS has been used to successfully identify >60 novel disease genes in the past 4 years.

Data type: Genetic Variant, Phenotype,
Contact: Stephan Zuchner: szuchner@med.miami.edu
Genome Asia 100K

GenomeAsia100K is a non-profit consortium that aims to generate genomic information for Asian populations and promote genetic understanding to support research and discovery, by sequencing 100,000 individuals. It is intended to initially include populations from 12 South Asian countries and at least 7 of North and East Asian countries.

Product duration: Ongoing
Scale International
Cohort size: 100000
Cohort description:

Individuals from across Asia

Data type: Whole Genome,
Function role: Data sharing (Genomic Research),
Genome in a Bottle

The Genome in a Bottle Consortium is a public-private-academic consortium hosted by the National Institute of Standards and Technology (NIST) to develop the technical infrastructure (reference standards, reference methods, and reference data) to enable translation of whole human genome sequencing to clinical practice. The priority of GIAB is authoritative characterization of human genomes for use in analytical validation and technology development, optimization, and demonstration

Product duration: 2018 - ongoing
Scale International
Cohort size: 7
Cohort description:

Small number of extensively characterized human genomes by many technologies, along with high-confidence characterization for use in benchmarking variant calls. Most genomes are distributed both as NIST Reference Materials and as cell lines and DNA from the Coriell Institute for Medical Research, and are consented under the Personal Genome Project for public data sharing and commercial use and redistribution. Current samples are from germline cell lines, and future samples may include germline

Data type: Whole Genome, Whole Exome, Gene Panel, Variants/Genotyping,
Function role: Data sharing (Genomic Research), Standards,
Genome in a Bottle

Category: eHealth

The Genome in a Bottle Consortium is a public-private-academic consortium initiated by NIST to develop the technical infrastructure (reference standards, reference methods, and reference data) to enable translation of whole human genome sequencing to clinical practice.

Product duration: Started 2018
Genomic Data Commons (GDC)

Initiative type: Database, GA4GH Driver Project

Disease area: Cancer

Established by the National Cancer Institute (NCI), the NCI Genomic Data Commons seeks to store, analyze and distribute cancer genomics data generated by NCI and other research organizations. The database will be interoperable and publicly available to qualified researchers. Anyone will be able to submit data for consideration. Initially, the GDC will house data from: Cancer Genome Characterization Initiative; The Cancer Genome Atlas; Therapeutically Applicable Research to Generate Effective Treatments, or TARGET; and The Cancer Cell Line Encyclopedia. Based out of University of Chicago.

Product duration: Ongoing
Scale National
Function role: Data sharing (Genomic Research), Expert resource,
Genomic Medicine Alliance

The Genomic Medicine Alliance aims to create collaboration ties between academics, researchers, regulators, and the general public interested in all aspects of genomics and personalized medicine. The Alliance provides the means to establish networks and to encourage collaborative work towards advancing the Genomic Medicine discipline, focusing in particular on translating results from academic research into clinical practice.
In particular, the Genomic Medicine Alliance aims to:
Encourage and catalyze multidisciplinary collaborative research between partner institutions and scientists, particularly from emerging countries.
Liaise among research organizations, clinical entities and regulatory agencies in areas related to genomic medicine.
Facilitate the introduction of pharmacogenomics

Contact: George P. Patrinos: gma@goldenhelix.org
Genomics England

Initiative type: National Initiative

Disease area: Cancer, Rare Disease

Genomics England has been established to deliver the 100,000 Genomes Project. This flagship project will sequence 100,000 whole genomes from ~70,000 NHS patients and their families. Genomics England is a company wholly owned and funded by the Department of Health; this programme was made possible by the National Institute for Health Research, NHS England, Public Health England and Health Education England.

Product duration: Finished/finishing 2017
Scale National
Cohort size: 100000
Cohort description:

Genomes derived from 70,000 rare disease and cancer patients and their relatives

Data type: Whole Genome,
Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine), Ecosystem,
Genomics England

Category: eHealth

Genomics England is a company owned by the UK Department of Health and was set up to deliver the 100,000 Genomes Project. This flagship project is sequencing 100,000 whole genomes from NHS patients with rare diseases, and their families, as well as patients with common cancers. The Project has four main aims: to bring benefit to patients, to create an ethical and transparent programme based on consent, to enable new scientific discovery and medical insights and to kickstart the development of a UK genomics industry. 13 NHS Genomic Medicine Centres (GMCs) have been set up across the country to recruit patients, take the samples and provide medical information to the project. Visit our website for further information, including how to access the 100,000 Genomes Project dataset.

Genomics Research and Innovation Network (GRIN)

Inspired by a common vision of accelerated genomic discovery, collaboration, and improved clinical outcomes, leaders at Boston Children_s Hospital (BCH), Cincinnati Children_s Hospital Medical Center (CCHMC) and the Children_s Hospital of Philadelphia (CHOP) have come together to propose the creation of _GRIN_, a common, shared community of practice for collaborative genomic studies. GRIN researchers are collaborating to create a broad knowledge base of annotated genomic and clinical data for variant interpretation and establishing a _big data_ environment to benefit discovery, translational science, and trainee development.

Product duration: Ongoing
Scale National
Cohort size: 100000
Cohort description:

Targeted pediatric populations and familial studies.

Data type: Whole Genome, Whole Exome, Gene Panel, Variants/Genotyping,
Function role: Data sharing (Genomic Research),
Global Alliance for Genomics and Health (GA4GH)

Category: eHealth

The Global Alliance for Genomics and Health (Global Alliance) is an international coalition, dedicated to improving human health by maximizing the potential of genomic medicine through effective and responsible data sharing. The promise of genomic data to revolutionize biology and medicine depends critically on our ability to make comparisons across millions of human genome sequences, but this requires coordination across organizations, methods, diseases, and even countries. The members of the Global Alliance for Genomics and Health are working together to create interoperable approaches and catalyze initiatives that will help unlock the great potential of genomic data.

Global Genomic Medicine Collaborative (G2MC)

The Global Genomic Medicine Collaborative (G2MC) is an organization of global leaders in the implementation of genomic medicine in clinical care, arising from an international symposium in Washington, D.C. in January, 2014 convened by the National Human Genome Research Institute and hosted by the US Institute of Medicine. It is an international genomic medicine community formed to unite and catalyze the implementation of genomic tools and knowledge into health care delivery globally. Specifically, it is intended to:
Serve as nexus, clearinghouse, and knowledge base for genomic medicine activities globally;
Develop opportunities for global genomic medicine demonstration projects (implementation and outcomes research);
Capture and disseminate best practices for genomic medicine (in bio

Data type: Genomics,
Contact: Adam Berger: genomics@nas.edu
Global Genomic Medicine Collaborative (G2MC)

Category: eHealth

The Global Genomic Medicine Collaborative (G2MC) evolved out of the 2014 Global Leaders in Genomic Medicine Summit to identify opportunities and foster global collaborations for enabling the demonstration of value and the effective use of genomics in medicine. Engaging multiple stakeholders across the globe, the G2MC group, under the auspices of the IOM Roundtable on Translating Genomic-Based Research for Health, seeks to improve global health by implementing genomic tools and knowledge into health care delivery. To accomplish these goals, seven working groups were created, including communications, education, evidence, IT/bioinformatics, pharmacogenomics, policy, and a steering group to guide and support efforts among working groups.

Contact: Adam Berger
GoT2D

The GoT2D consortium aims to understand the allelic architecture of type 2 diabetes through whole-genome sequencing, high-density SNP genotyping, and imputation. The reference panel based on this work is intended as a comprehensive inventory of low-frequency variants in Europeans, including SNPs, small insertions and deletions, and structural variants.

Product duration: Ongoing
Scale International
Cohort description:

Multiple case-control cohorts

Data type: Whole Genome, Whole Exome, Variants/Genotyping,
Function role: Data sharing (Genomic Research),
GTEx

The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. This project will collect and analyze multiple human tissues from donors who are also densely genotyped, to assess genetic variation within their genomes. By analyzing global RNA expression within individual tissues and treating the expression levels of genes as quantitative traits, variations in gene expression that are highly correlated with genetic variation can be identified as expression quantitative trait loci, or eQTLs. The GTEx Consortium Analysis Working Group (AWG) is open to all academic, government and private sector scientists interested in participating in a collaborative open p

Cohort size: 8555
Cohort description:

Samples, derived from 544 donors

Data type: Whole Genome, Whole Exome, Variants/Genotyping,
H3Africa

The Human Heredity and Health in Africa (H3Africa) Initiative aims to facilitate a contemporary research approach to the study of genomics and environmental determinants of common diseases with the goal of improving the health of African populations. To accomplish this, the H3Africa Initiative aims to contribute to the development of the necessary infrastructure and expertise among African scientists, and to establish networks of African investigators.

Product duration: Ongoing
Scale International
Cohort size: 60000
Cohort description:

There are multiple cohorts (see H3Africa website)

Data type: Whole Genome, Whole Exome, Variants/Genotyping,
Function role: Data sharing (Genomic Research), Expert resource,
Health Level 7 Clinical Genomics Working Group

Category: eHealth

Initiative type: Standards

This group supports the HL7 mission to create and promote its standards by enabling the communication between interested parties of the clinical and personalized genomic data. The focus of clinical genomics work is the personalization (differences in individual’s genome) of the genomic data and the linking to relevant clinical information.
This Work Group will facilitate the development of common standards for clinical research information management across a variety of organizations — including national and international government agencies and regulatory bodies, private research efforts, and sponsored research — and thus the availability of safe and effective therapies by improving the processes and efficiencies associated with regulated clinical research.

Health Level 7 Terminology Authority

Category: eHealth

Initiative type: Standards

The HTA, as a representative body of HL7 International, shall ensure that HL7 provides timely and high quality terminology products and services to meet its business needs. The HTA shall serve as the single point of contact with any external terminology standards development organizations (SDO) with which HL7 has established, or in the future shall establish, formal relationships.

Health Level Seven International (HL7)

Category: eHealth

Initiative type: Standards

Founded in 1987, Health Level Seven International (HL7) is a not-for-profit, ANSI-accredited standards developing organization dedicated to providing a comprehensive framework and related standards for the exchange, integration, sharing, and retrieval of electronic health information that supports clinical practice and the management, delivery and evaluation of health services. HL7’s 2,300+ members include approximately 500 corporate members who represent more than 90% of the information systems vendors serving healthcare.

HUGO Gene Nomenclature Committee (HGNC)

Category: eHealth

HGNC is responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication.

Function role: Publishes Ontologies,
Human Genome Variation Society (HGVS)

The Society aims to foster discovery and characterization of genomic variations including population distribution and phenotypic associations. HGVS promotes collection, documentation and free distribution of genomic variation information and associated clinical variations. It endeavor to foster the development of the necessary methodology and informatics. HGVS runs a database of locus-specific databases (LSDBs), available at: http://www.hgvs.org/locus-specific-mutation-databases

Product duration: Ongoing
Scale International
Data type: Whole Genome,
Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine), Standards, Ecosystem,
Contact: Rania Horaitis: rania@variome.org
Human Longevity, Inc. (HLI)

Human Longevity, Inc. (HLI) is a genomics-based, technology-driven company creating the world_s largest and most comprehensive database of whole genome, phenotype and clinical data. HLI is developing and applying large scale computing and machine learning to make novel discoveries to revolutionize the practice of medicine. HLI is concentrating on cancer, diabetes and obesity, heart and liver diseases, and dementia. HLI_s business also includes the HLI Health Nucleus, a genomic powered clinical research program which uses whole genome sequence analysis, advanced clinical imaging and innovative machine learning, along with curated personal health information, to deliver the most complete picture of individual health.

Product duration: Ongoing
Data type: Whole Genome,
Human Phenotype Ontology (HPO)

…The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Terms in the HPO describes a phenotypic abnormality, such as atrial septal defect.
The HPO was initially developed using information from Online Mendelian Inheritance in Man (OMIM) and is now using information from OMIM and the medical literature and contains approximately 10,000 terms. Over 50,000 annotations to hereditary diseases are available for download or can be browsed using the PhenExplorer.

Product duration: Started 2018
Data type: Phenotype Ontology,
Function role: Develops data Interchange Standards, Publishes Ontologies, Publishes Data Models,
Contact: Peter Robinson: peter.robinson@charite.de
Human Variome Project

The Human Variome Project focuses on increasing both the quality and quantity of genomic knowledge that is collected, curated, interpreted and shared in order to improve global health outcomes.
The Human Variome Project acts as an umbrella organisation across multiple countries, institutions and initiatives to establish collaboration around its central vision—the responsible, open, online publishing of the international consensus on genomic variant pathogenicity.
Variant data is generated every day in diagnostic labs, clinical centres and research institutions around the world. The Human Variome Project recognises the importance of sharing high quality genetic variant data to expedite the diagnosis and treatment of patients with genetic diseases worldwide. Integral to this is the process

i2b2

Category: eHealth

Initiative type: Tool

Informatics for Integrating Biology & the Bedside is developing a scalable informatics framework that will enable clinical researchers to use existing clinical data for discovery research and, when combined with IRB-approved genomic data, facilitate the design of targeted therapies for individual patients with diseases having genetic origins.

Product duration: Started 2018
Icahn Institute for Genomics and Multiscale Biology at Mount Sinai

Category: eHealth

At the Icahn Institute, our vision is to integrate the digital universe of information to better diagnose, treat, and prevent disease. The Icahn Institute was founded in 2011 to help advance precision medicine with cutting-edge technologies, novel partnerships between the public and private sectors, and world class computational and analytical resources. At Mount Sinai, our research and clinical teams work together to translate research insights to improve patient diagnostics and treatment.

Contact: Eric Schadt
Implementing Genomics in Practice (IGNITE)

IGNITE was created to enhance the use of genomic medicine by supporting the development of methods for incorporating genomic information into clinical care and exploration of the methods for effective implementation, diffusion and sustainability in diverse clinical settings. Six genomic medicine demonstration projects were selected for 4 years of funding. These demonstration projects will incorporate genomic information into the electronic medical record (EMR) and provide clinical decision support (CDS) for implementation of appropriate interventions or clinical advice. The sites will work together to develop new methods and projects and disseminate their findings to the public. Dissemination of these methods and developing best practices for implementation is a key goal so that the inform

Product duration: Finished/finishing 2018
Scale National
Cohort size: 73000
Cohort description:

Duke: 7,000 patients from primary care clinics. Mt. Sinai: 1,800 adults of African ancestry with hypertension at risk for chronic kidney disease. Vanderbilt: 50,000 cardiac catherization laboratory patients; genotype-guided therapy to identify patients at risk for particular anti-platelet medications. Florida: 7,500 cardiac catherization laboratory patients; genotype-guided therapy for clopidogrel. Indiana: 6,000 randomized intervention study; adult patients. Maryland: 700 diabetic patients who

Data type: Gene Panel, Variants/Genotyping,
Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine), Standards, Expert resource,
International Cancer Genome Consortium (ICGC)

The International Cancer Genome Consortium (ICGC) has been organized to launch and coordinate a large number of research projects that have the common aim of elucidating comprehensively the genomic changes present in many forms of cancers that contribute to the burden of disease in people throughout the world. The goals of the ICGC are to generate comprehensive catalogues of genomic abnormalities (somatic, expression, epigenetic) across 50 cancer types, and make the data available to the entire research community as rapidly as possible.

Product duration: Ongoing
Scale International
Function role: Data sharing (Genomic Research),
International Consortium for Human Phenotype Terminologies (ICHPT)

Website forthcoming (a common set of terms are being mapped across all ontologies)

Data type: Phenotype Ontology,
Contact: Peter Robinson (main): peter.robinson@charite.de Ségolène Aymé: segolene.ayme@inserm.fr Ana Rath: an
International Genomics of Alzheimer's Project (IGAP)

The aim of the International Genomics of Alzheimer_s Project (IGAP) consortium is to discover and map the genes that contribute to Alzheimer_s disease (AD). The effort spans several consortia focused on AD and includes universities from Europe and the U.S. The goal is to create a shared resource database that includes genetic data for the more than 40,000 individuals with AD. IGAP was started in 2011 by four of the largest AD research consortia _ the Alzheimer_s Disease Genetics Consortium (ADGC), the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE), the European Alzheimer Disease Initiative (EADI), and the Genetic and Environmental Research in Alzheimer Disease (GERAD) consortium. Currently there is no public access to the raw individual-level genetic data because of

Product duration: Ongoing
Scale International
Cohort size: 40000
Cohort description:

Patients with Alzheimer’s disease

Function role: Data sharing (Genomic Research),
International Health Terminology Standards Development Organization (SDO)

Category: eHealth

IHTSDO is the not-for-profit association that owns and maintains SNOMED CT.

International Inflammatory Bowel Disease Genetics Consortium (IIBDGC)

IIBDGC is focused on collecting large datasets from a diverse set of countries via world-wide collaboration. In addition to enabling the discovery of all associated genes, IIBDGC also tries to dig a little deeper into what these associations actually mean. Prospective members are asked to bring high quality genomic DNA and phenotypic information from a minimum of 500 patients with a confirmed diagnosis of IBD as well as 500 population-matched healthy controls.

Scale International
International Multiple Sclerosis Genetics (IMSG) Consortium

The International Multiple Sclerosis Genetics Consortium (IMSGC) was formed in 2003 with funding from the National Multiple Sclerosis Society and published results from the first genome-wide association study (GWAS) in 2007 that identified the second and third susceptibility genes known to predispose people to developing multiple sclerosis (MS). IMSGC later expanded to include more research groups from more countries, receiving grants to conduct larger GWAS studies.

Product duration: Ongoing
Scale International
Cohort size: 50000
Cohort description:

Patients with multiple sclerosis

Data type: Variants/Genotyping,
International Parkinson's Disease Genomics Consortium (IPDCG)

Members of the IPDGC have led the effort to define and understand the genetic basis of PD, identifying the majority of known genetic risk factors for this disease. Their work is being extended to include biomarker identification, risk prediction, disease subtyping, and the molecular basis of disease. To date, the largest genome-wide association analysis for PD was performed by IPDGC members.

Scale International
International Rare Diseases Research Consortium (IRDiRC)

The International Rare Diseases Research Consortium (IRDiRC) teams up researchers and organizations investing in rare diseases research in order to achieve two main objectives by the year 2020, namely to deliver 200 new therapies for rare diseases and means to diagnose most rare diseases.
A number of grand challenges are being addressed through collaborative actions to reach these 2020 goals such as:
establishing and providing access to harmonized data and samples,
performing the molecular and clinical characterization of rare diseases,
boosting translational, preclinical and clinical research,
and streamlining ethical and regulatory procedures.

Product duration: Ongoing
Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine), Standards, Expert resource,
Contact: contact@irdirc.org
International Stroke Genetics Consortium (ISGC) Portal

The ISGC is an international collaboration of stroke physicians and scientists who have agreed to pool resources and expertise in an effort to unravel the genetic basis of stroke. This will be a first step to developing both more effective treatments and allowing earlier intervention for stroke treatment as well as potentially identifying new targets for drug treatment. Currently there are >200 members across 50 countries.

Product duration: Ongoing
Scale International
Data type: Whole Genome, Single Gene, Variants/Genotyping,
Function role: Expert resource,
IOM Action Collaborative - Rountable on Translating Genomic-Based Research for Health

Category: eHealth

Upcoming Workshop: Genomics-Enabled Learning Health Care Systems: Gathering and Using Genomic Information to Improve Patient Care and Research – December 8, 2014
…With the significant promise that combining genomic and other health data holds to derive new knowledge about disease biology, treatment efficacy, outcomes, and drug safety, there are still several challenges to using these data to their full potential. The EHR, for example, could be used as a valuable tool to store and access clinical genomic information, as could other data sources like self-reported databases and social media. However, the current health care system is largely unprepared to handle this large-scale information. There is a lack of standards for the data, and interoperability, scalability, privacy, security, a

Product duration: Started 2018
Contact: Adam Berger / Sarah Beachy
ISO/IEEE 11073

Category: eHealth

Initiative type: Standards

Family of Medical-Device Communication Standards. Health informatics – Medical / health device communication standards enable communication between medical/health care devices. Works closely with HL7.

Kaiser Permanente Research Program on Genes, Environment, and Health (RPGEH)

RPGEH is a scientific research program at Kaiser Permanente, California. Based on the over six million-member Kaiser Permanente Medical Care Plan of Northern California (KPNC) and Southern California (KPSC), the completed resource will link together comprehensive electronic medical records, data on relevant behavioral and environmental factors, and biobank data (genetic information from saliva and blood) from 500,000 consenting health plan members. The end product will be one of the largest population-based biobanks in the US.

Product duration: Ongoing
Scale Regional
Cohort size: 500000
Cohort description:

Health plan members at Kaiser Permanente

Data type: Genomics,
Kanter Health - The Joseph H. Kanter Family Foundation

Category: eHealth

Develop a National Health Outcomes Data Sharing Network
The Joseph H. Kanter Family Foundation / Health Legacy Partnership (KFF) is perhaps the longest standing, most committed organization to advancing patient-centered outcomes research by developing a National Health Outcomes Data Sharing Network. KFF promises to bring a number of invaluable resources and capabilities to the data sharing network’s development. KFF is an established, respected, and trusted convener of top leaders, key experts, and diverse stakeholders across the healthcare, health information technology (IT), and health policy communities as an objective consumer representative. It has a proven track record of generating bipartisan political interest in and public support for outcomes research and the promise of interope

Kaviar

Initiative type: Database

Kaviar (~Known VARiants) is a compilation of SNVs, indels, and complex variants observed in humans, designed to facilitate testing for the novelty and frequency of variants observed in individual genomes. Kaviar excludes cancer genomes but includes some data from cell lines and individuals affected by disease. Access methods include a web interface, an API, downloadable VCFs, and a draft iOS app.

Product duration: Ongoing
Cohort description:

Integration of many different cohorts and data sources.

Data type: Variants/Genotyping,
Function role: Data sharing (Genomic Research),
Leiden Open Variation Database (LOVD)

LOVD stands for Leiden Open (source) Variation Database.
Purpose : provide a flexible, freely available tool for gene variant and phenotype collection, display and curation. On the Leiden server LOVD offers free hosting and support of LOVD-powered gene variant databases. LOVD is open source, released under the GPL license, and is actively being improved. Several version of the software are available. LOVD 3.0 is actively developed, currently we have releases every month.

Product duration: Ongoing
Scale International
Cohort size: 290000
Cohort description:

LOVD currently has ~2000 registered contributors that have collected data on >2,500,000 unique variants from >290,000 individuals. Human, genome wide: individuals, all phenotypes and all variants

Data type: Genetic Variant, Phenotype,
Function role: Data sharing (Genomic Research),
Contact: Johann Den Dunnen: LOVD@JohanDenDunnen.nl
Logical Observation Identifiers Names and Codes (LOINC)

Category: eHealth

The LOINC effort is housed in the Regenstrief Institute, an internationally respected non-profit medical research organization associated with Indiana University. LOINC was initiated in 1994 by the Regenstrief Institute and developed by Regenstrief and the LOINC committee as a response to the demand for electronic movement of clinical data from laboratories that produce the data to hospitals, physician’s offices, and payers who use the data for clinical care and management purposes.
The purpose of the LOINC® database is to facilitate the exchange and pooling of results for clinical care, outcomes management, and research. Currently, most laboratories and clinical services use HL7 to send their results electronically from their reporting systems to their care systems. However, the tests in

Initiative type: Database

The Winter-Baraitser Dysmorphology Database: The Winter-Baraitser Dysmorphology Database (WBDD) currently contains information on over 4700 dysmorphic, multiple congenital anomaly and mental retardation syndromes. It includes single gene disorders, sporadic conditions, and those caused by environmental agents…
The Baraitser-Winter Neurogenetics Database: The Baraitser-Winter Neurogenetics Database (BWND) currently contains information on over 4250 syndromes involving the central and peripheral nervous system seen in adults and children…
The Photo Library: Now integrated into WBDD and BWND, the Photo Library is a superb collection of over 20000 photographs that show the main dysmorphic features of the syndrome and other relevant images, such as skeletal radiographs, hair microscopy, e

Data type: Phenotype Ontology,
Contact: info@lmdatabases.com
Lung Genomics Research Consortium (LGRC)

The Lung Genomics Research Consortium (LGRC) is a group of top scientists from five U.S. institutions, whose mission is to transform the understanding of chronic lung diseases such as chronic obstructive pulmonary disease (COPD) and interstitial lung disease (ILD) by using the advanced genomic technologies that have emerged from the Human Genome Project.

Product duration: Ongoing
Scale National
Matchmaker Exchange

Initiative type: GA4GH Driver Project

Disease area: Rare Disease

Matchmaker Exchange involves a large and growing number of teams and projects working towards a federated platform (Exchange) to facilitate the matching of cases with similar phenotypic and genotypic profiles (matchmaking) through standardized application programming interfaces (APIs) and procedural conventions.

Product duration: Ongoing
Scale International
Data type: Variants/Genotyping,
Function role: Data sharing (Genomic Medicine), Ecosystem,
MedGen

MedGen is NCBI’s portal to information about human disorders and phenotypes having a genetic component. The purpose of MedGen is harmonize phenotype terminologies, support computational access to phenotype data, and add value through a variety of data elements. MedGen aggregates terms from multiple vocabulary sources into a specific concept and assigns a unique, stable identifier (Concept Unique Identifier; CUI) to that concept – where possible, the same identifier used by UMLS. MedGen provides multiple types of descriptors for concepts including names, synonyms, acronyms, semantic type, abbreviations, sources of descriptors, attribution and identifiers (e.g., from OMIM, HPO and Orphanet), textual definitions from multiple sources, hierarchical relationships between terms, cytogenetic l

Data type: Phenotype Ontology,
Function role: Publishes Ontologies,
Contact: Wendy Rubinstein: rubinstw@ncbi.nlm.nih.gov
Medulloblastoma Advanced Genomics International Consortium (MAGIC)

In this project, genomic analyses of pediatric medulloblastoma samples, obtained through the international medulloblastoma consortium, will be performed. Genomic analysis of high risk subgroup cases are supporting the discovery of subgroup specific somatic mutations in order to inform current clinical trials of targeted therapies, and to identify genes and pathways already targeted in other diseases. Such therapies could be rapidly transitioned to Phase II trials in medulloblastoma. Furthermore, the discovery of somatic mutations could be used for developing as well as validating specific biomarkers.

Scale International
Cohort size: 300
Cohort description:

High-risk pediatric medulloblastoma cases

Million Veteran Program

MVP is a national, voluntary research program funded entirely by the Department of Veterans Affairs Office of Research & Development. The goal of MVP is to partner with Veterans receiving their care in the VA Healthcare System to study how genes affect health. To do this, MVP will build one of the world’s largest medical databases by safely collecting blood samples and health information from one million Veteran volunteers.

Product duration: Ongoing
Scale National
Cohort size: 1000000
Cohort description:

Veterans from USA

Data type: Variants/Genotyping,
Monarch Initiative

The Monarch Initiative is a collaborative, open science effort that aims to semantically integrate genotype–phenotype data from many species and clinical sources in order to support precision medicine, disease modeling, and mechanistic exploration. Our integrated knowledge graph, analytic tools, and web services enable diverse users to explore relationships between phenotypes and genotypes across species. The Human Phenotype Ontology (HPO) is developed as part of the Monarch Initiative, and is the de facto standard for rare disease phenotyping and exome analysis. The Exomiser tool leverages the HPO and Monarch data to support improved diagnosis of rare disease. The GA4GH Matchmaker Exchange also leverages the HPO for matching patient phenotypes, and Monarch also co-develops the Phenopacket

Contact: info@monarchinitiative.org
MSSNG

Initiative type: Research Network/Project

Disease area: Neurological Disease

MSSNG is a groundbreaking collaboration between Google and Autism Speaks to create the world_s largest genomic database on autism. Using the Google Cloud, this vast sea of information will be made accessible for free to researchers focusing specifically on autism.

Scale International
Cohort size: 10000
Cohort description:

Families affected with autism

Data type: Whole Genome,
Function role: Data sharing (Genomic Research),
Multiple Myeloma Genomics Initiative

Disease area: Cancer

MMGI is a collaboration of The Multiple Myeloma Research Consortium, The Broad Institute of MIT and Harvard, and the Translational Genomics Research Institute (TGen). Funding is provided by the Multiple Myeloma Research Foundation. Development of the portal and data curation was performed by the portal team of the Broad Institute and Dana Farber Cancer Center. The Multiple Myeloma Genomics Portal (MMGP) has been made available to provide access to and limited analysis of the MMGP portal data sets. These include the MMRC funded reference aCGH and gene expression data and additional public multiple myeloma datasets. The MMGP will be updated with new features such as additional data and analysis tools as they become available. There are ~2,000 registered users.

Scale Regional
Cohort size: 17123
Cohort description:

Multiple myeloma samples

MyCode Community Health Initiative

The MyCode® Community Health Initiative is a precision medicine project at Geisinger that includes a system-wide biobank designed to store blood and other samples for research use by Geisinger and Geisinger collaborators. Samples and information in the biobank are used to do health research. Geisinger & Regeneron have agreed to an initial 5-year partnership, which may be extended to 10 years.

Product duration: Finished/finishing 2019
Scale Regional
Cohort size: 250000
Cohort description:

Patients from Geisinger

Data type: Whole Genome, Whole Exome, Variants/Genotyping,
MyGene2

MyGene2 is a free, public, searchable site developed by families with rare conditions, clinicians, and researchers to publicly share health and genetic information with one another by creating “family profiles.” This makes discovering the genetic basis of rare conditions and their diagnosis easier by facilitating data sharing and case-matching.

Families can create profiles to share photos, stories, candidate variants, health information, and even genetic data from exome or genome sequencing so that they can find or match with other families with the same condition or candidate gene; make their data available for re-analysis if no causal variant(s) were found; and find researchers and clinicians who may be interested in studying their condition. Researchers and clinicians/genetic counse

Product duration: Ongoing
Scale International
Cohort size: 500
Cohort description:

MyGene2 profiles are created by families with a rare disease or condition, clinicians/genetic counselors on behalf of such families, or researchers studying a rare condition. The MyGene2 website and profiles in it are free, public, and available internationally.

Data type: Whole Genome, Whole Exome, Gene Panel, Single Gene, Variants/Genotyping, RNAseq, mtDNA,
Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine), Expert resource, Ecosystem,
National Center for Biomedical Ontologies (NCBO)

Category: eHealth

Hosts BioPortal, the world’s most comprehensive repository of biomedical ontologies.

National Institute of Health Big Data to Knowledge Initiative (BD2K)

Category: eHealth

The ability to harvest the wealth of information contained in biomedical Big Data will advance our understanding of human health and disease; however, lack of appropriate tools, poor data accessibility, and insufficient training, are major impediments to rapid translational impact. To meet this challenge, the National Institutes of Health (NIH) launched the Big Data to Knowledge (BD2K) initiative in 2012.

BD2K is a trans-NIH initiative established to enable biomedical research as a digital research enterprise, to facilitate discovery and support new knowledge, and to maximize community engagement.

The BD2K initiative addresses four major aims that, in combination, are meant to enhance the utility of biomedical Big Data:

To facilitate broad use of biomedical digital assets by m

National Institute of Standards and Technology (NIST) Applied Genetics Group

Category: eHealth

Initiative type: Standards

Applied Genetics Group

Welcome
Since the late 1980s, NIST has had scientists involved in DNA testing. Early concerns over measurement accuracy and issues with poor quality control of forensic DNA tests caused the Department of Justice to call upon NIST scientists to help with standards development and technology evaluation. For the past several years, our Forensic Genetics Project Team has been part of the Applied Genetics of the Biomolecular Measurements Division at NIST. The Applied Genetics Group was formed to focus on developing standards and technology to aid human, plant, and animal identification and to benefit agricultural, law enforcement, and clinical applications using genetic information.
Our work is primarily nucleic acid-based and focuses on the characterization of genet

Neuromics

Neuromics is a research consortium which brings together the leading research groups in Europe, five highly innovative SMEs as well as overseas experts in the relevant fields. Using the most sophisticated -omics technologies, this consortium will revolutionize diagnostics and develop new treatments for ten major neurodegenerative and neuromuscular diseases affecting the cortex, basal ganglia, cerebellum, spinal cord, peripheral nerves, neuromuscular junction, and muscle…

The Neuromics research efforts will interact closely with a similar project in the field of rare kidney diseases – EURenOmics, sharing skills, experiences and infrastructure where possible. Both will work closely with RD-Connect, a recently funded project which will create an integrated platform connecting databases,

Contact: Olaf Riess: olaf.riess@med.uni-tuebingen.de
Newborn Sequencing in Genomic Medicine and Public Health (NSIGHT)

The purpose of NSIGHT is to explore, in a limited but deliberate manner, the implications, challenges and opportunities associated with the possible use of genomic sequence information in the newborn period.

Product duration: Ongoing
Scale National
NHGRI Genomic Medicine Activities

Category: eHealth

NHGRI held a series of Genomic Medicine meetings gathering genomics researchers, clinicians, and other experts from over U.S. institutions involved with the implementation of genomic medicine programs. The goal of these meetings includes identifying research gaps and opportunities; sharing approaches to genomic medicine implementation, and facilitating development of an active research community and possible collaborative projects.

NHLBI Exome Sequencing Project (ESP) and Exome Variant Server (ESS)

Initiative type: Tool

The goal of the NHLBI GO Exome Sequencing Project (ESP) is to discover novel genes and mechanisms contributing to heart, lung and blood disorders by pioneering the application of next-generation sequencing of the protein coding regions of the human genome across diverse, richly-phenotyped populations and to share these datasets and findings with the scientific community to extend and enrich the diagnosis, management and treatment of heart, lung and blood disorders.

Data type: Genetic Variant,
Contact: Debbie Nickerson: debnick@u.washington.edu
NIH Big Data to Knowledge (BD2K)

Category: eHealth

Initiative type: Database

The NIH Big Data to Knowledge (B2K) initiative is considering the development of a biomedical Data Catalog to make biomedical research data findable and citable, as PubMed does for scientific publications.

Office of the National Coordinator (ONC) for Health Information Techology

Category: eHealth

The Office of the National Coordinator for Health Information Technology (ONC) Certification Program helps to ensure that Electronic Health Record (EHR) technologies meet the standards and certification criteria adopted by the Secretary of Health and Human Services to allow providers and hospitals achieve meaningful use and participate in the CMS EHR Incentive Programs.

The Office of Certification was established to develop and oversee national programs for the certification of health information technology by the Health Information Technology for Economic and Clinical Health (HITECH) Act. For more information about the establishment of the ONC HIT Certification Program, please see the Establishment of the Permanent Certification Program for Health Information Technology, Final Rule.

Function role: Shapes Incentives,
Online Mendelian Inheritance in Man (OMIM)

Initiative type: Database

OMIM is a comprehensive, authoritative compendium of curated descriptions of human genes and phenotypes and the relationships between them. OMIM also includes gene-phenotype relationship tables and synopses of clinical features of phenotypes. The knowledgebase is freely available and updated daily. OMIM entries are given stable 6-digit identifiers (MIM numbers) that are widely referenced in the biomedical literature and integrated into other electronic resources. In addition, OMIM.org provides focused links to information in other clinical and genomic resources, and the MIMmatch utility facilitates information dissemination and collaboration.

Data type: Genotype, Phenotype,
Online Mendelian Inheritance of Man (OMIM)

Category: eHealth

Initiative type: Database

OMIM is a comprehensive, authoritative compendium of curated descriptions of human genes and phenotypes and the relationships between them. OMIM also includes gene-phenotype relationship tables and synopses of clinical features of phenotypes.
The knowledgebase is freely available and updated daily. OMIM entries are given stable 6-digit identifiers (MIM numbers) that are widely referenced in the biomedical literature and integrated into other electronic resources. In addition, OMIM.org provides focused links to information in other clinical and genomic resources, and the MIMmatch utility facilitates information dissemination and collaboration.

Open Clinical Decision Support Tools and Resources (OpenCDS)

Category: eHealth

Initiative type: Standards

Multi-institutional, collaborative effort to develop open-source, standards-based clinical decision support (CDS) tools and resources that can be widely adopted to enable CDS at scale.

openSNP

Initiative type: Database

openSNP allows customers of direct-to-customer genetic tests to publish their test results, find others with similar genetic variations, learn more about their results by getting the latest primary literature on their variations, and help scientists find new associations.

Product duration: Ongoing
Cohort size: 2500
Cohort description:

Genotypes from direct-to-consumer customers

Data type: Variants/Genotyping,
Orphanet

Orphanet is the reference portal for information on rare diseases and orphan drugs, for all audiences. Orphanet’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases.Orphanet offers a range of freely accessible services: A multi-lingual inventory of rare diseases and a classification of diseases elaborated using existing published expert classifications. An encyclopaedia of rare diseases in English, progressively translated into French, German, Spanish, Portuguese, Italian and Dutch. An inventory of orphan drugs at all stages of development. A directory of expert resources, providing information on expert centres, medical laboratories, ongoing research projects, clinical trials, registries, networks, technological platforms and patient organisations, in

Contact: Ana Rath: ana.rath@inserm.fr
Orphanet Rare Disease Ontology (ORDO)

The Orphanet Rare Disease ontology (ORDO) is jointly developed by Orphanet and the European Bioinformatics Institute to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It is derived from the Orphanet database (www.orpha.net), a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA),databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) or classifications (ICD10). Orphanet classif

Data type: Phenotype Ontology,
Contact: Ana Rath (main): ana.rath@inserm.fr Annie Olry: annie.olry@inserm.fr
Patient-Centered Outcomes Research Institute (PCORI)

Category: eHealth

We began funding research in December 2012 and have a sizeable and growing portfolio of projects designed to improve patient care and outcomes through patient-centered comparative clinical effectiveness research, or CER. The research we fund is guided by our five National Priorities for Research and Research Agenda. The work under these priorities is managed by our scientific programs, which track it and evaluate its effectiveness.

We are also charged with developing and improving the science and methods of CER because methods matter when it comes to producing valid, trustworthy, and useful information that will lead to better healthcare decisions and, ultimately, to improved patient outcomes. Our Methodology Committee oversees our work on methods.

Our strong emphasis on engaging pat

Function role: Fund Initiatives,
Personal Connected Health Alliance

Category: eHealth

The Personal Connected Health Alliance (PCHA) is at the forefront of health and wellness in today’s society, driving advancements in mobile and communications technologies, and the growing use of new devices, health trackers and apps by consumers and healthcare providers. No longer is a doctor’s visit the only way to check up on your health. Thanks to readily-available consumer technologies — such as smartphones, sensors and tablets — consumers are taking charge of their health and wellness. PCHA brings together the critical elements needed to ensure that these technologies are user-friendly, secure and can easily collect, display and relay personal health data. In PCHA’s vision for healthcare, consumers can use readily available technologies to access their personal health data, receive

PersonalGenomes.org

Initiative type: Database

PersonalGenomes.org is a charitable organization working to generate, aggregate and interpret human biological and trait data on an unprecedented scale. Their mission is to make a wide spectrum of data about humans accessible to increase biological literacy and improve human health. PersonalGenomes.org’s efforts are informed by values encouraging greater transparency and collaboration between researchers and participants. The organization supports the Personal Genome Project (PGP) global network; they also produce the annual Genomes, Environments and Traits (GET) Conference.

Product duration: Ongoing
Scale International
Pharmacogenetics Knowledge Base (PharmGKB)

Initiative type: Database

The PharmGKB is a pharmacogenomics knowledge resource that encompasses clinical information including dosing guidelines and drug labels, potentially clinically actionable gene-drug associations and genotype-phenotype relationships. PharmGKB collects, curates and disseminates knowledge about the impact of human genetic variation on drug responses through the following activities:

Annotate genetic variants and gene-drug-disease relationships via literature reviews
Summarize important pharmacogenomic genes, associations between genetic variants and drugs, and drug pathways
Curate FDA drug labels containing pharmacogenomic information
Enable consortia examining important questions in pharmacogenomics
Curate and participate in writing pharmacogenomic-based drug dosing guidelines
Cont

Data type: Genomics,
Contact: Teri E. Klein: teri.klein@stanford.edu
Pharmacogenomics Research Network (PGRN)

The mission of the Pharmacogenomics Research Network (PGRN) is to catalyze and lead research in precision medicine for the discovery and translation of genomic variation influencing therapeutic and adverse drug effects. To this end, the PGRN hosts various activities that stimulate collaborative research in pharmacogenomics and precision medicine.

Product duration: Ongoing
Scale International
Cohort size: 200
Cohort description:

Pharmacogenomics Research in various drugs response and disease areas. Please see pgrn.org

Data type: Variants/Genotyping,
Pharmacogenomics Research Network (PGRN)

Category: eHealth

Vision: To lead discovery and advance translation in genomics, in order to enable safer and more effective drug therapies
Major Indicators of Success
Discovery of novel insights into mechanisms relating genomic variation to differences in drug responses
Demonstration of the use and utility of genomic information to improve outcomes for drug therapies
Incorporation of genomic data to predict and personalize medicine use into routine clinical practice
Mission of the PGRN
PGRN investigators, individually and collectively, will:
Implement studies in basic, translational, and clinical science to advance the scientific vision
Develop novel experimental methods and tools to solve pharmacogenomic problems
Share data and, where feasible, biological samples in collaborations
Foster cross-d

PhEMA - Phenotype Execution and Model Architecture

Category: eHealth

Initiative type: Tool

Early stage project plans to adapting QDM frameworks for NLP, more robust logic, etc. Also planning to build interfaces with KNIME to/from QDM.

PhenoDB

To interpret whole exome/genome sequence data for clinical and research purposes, comprehensive phenotypic information, knowledge of pedigree structure, and results of previous clinical testing are essential. With these requirements in mind and to meet the needs of the Centers for Mendelian Genomics project, we have developed PhenoDB (http://researchphenodb.net and http://phenodb.org), a secure, Web-based portal for entry, storage, and analysis of phenotypic and other clinical information. The phenotypic features are organized hierarchically according to the major headings and subheadings of the Online Mendelian Inheritance in Man (OMIM®) clinical synopses, with further subdivisions according to structure and function. Every string allows for a free-text entry. All of the over 3,600 featur

Data type: Genetic Variant, Phenotype,
Contact: Ada Hamosh: ahamosh@jhmi.edu
Phenome Knowledge Base (PheKB)

Category: eHealth

Initiative type: Database

The Phenotype Knowledgebase website, PheKB, is a collaborative environment to building and validating electronic phenotype algorithms. PheKB was functionally designed to enable such a workflow and has purposefully integrated tools and standards that guide the user in efficiently navigating each of these stages from early stage development to public sharing and reuse. PheKB has tools to enable cross-site collaboration for algorithm development and validation.

PhenomeCentral

PhenomeCentral is a repository for secure data sharing targeted to clinicians and scientists working in the rare disorder community. PhenomeCentral encourages global scientific collaboration while respecting the privacy of patients profiled in this centralized database.

Why is it useful?

PhenomeCentral enables the discovery of multiple individuals affected by the same unnamed disorder. Undiagnosed disorders may be present in only a handful of individuals seen at different hospitals and sequenced by different centers. The PhenomeCentral collaboration model enables effective and secure data-sharing techniques that allow clinicians and scientists to learn about the existence of cases similar to theirs, which eventually may help improve the understanding of disorder manifestations and

PhenoTips

PhenoTips is an open source software tool for collecting and analyzing phenotypic information for patients with genetic disorders. The user interface closely mirrors clinician workflows so as to facilitate the recording of observations made during the patient encounter. This easy-to-use front-end, compatible with any device that runs a Web browser, is coupled with with a standardized database back-end where phenotypic information is represented using the Human Phenotype Ontology (HPO).

Collected data include demographics, medical history, family history, physical and laboratory measurements, physical findings, and free-form notes.

In addition to data collection, PhenoTips automatically analyzes a wide range of measurements and plots live the corresponding growth curves. It also suppo

Data type: Phenotype Ontology,
Contact: Mike Brundo: brundo@cs.toronto.edu
Phenotype KnowledgeBase

Category: eHealth

Initiative type: Database

Collection of phenotype algorithms, validations, data validation tools to help mine EHR phenotypes

PheWAS Catalog

Category: eHealth

Initiative type: Database

Graphable, searchable, downloadable catalog of EHR phenotype-genotype association results

Precision Link

Precision Link drives coherence between the BCH research and clinical missions by establishing the technology, policies and workflows to engage our patients in research, and treating each visit as an opportunity to build a learning health system culture. Precision Link strives to build a knowledge base of both omics and phenotypic data on the patients walking through our doors–for use in population research as well as in care.

Product duration: Ongoing
Cohort size: 200000
Cohort description:

Targeted pediatric populations.

Data type: Whole Genome, Whole Exome, Gene Panel, Single Gene, Variants/Genotyping,
Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine), Standards, Expert resource, Ecosystem,
Psychiatric Genomics Consortium (PGC)

The purpose of the Psychiatric Genomics Consortium (PGC) is to conduct mega-analyses of genome-wide genetic data for psychiatric disorders. From 2007 to 2011, PGC focused on autism, attention-deficit hyperactivity disorder, bipolar disorder, major depressive disorder, and schizophrenia. It now includes large studies of anorexia nervosa, drug use disorders, obsessive compulsive disorder (OCD)/Tourette_s, and posttraumatic stress disorder. Initially, PGC focused on common single nucleotide polymorphisms. Its focus has expanded to include copy number variation and uncommon/rare genetic variation. The PGC includes over 800 investigators from 38 countries.

Product duration: Ongoing
Scale International
Cohort size: 170000
Cohort description:

Psychiatric patients

Data type: Variants/Genotyping,
Public Health Genomics Knowledge Base (PHGKB)

The CDC Public Health Genomics Knowledge Base is an open-access, online, searchable database of published scientific literature, CDC resources, and other materials that address the translation of genomic discoveries into improved health care and disease prevention. The Knowledge Base, co-sponsored by the Division of Cancer Control and Population Sciences at the National Cancer Institute, is curated by CDC staff and is regularly updated to reflect ongoing developments in the field. This compendium of databases can be searched for genomics-related information on any specific topic.

Cohort description:

Published population-based study data

Public Population Project in Genomics and Society (P3G)

The Public Population Project in Genomics and Society (P³G) is a not-for-profit, international consortium dedicated to supporting the development and management of multi-disciplinary research infrastructures, to compare and merge results from studies, biobanks, research databases and other similar health and social research infrastructures around the world. Through its tools, support and network, P³G helps the international research community to develop more effective health care strategies aimed at disease prevention, tailoring treatments and promoting the health of individuals, families and communities. P³G’s mission is to lead, catalyze, and coordinate international efforts and expertise to optimize the use of studies, biobanks, research databases and other similar health and social res

Scale International
Function role: Standards, Expert resource,
Qatar Genome Project

Researchers at Weill Cornell Medicine-Qatar (WCM-Q) have mapped the genomes of more than 1,161 Qataris, giving the country its own population-specific genome resource for the indigenous Arab population of Qatar (QTRG). This gives scientists a powerful reference tool that will facilitate efforts to identify genetic variations that cause serious and distressing conditions such as cystic fibrosis, sickle cell anaemia and muscular dystrophy among the local population. It will also help doctors treating Qataris to more effectively practice _precision medicine,_ and predict, diagnose and treat disease.
The project, entitled The Qatar Genome: A Population-Specific Tool for Precision Medicine in the Middle East, is the work of a research team comprising scientists from WCM-Q, Weill Cornell Medi

Product duration: Ongoing
Scale National
Cohort size: 1161
Cohort description:

Qataris from Hamad Medical Corporation clinics

Data type: Whole Genome, Whole Exome,
RD-Connect

Initiative type: Tool, Database

Disease area: Rare Disease

RD-Connect is a global platform for rare disease data that links databases, registries, biobanks, and clinical bioinformatics data used in rare disease research into a central resource for researchers worldwide. Genomic data from rare disease research projects is made accessible through an online analytical interface for gene discovery and combined with detailed phenotypic profiles, other omics datasets and sample availability. Funded by the EU and linked with the European biomedical research infrastructures ELIXIR and BBMRI, the RD-Connect platform is open to all researchers, and in particular to research funded under the International Rare Diseases Research Consortium (IRDiRC).

Product duration: Ongoing
Scale International
Cohort size: 2500
Cohort description:

Omics data and HPO-coded phenotypic data from individuals with rare mendelian disease and family members. Currently enriched for neuromuscular, neurodegenerative and kidney disease phenotypes but any rare disease is eligible.

Data type: Whole Genome, Whole Exome, Gene Panel, RNAseq,
Function role: Data sharing (Genomic Research), Standards, Expert resource,
Reference Variant Store (RVS)

Initiative type: Database

The Reference Variant Store holds information on more than 520 million genetic variants using various methods of annotation. Sources for variants in RVS are re-sequencing projects such as the 1000 Genomes, ESP6500, UK10K, TCGA, Scripps Wellderly; clinical annotation databases such as ClinVar and HGMD; and hypothetical, amino-acid changing single-point mutations from dbNSFP. RVS provides annotations on low level effects, phenotypes and diseases, population frequencies, and predictive functional impact scores.

Repositive

Repositive is a free platform which enables researchers to search multiple human genomic data repositories for the data they need, all within one interface. It allows researchers to request datasets that they need, to register their own datasets and let other researchers know that they have them, to interact with each other and form collaborations.

Product duration: Ongoing
Scale International
Data type: Whole Genome, Whole Exome, Gene Panel, Single Gene, Variants/Genotyping, RNAseq, mtDNA,
Function role: Data sharing (Genomic Research), Ecosystem,
Research Data Alliance (RDA)

Category: eHealth

The Research Data Alliance (RDA) builds the social and technical bridges that enable open sharing of data. The RDA vision is researchers and innovators openly sharing data across technologies, disciplines, and countries to address the grand challenges of society.

ResearchPhenoDB

Category: eHealth

ResearchPhenoDB is a research tool developed by the Baylor-Hopkins Center for Mendelian Genomics for the Centers for Mendelian Genomics. It is comprised of Phenotype Module which is designed to collect, store and analyze standardized phenotypic information and an ELSI Module to collect consents and committee discussions. These are described in: Hamosh A, Sobreira N, Hoover-Fong J, Sutton VR, Boehm C, Schiettecatte F, Valle D. PhenoDB: a new web-based tool for the collection, storage, and analysis of phenotypic features. Hum Mutat. 2013 Apr;34(4):566-71. doi: 10.1002/humu.22283. Epub 2013 Mar 4. PMID: 23378291. In addition, ResearchPhenoDB also includes an Analysis Module for variant filtering and evaluation and a Sample Tracking Module for tracking consents and samples through the research

Resilience Project

As part of a pilot study for the ongoing Resilience Project, researchers at Mount Sinai’s Icahn Institute for Genomics and Multiscale Biology, Sage Bionetworks, and collaborators in the US, Canada, and China brought together targeted sequencing or genotyping data for nearly 900 genes in 589,306 individuals from a dozen large cohorts _ including 23andMe customers who consented to participate in research, individuals from several medical studies, and participants in 1,000 Genomes and UK10K projects. Though all of the participants were reportedly disease-free, the team identified 13 adult individuals with mutations associated with eight serious Mendelian conditions known to begin in childhood, from metabolic or developmental syndromes to cystic fibrosis. The results point to the possibility o

Product duration: Ongoing
Scale International
Cohort size: 589306
Cohort description:

Unaffected individuals

Data type: Whole Genome, Whole Exome, Variants/Genotyping,
RxNorm

Category: eHealth

RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, MediSpan, Gold Standard Drug Database, and Multum. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary.

Saudi Human Genome Program

The Saudi Human Genome Projects is a specific effort to solve genetic disease in the Kingdom, to lay the foundation for the development of Personalized Medicine and establish capacity for a Genomics industry more broadly. The project aims to sequence the genomes of 100,000 individuals representing patients and the general population. Of particular interest are rare, severe genetic diseases (impact 8% of births in the Kingdom) and common adult-onset diseases (e.g. diabetes), which impact 20% of the population. This will be the largest disease gene discovery project ever undertaken, and will therefore also establish the Kingdom as a world leader in disease genetics research and Personalized Medicine. The project plans to establish a network of 15 genome sequencing centres.

Product duration: Finished/finishing 2018
Scale National
Cohort size: 100000
Cohort description:

Patients and unaffected individuals from Saudi Arabia

Data type: Whole Genome,
Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine),
Scottish Genomes Partnership (SGP)

The Universities of Edinburgh and Glasgow are leading the Scottish Genomes Partnership (SGP) in collaboration with the NHS in both Scotland and England, and Genomics England. The Partnership will initially focus on rapid screening of cancer patients, diagnosing childhood illnesses, rare genetic diseases, disorders of the central nervous system and population studies.
The SGP was founded by the Universities of Edinburgh and Glasgow following a _15m investment in January 2015, which has led to installation of 10 state-of-the-art HiSeq X genome sequencing instruments divided between the sequencing hubs within the two Universities. A further _6m investment jointly awarded by Scotland_s Chief Scientist Office (_4m) and the UK_s Medical Research Council (_2m) in February 2016 has boosted the p

Product duration: Ongoing
Scale National
Cohort size: 3000
Cohort description:

Individuals from Scotland

Data type: Whole Genome,
Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine), Standards, Expert resource, Ecosystem,
Sequence Bio 100K Genome Project

Initiative type: Research Network/Project

Disease area: Rare Disease

The 100k genome project is a community-based initiative enabling innovative science and improving the healthcare for the people of Newfoundland and Labrador, Canada. This is a unique, isolated population with a high incidence of rare and complex diseases, that benefits from a comprehensive EHR system and extended family pedigrees. Genomic data collected through this project will be used for drug development research to combat the medical challenges in this community. Full sequence data will be returned to participants (who retain data ownership), at no cost.

Product duration: Ongoing
Scale Regional
Cohort size: 100000
Cohort description:

Individuals from Newfoundland & Labrador, Canada

Data type: Whole Genome,
SHARP-SMART Consortium

Category: eHealth

International consortium of clinical, genomic, providers, and EHR vendors working on interactive apps that allow interoperability between EHR’s. SHARP-SMART Consortium uses the following standards: HL7, FHIR, Oauth, HTML, LOINC, SNOMED CT, RxNorm, REST API.

Data type: Genomics,
Function role: Provides Open Source Code,
SHARPn - Phenotype Portal

Category: eHealth

Initiative type: Tool

The Phenotype Portal is a tool funded by the SHARPn Project from the Office of the National Coordinator (ONC). It will enable clinicians and investigators to identify patient cohorts using electronic health record (EHR) data by leveraging informatics-based phenotyping processes. In turn, these cohorts will facilitate clinical trial enrollment, outcomes research, and inform clinical decision support. Currently, the field has various barriers in technological research and tool development, and Phenotype Portal is the first such platform for generating and executing Meaningful Use standards-based phenotyping algorithms that can be shared across multiple institutions and investigators. Traditionally, a patient’s medical information is stored inconsistently and in multiple locations, both elect

Data type: Phenotype,
SMART Genomics

Category: eHealth

Initiative type: Tool

The SMART Genomics API is a means to access genomic information for the use in the clinical realm. With the influx of data supporting personalized genetic medicine, a need arises to accommodate the use of this information in the electronic medical record, by point-of-care providers. Since a clinical API has been defined and supported by the SMART clinical initiative, it is natural to model the use of genomic data in a way similar to this established method. SMART Genomics uses the following standards: HL7, FHIR, Oauth, HTML, LOINC, SNOMED CT, RxNorm, REST API.

Data type: Genomics,
SMART Health IT

Category: eHealth

Initiative type: Tool

SMART Health IT is an open, standards based technology platform that enables innovators to create apps that seamlessly and securely run across the healthcare system. Using an electronic health record (EHR) system or data warehouse that supports the SMART standard, patients, doctors, and healthcare practitioners can draw on this library of apps to improve clinical care, research, and public health.

The SMART platform is composed of open standards, open source tools for developers building apps and a publicly accessible app gallery. To date, dozens of clinical applications have been built on this platform, and SMART applications are being used to provide clinical care at leading healthcare institutions, including Boston Children’s Hospital, Duke Medicine and Intermountain Healthcare.

T

Function role: Provides Open Source Code,
SNOMED CT

SNOMED CT is the most comprehensive and precise clinical health terminology product in the world. It is owned and distributed,under licence, around the world by The International Health Terminology Standards Development Organisation (IHTSDO) – www.ihtsdo.org. SNOMED CT has been developed collaboratively to ensure it meets the diverse needs and expectations of the worldwide medical profession and is now accepted as a common global language for health terms. SNOMED CT is a resource with comprehensive, scientifically validated clinical content, which enables consistent, processable representation of clinical content in electronic health records. SNOMED CT has maps available to other international standards and is in use in more than fifty countries worldwide, a figure that continues to grow.

Data type: Phenotype Ontology,
Function role: Publishes Ontologies,
Contact: Don Sweete: ceo@ihtsdo.org
SNPedia

Category: eHealth

SNPedia is a wiki investigating human genetics. We share information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used byPromethease to create a personal report linking your DNA variations to the information published about them. Please see the SNPedia:FAQ for answers to common questions.

Stanley Center for Psychiatric Research

Initiative type: Research Network/Project

Disease area: Neurological Disease

The mission of the Stanley Center for Psychiatric Research at Broad Institute is to reduce the burden of serious mental illness through research. Based on a conjunction of powerful new enabling technologies, interdisciplinary faculty from the Harvard, MIT, the Broad Institute, and Harvard-affiliated hospital communities, and the remarkable philanthropy of Ted Stanley, the Stanley Center is galvanized to make progress against the ravages of severe mental illness. Our primary scientific focus is on the severe psychiatric disorders schizophrenia, bipolar disorder, and autism, and the frequently comorbid neurodevelopmental disorder, attention deficit hyperactivity disorder (ADHD).

Product duration: Ongoing
Scale National
Data type: Variants/Genotyping,
Stratified Medicine Scotland - Innovation Centre (SMS-IC)

The Stratified Medicine Scotland Innovation Centre (SMS-IC) aspires to be a world-class centre of research, innovation and commercialisation in stratified medicine. Stratified medicine involves examining the genetic makeup of patients and their differing responses to drugs designed to treat specific diseases. By building up an understanding of the ‘strata’ of responses and the genetics of the diseases, medical researchers hope to create more personalised and effective forms of treatment for groups of patients most likely to benefit. SMS-IC is a unique partnership comprising the Universities of Glasgow, Edinburgh, Dundee and Aberdeen; NHS Greater Glasgow and Clyde, NHS Grampian, NHS Lothian and NHS Tayside; and the key business partners, global biotechnology company, ThermoFisher Scientific

Sync for Genes (S4Genes)

Category: eHealth

Sync for Genes seeks “to improve genomic information sharing—including data from next generation sequencing (NGS) laboratories—in a consistent and usable way via point-of-care applications as well as ‘create a foundation for widespread use of genomic data to be shared in the All of Us research program and future studies'”
Source: https://www.healthdatamanagement.com/news/onc-announces-five-pilot-sites-for-sync-for-genes-program

T2D-GENES

T2D-GENES (Type 2 Diabetes Genetic Exploration by Next-generation sequencing in multi-Ethnic Samples) is a large collaborative effort to find genetic variants that influence risk of type 2 diabetes. The group is pursuing three projects: (1) deep whole-exome sequencing in 10,000 people from five ethnicities (African-American, East Asian, South Asian, European, and Hispanic); (2) deep whole-genome sequencing of 600 individuals selected from extended Mexican American pedigrees; and (3) a trans-ethnic fine-mapping “mega-meta-analysis.”

Product duration: Ongoing
Scale International
Cohort size: 10600
Cohort description:

10,000 patients and controls representing 5 ethnicities (African-American, East Asian, South Asian, European, and Hispanic), plus 600 individuals from extended Mexican American pedigrees.

Data type: Whole Genome, Whole Exome,
Function role: Data sharing (Genomic Research),
TBResist

TBResist is a consortium of labs and research groups dedicated to understanding and counteracting genomic drug resistance in Mycobacterium tuberculosis. TBResist analyzes the genome sequence data of MDR, XDR, and TDR TB strains. TBResist is seeking new partners with the ability to enhance our database and our analytical capabilities through collaboration and large-scale data sharing. Founding members include Laboratory Information for Public Health Excellence (LIPHE), NIAID of the NIH, BROAD, and IBM.

Scale International
Cohort size: 2600
Cohort description:

Samples

Function role: Data sharing (Genomic Research),
The Clinical Genome Resource (ClinGen)

ClinGen is a National Institutes of Health (NIH)-funded resource dedicated to building an authoritative central resource that defines the clinical relevance of genes and variants for use in precision medicine and research.

Product duration: Ongoing
Scale National
Data type: Single Gene, Variants/Genotyping,
Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine), Expert resource,
The Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA)

Disease area: Cancer

The Consortium of Investigators of Modifiers of BRCA1/2 is a collaborative group of researchers working on genetic modifiers of cancer risk in BRCA1 and BRCA2 mutation carriers. The aim of CIMBA is to provide sufficient sample sizes to allow large scale studies (e.g. GWAS) in order to evaluate reliably the effects of genetic modifiers

Product duration: Ongoing
Scale International
Cohort size: 46000
Cohort description:

BRCA1 (n=>28,500) and BRCA2 (n=17,500) mutation carriers

Data type: Variants/Genotyping,
Function role: Data sharing (Genomic Research), Expert resource,
The National Academies Genomic Roundtables Displaying and Integrating Genetic Results Through the EH

Category: eHealth

Bring together vendors, AMCs, laboratories, standards bodies, patient groups, government agencies and other interested parties to create a framework for expanding genetic support in the EHR environment. Initially focused on cross industry data transfers needed to enable broad pharmacogenomic clinical decision support

The Pharmacogenomics Knowledge Base (PharmGKB)

Category: eHealth

Initiative type: Database

PharmGKB is a comprehensive resource that curates knowledge about the impact of genetic variation on drug response for clinicians and researchers.

Tohoku Medical Megabank Project

The project will develop a biobank that combines medical and genome information during the process of rebuilding the community medical system and supporting health and welfare in the Tohoku area. Types of data collected will include: whole-genome sequence, metabolomic and proteomic data, epigenomic data, baboratory test data, questionnaire data (Life style, Exposure), physiological measures (MRI image data), and clinical data.

Product duration: Finished/finishing 2022
Scale National
Cohort size: 150000
Cohort description:

A population-based adult cohort study and a birth and three-generation cohort study.

Data type: Whole Genome, Gene Panel, Variants/Genotyping,
Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine), Standards,
Trans-Omics for Precision Medicine (TOPMed) Whole-Genome Sequencing project

To support the NHLBI Precision Medicine Initiative, the TOPMed program will couple whole-genome sequencing (WGS) and other _omics (e.g., metabolic profiles, protein and RNA expression patterns) data with molecular, behavioral, imaging, environmental, and clinical data from studies focused on heart, lung, blood and sleep (HLBS) disorders. In doing so, this program seeks to uncover factors that increase or decrease the risk of disease, identify subtypes of disease, and develop more targeted and personalized treatments. The WGS project will collect whole-genome sequencing data from individuals with well characterized phenotypes and existing clinical outcome data. This project aims to identify genetic markers of increased or decreased risk of disease, as well as those that help define disease

Product duration: Ongoing
Scale National
Cohort size: 20000
Cohort description:

Individuals with heart, lung, blood, and sleep disorders from across 26 NHLBI studies

TRANSFoRm

Category: eHealth

TRANSFoRm aims to develop the technology that facilitates a learning healthcare system, bringing together a highly multidisciplinary consortium where three carefully chosen clinical ‘use cases’ will drive, evaluate and validate the approach to the ICT challenges

Transforming Genetic Medicine Initiative (TGMI)

The Transforming Genetic Medicine Initiative (TGMI) is building the knowledge base, tools and processes needed to deliver genetic medicine. The TGMI brings together a dedicated, experienced multi-disciplinary group of scientific and clinical experts focussed on ensuring the promise of genetic medicine can be realised.

Product duration: Ongoing
Scale International
Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine),
Transmart

Category: eHealth

Initiative type: Tool

The tranSMART Foundation enables effective sharing, integration, standardization and analysis of heterogeneous data from collaborative translational research by mobilizing the tranSMART open-source and open-data community.

Treat-NMD Neuromuscular Network

TREAT-NMD is a network for the neuromuscular field that provides an infrastructure to ensure that the most promising new therapies reach patients as quickly as possible. Since its launch in January 2007 the network’s focus has been on the development of tools that industry, clinicians and scientists need to bring novel therapeutic approaches through preclinical development and into the clinic, and on establishing best-practice care for neuromuscular patients worldwide.

Contact: Volker Straub: volker.straub@newcastle.ac.uk
Treehouse Childhood Cancer Initiative

Disease area: Cancer

Treehouse Childhood Cancer Initiative is a data sharing initiative researching the feasibility of real-time pan-cancer analysis for difficult-to-treat pediatric cancer patients

Scale International
Data type: Whole Genome, Whole Exome, Gene Panel, Variants/Genotyping, RNAseq,
Type 2 Diabetes Knowledge Portal

Initiative type: Database, Tool

Disease area: Complex Diseases

The Type 2 Diabetes Knowledge Portal is an open-access repository for data on human genetic variants associated with T2D. Data aggregated by the project are stored in a Data Coordinating Center (DCC) at the Broad Institute and will additionally be stored at connected federated nodes in the near future. The Portal knowledgebase contains T2D association studies from all the large-scale T2D consortia and projects, covering more than 260,000 individuals, along with harmonized genome-wide association study (GWAS) meta-analysis data from over 600,000 samples for an additional 25 relevant traits. Major contributors of data to the Portal include the GoT2D, T2D-GENES, and SIGMA consortia. New data sets will be added to the knowledgebase as they are generated, continually increasing the power of ana

Product duration: Ongoing
Scale International
Cohort description:

Multiple case-control cohorts; see Description

Data type: Whole Genome, Whole Exome, Variants/Genotyping,
Function role: Data sharing (Genomic Research),
U.S. All of Us Research Program

The PMI Cohort Program will seek to extend precision medicine to all diseases by building a national research cohort of one million or more U.S. participants. The PMI Cohort Program will be a participant-engaged, data-driven enterprise supporting research at the intersection of human biology, behavior, genetics, environment, data science and computation, and much more to produce new knowledge with the goal of developing more effective ways to prolong health and treat disease. The cohort will broadly reflect the diversity of the U.S. population by including participants from diverse social, racial/ethnic, and ancestral populations living in a variety of geographies, social environments, and economic circumstances, and from all age groups and health statuses. The longitudinal information ga

Product duration: Ongoing
Scale National
Cohort size: 1000000
Cohort description:

Participants from USA

Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine), Ecosystem,
Ubiquitous Pharmacogenomics (U-PGx)

The U-PGx consortium will address major challenges and obstacles for implementation of PGx testing in patient care, taking into account the diversity of healthcare systems and citizens across Europe. Specifically, U-PGx will investigate if the emerging approach of pre-emptive genotyping of an entire panel of important PGx markers is cost-effective and results in a better outcome for patients. We want to improve the safety and efficacy of pharmacotherapy for every European patient by enabling clinical pharmacogenomics. The new model of personalised medicine through pre-emptive PGx-testing will be conducted at a large scale in seven existing European health care environments (The Netherlands, Spain, UK, Italy, Austria, Greece, Slovenia).

Scale International
UK Biobank

UK Biobank is a major national health resource and a registered charity, with the aim of improving the prevention, diagnosis and treatment of a wide range of serious and life-threatening illnesses _ including cancer, heart diseases, stroke, diabetes, arthritis, osteoporosis, eye disorders, depression and forms of dementia. UK Biobank recruited 500,000 people aged 40-69 years in 2006-2010 from across the country to take part in this project, and is currently working with Affymetrix to genotype the 500,000 participants. Genotype data on all participants is expected to be available towards Q3 of 2016; visit http://www.ukbiobank.ac.uk/scientists-3/genetic-data/

Product duration: Ongoing
Scale International
Cohort size: 500000
Cohort description:

Individuals, aged 40-69 years, from across the UK

Data type: Variants/Genotyping,
UK Health Informatics Network

Category: eHealth

Responding to the issues highlighted in the report, a consortium of ten UK government and charity research funders launched a call, co-ordinated by MRC, to establish Centres of Excellence in research linking electronic health data. Four Health Informatics Research Centres (HIRCs) were funded at a total budget of £17.5m over 5 years…

To add value to the HIRCs and support health informatics research in the UK more widely, a further £1.5m was allocated by the funders’ consortium to fund a UK health informatics research network.

The objectives of the Network are to:
harness expertise in the wider UK research community
develop methodologies
share best practice
provide a central route for collaborating with industry, the NHS and policy
engage with the public to promote the ben

UK10K

The UK10K project will enable researchers in the UK and beyond to better understand the link between low-frequency and rare genetic changes, and human disease caused by harmful changes to the proteins the body makes.

Product duration: Ongoing
Scale National
Cohort size: 10000
Cohort description:

Participants (6,000 patients, and 4,000 controls)

Data type: Whole Genome, Whole Exome,
Function role: Data sharing (Genomic Research),
Undiagnosed Diseases Network (UDN)

UDN is designed to accelerate discovery and innovation in the way we diagnose and treat patients with previously undiagnosed diseases. The specific goals of the network are to: (1) improve the level of diagnosis and care for patients with undiagnosed diseases through the development of common protocols designed by a large community of investigators; (2) facilitate research into the etiology of undiagnosed diseases, by collecting and sharing standardized, high-quality clinical and laboratory data including genotyping, phenotyping, and documentation of environmental exposures; and (3) create an integrated and collaborative community across multiple clinical sites and among laboratory and clinical investigators prepared to investigate the pathophysiology of these new and rare diseases. UDN pa

Product duration: Ongoing
Scale National
Cohort size: 8000
Cohort description:

Individuals with a disease or condition that remains undiagnosed despite thorough evaluation, ongoing care and follow up by a healthcare provider. UDN is actively recruiting (estimated enrollment is 8000 individuals, which includes unaffected relatives enrolled for family sequencing studies).

Data type: Whole Genome, Whole Exome,
Function role: Data sharing (Genomic Research), Data sharing (Genomic Medicine), Standards,
Contact: Anastasia Wise: anastasia.wise@nih.gov
Universal Mutation Database (UMD) and BRCA Share

The Universal Mutation Database (UMD) databases are dedicated to the collection of mutations in human genes associated with genetic diseases. Most of these locus specific databases are freely accessible but some can only be accessed by a password. UMD was developed as a generic software to create locus-specific databases (LSDBs), including BRCA1/2 LSDBs. The BRCA1/2 LSDS became ‘BRCA Share’ in April 2015 – a novel gene datashare initiative that provides scientists and commercial laboratory organizations around the world with open access to BRCA1 and BRCA2 genetic data; co-founded by Inserm and Quest Diagnostics).

Product duration: Ongoing
Scale International
Data type: Variants/Genotyping,
Function role: Data sharing (Genomic Research),
Vanderbilt's BioVU

Initiative type: Biobank/Repository

BioVU is Vanderbilt’s collection, or _bank,_ of de-identified DNA samples derived from excess material from routine blood testing (consenting cases only). Researchers are using these samples to study the links between genes and disease and between genes and how a patient might respond to a prescribed medication. >160 on-going research projects use this biobank.

Product duration: Ongoing
Cohort size: 215000
Cohort description:

Samples

W3C

Category: eHealth

Semantic Web Health Care and Life Sciences Interest Group (HCLS IG) has the goal of developing, advocating for, and supporting the use of Semantic Web technologies across health care, life sciences, clinical research and translational medicine.

World Wide Web Consortium (W3C) Clinical Pharmacogenomics Task Force

Category: eHealth

Initiative type: Standards

Capture use cases for pharmacogenomic clinical research and medicine
Formalize the representation of pharmacogenomics-related information using Semantic Web technologies and ontologies
Demonstrate the integration of (genomic) patient data with biomedical resources (SNPs, drugs, genes, trials, treatments, adverse events)
Demonstrate a working interface to explore and query pharmacogenomic knowledge
Demonstrate how such representations can be used for clinical decision support

There are no matches for your search criteria