Partners with the Common Fund Data Ecosystem (CFDE)

The CFDE Coordinating Center oversees CFDE activities and works closely with participating data coordinating centers from other Common Fund Programs (or partners) on an initial subset of data sets, with plans to expand to additional CF data sets in the future. The CFDE portal is also developing and deploying a number of resources and tools, including training materials, to empower the research community to use CF data sets for novel scientific research that was not possible before. This may include hypothesis generation, discovery, or validation that leads to new insights in health and disease.

The goal of the 4D Nucleome (4DN) program is to study the three-dimensional organization of the nucleus in space and time (the 4th dimension). The nucleus of a cell contains DNA, the genetic “blueprint” that encodes all of the genes a living organism uses to produce proteins needed to carry out life-sustaining cellular functions.

The goal of the Acute to Chronic Pain Signatures (A2CPS) program is to develop a set of objective biomarkers that provide “signatures” to predict if chronic pain is likely to develop or be resolved after acute pain, like an injury or after a surgery. These signatures are greatly needed because prevention of chronic pain is a major challenge in pain management. For most people, acute pain resolves as the injury that caused it heals. Yet in many other people, pain from an injury, surgery, or disease persists lasts for years or even throughout life becoming a chronic condition. This high prevalence of chronic pain has in part contributed to the current opioid epidemic in the US. A signature that could be identified before the transition from acute to chronic pain could help accelerate therapy development and ultimately guide pain prevention strategies.

The Extracellular RNA Communication (ERC) program is exploring the biology of extracellular RNA (exRNA). Once thought to exist only within cells, in a paradigm shift for science, RNA is now known to be exported from cells as “extracellular RNA” and to play a role in cell-to-cell communication. Since its founding, the program has established data standards, a data portal, and tools and reagents available to the scientific community. The program cataloged exRNA molecules found in human biofluids like plasma, saliva, and urine from over 2000 donors. It also identified potential exRNA biomarkers for nearly 30 diseases, including cardiovascular disease, pregnancy complications, glaucoma, diabetes, and multiple types of cancer.

The goal of the Common Fund’s Glycoscience program is to create new resources, tools, and method to make the study of glycans (sugars) more accessible to the broader research community. Glycans play a critical role in nearly all aspects of biology, ranging from how our bodies recognize and fight viruses and bacteria to how proteins are moved throughout our cells to perform different tasks. Despite being an important part to nearly all biological functions, the study of glycans and the roles they play is limited due to the complexity surrounding the chemistry to make, study, and sequence all the different glycans in our body. To combat this, the Glycoscience program has developed a variety of tools, resources, and information for researchers unfamiliar with glycans to incorporate them into their studies. This includes techniques for identifying especially difficult glycans, probes to study glycans in bacterial cell walls, standards for glycan chemical synthesis, methods for high-throughput glycan studies, and glycoscience educational materials.

The Genotype-Tissue Expression (GTEx) project is an ongoing effort to build a comprehensive public resource to study tissue-specific gene expression and regulation. Samples were collected from 54 non-diseased tissue sites across nearly 1000 individuals, primarily for molecular assays including WGS, WES, and RNA-Seq. Remaining samples are available from the GTEx Biobank. The GTEx Portal provides open access to data including gene expression, QTLs, and histology images.

The Human BioMolecular Atlas Program (HuBMAP) is committed to developing the next generation of molecular analysis technologies, computational tools, and to generate foundational tissue maps in order to accelerate the construction of an atlas of the human body for the understanding the relationship between tissue organization and function. HuBMAP values secure, open sharing, and collaboration with the wider research community.\n

The Gabriella Miller Kids First Data Resource Center enables researchers, clinicians, and patients to work together to accelerate research and promote new discoveries for children affected with cancer and structural birth defects. Data from over 11,000 samples, including DNA and RNA, is available to empower your research today. Data collected from more than 30,000 samples are expected to be available in the next few years.

The LINCS project is based on the premise that disrupting any one of the many steps of a given biological process will cause related changes in the molecular and cellular characteristics, behavior, and/or function of the cell – the observable composite of which is known as the cellular phenotype. Observing how and when a cell’s phenotype is altered by specific stressors can provide clues about the underlying mechanisms involved in perturbation and, ultimately, disease.

The goal of the Metabolomics program is to inform basic, translational, and clinical research. Metabolomics is the scientific study of the chemical reactions that occur in organisms, cells, or tissues. Each reaction produces small chemicals called metabolites, which play critical roles in keeping our cells healthy and functioning properly. Improving metabolomics methods and making them more accessible to different researchers may allow for more personalized diagnosis of disease and treatment methods.\n

Molecular Transducers of Physical Activity Consortium (MoTrPAC) is a national research consortium designed to discover and perform preliminary characterization of the range of molecular transducers (the "molecular map") that underlie the effects of physical activity in humans. The program's goal is to study the molecular changes that occur during and after exercise and ultimately to advance the understanding of how physical activity improves and preserves health.

The Stimulating Peripheral Activity to Relieve Conditions (SPARC) program aims to transform our understanding of nerve-organ interactions with the intent of advancing bioelectronic medicine towards treatments that change lives.

The overall mission of the Integrative Human Microbiome Project is to generate resources to facilitate characterization of the human microbiota to further our understanding of how the microbiome impacts human health and disease. In the second phase of the HMP, the iHMP will create integrated longitudinal datasets from the microbiome and host from three different cohort studies of microbiome-associated conditions using multiple ‘omics technologies.

The Knockout Mouse Phenotyping Program (KOMP2) collaborates with the International Mouse Phenotyping Consortium (IMPC) to knockout and characterize all protein-coding genes in the mouse genome. Knocking out the activity of a gene provides valuable clues about what that gene normally does but creating mice with gene knockouts is a time-consuming and difficult process, and often is done by individual research labs with varied approaches. Since the founding of the program, KOMP2 scientists established and adhered to uniform characterization – or phenotyping – protocols, data collection, and reporting standards, and made all data available via a data portal. KOMP2 awardees, in conjunction with the IMPC, published over 120 peer-reviewed publications, including papers systematically describing genes with previously unknown function in hearing, embryonic development, and metabolism. Overall, this effort helps scientists explain the genetic basis of many different types of diseases in mice that also occur in humans, including rare diseases that have been under-studied as well as some common chronic diseases that affect much of the human population.

The Common Fund’s Undiagnosed Diseases Network (UDN) is a research study to improve the level of diagnosis of rare and undiagnosed conditions. In the United States, it has been estimated that approximately 25 million Americans suffer from a rare disorder. The UDN established a nationwide network of clinicians and researchers who use both basic and clinical research to uncover the underlying disease mechanisms associated with these conditions. In its first 20 months, the UDN accepted 601 participants undiagnosed by traditional medical practices. Of those who completed their UDN evaluation during this time, 35% were given a diagnosis. Many of these diagnoses were rare genetic diseases including 31 previously unknown syndromes.