Research Category: Scientific Coordination
The Gray Foundation
The First 1000 Days 1kD
imCORE Network Data Repository
TREAT-AD
PsychENCODE Consortium
The PsychENCODE Consortium is a collaboration between 16 institutions working to provide an enhanced framework of regulatory genomic elements in individuals with neuropsychiatric disorders.
The collaboration has resulted in a comprehensive set of manuscripts published in Science providing new insights into the biology of the developing, adult, and diseased human brain.
The PsychENCODE program is funded by the NIMH with the goal of accelerating discovery of non-coding functional genomic elements in human brain, and elucidating their role in the molecular pathophysiology of psychiatric disorders. The Consortium investigators are producing a public resource of multi-dimensional genomic data using unbiased genome-wide approaches on tissue and cell-type specific samples from approximately 1000 phenotypically well-characterized healthy and diseased human post-mortem brains. The Consortium is also sharing data from functional characterization of disease-associated regulatory elements and variants in in-vitro and in-vivo model systems.
NF Open Science Initiative
The Portal and the NF-OSI
The NF Data Portal is designed to help openly explore and share NF datasets, analysis tools, resources, and publications related to neurofibromatosis. Anyone can join the NF Open Science Initiative (NF-OSI) to participate! We welcome contributions from anyone in the neurofibromatosis and schwannomatosis research community, such as original datasets generated by the community or analyses of data from the NF Data Portal. Contact the NF-OSI data coordination team at nf-osi@sagebionetworks.org with a brief summary of your contribution to begin the process. If you are a CDMRP NFRP Investigator Initiated Award applicant, please read more about NF-OSI data sharing here and contact us at nfrp-requests@sagebionetworks.org.
Neurofibromatosis and Schwannomatosis
Neurofibromatosis (NF) is a group of diseases including neurofibromatosis type 1 (NF1), neurofibromatosis type 2 (NF2), and schwannomatosis (SCH). These syndromes can afflict patients with a broad range of symptoms including tumors, developmental hardships, and pain. Many of these symptoms have few or no treatment options. Learn more about this family of diseases here.
Accessing the Data
Accessing the data in this portal requires a Synapse account. To establish a Synapse account, please follow the instructions on this page. If you have suggestions or feedback about the NF Data Portal, please contact us at nf-osi@sagebionetworks.org.
Supporting Organizations
The NF Data Portal is a central component and the first major milestone of the NF-OSI. The Portal is funded by the Children’s Tumor Foundation (CTF) and the Neurofibromatosis Therapeutic Acceleration Program (NTAP). The Portal is maintained by Sage Bionetworks.
Human Tumor Atlas Network (HTAN)
Accelerating Medicine Partnership in Alzheimer’s Disease
The Accelerating Medicine Partnership for Alzheimer’s Disease Knowledge Portal is a premier repository and workspace for multi-omic data generated through the AMP-AD consortia – a public- private partnership between academic research groups, industry partners, and non-profit partners. The primary goal of the consortia is to generate and test hypotheses to identify new targets for intervention in the treatment of Alzheimer’s disease. Deposited data includes gene expression, genotype, methylation, CHiP-Seq, DNA methylation, miRNA profiles, and clinical data, among others from human participants as well as animal and cell line model systems. Data is publically released on an aggressive schedule, with data releases occurring every quarter, starting in March 2015.
Learn more about the datasets, collaborators or external research projects by visiting the AD Knowledge Portal on Synapse.
AACR Project GENIE
AACR GENIE is a pilot project that seeks to identify and validate genomic biomarkers relevant to cancer treatment by linking tumor genomic data from clinical sequencing efforts with longitudinal clinical outcomes. GENIE will serve as a prototype for aggregating and harmonizing next-generation sequencing data from clinical specimens from multiple national and international institutions obtained in routine medical practice. The resulting “clinical cancer genomics meta-database”, which is expected to include ~100,000 tumors within 5 years, will complement existing efforts such as TCGA and ICGC, which have focused on generating more comprehensive genomic datasets on smaller numbers of tumors using optimized samples collected and processed by select institutions under very controlled conditions.
The GENIE platform was designed to integrate and link clinical-grade cancer genomic data with clinical outcomes data for tens of thousands of cancer patients treated at multiple institutions worldwide. Sage serves as the data hosting and integration hub for Project GENIE and maintains databases on Synapse that host the sample and clinical level information and associated genomic data, including somatic variants, copy-number alterations, and fusion data. To harmonize information across eight large academic centers, Sage developed and deployed detailed data dictionaries, formats, and SOPs describing the workflow streams required of each institution as well as data processing pipelines to validate and harmonize the data.
Learn more about Project GENIE:
- Project Genie video on the AACR Project GENIE website.
- Project GENIE consortium presents: Turning the Unknown into the Known – Data mining is increasingly used to prospect for rare-disease biology and treatments.
- AACR Project GENIE announces the first public release of cancer genomic data aggregated through its initiative known as GENIE. The data set includes nearly 19,000 de-identified genomic records collected from patients who were treated at eight international institutions, making it among the largest fully public cancer genomic data sets released to date.