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GoT2D: Genetics of Type 2 Diabetes, a study of the the genetic architecture of type 2 diabetes

The GoT2D study includes ~2800 samples, half T2D cases and half T2D controls, of Northern European ancestry sequenced over 3 three technologies: deep whole exome sequencing, low-pass (4x) whole genome sequencing, and OMNI 2.5M genotyping. Samples were ascertained to be phenotypically "extreme" (e.g. leaner, younger cases and older, more obese controls). Genotypes (SNVs, INDELs, and SVs) were called separately for each technology and then integrated via genotype refinement into a single phased reference panel; samples and variants were then excluded based on QC procedures described in Fuchsberger et al. Please note that 2 of the samples in the GoT2D vcf do not have phenotype data.

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This agreement governs the terms on which access will be granted to the phenotype and genotype data stewarded by the Broad Institute (‘Broad”) on behalf of the GoT2D/T2D-GENES Project (“Project”). In signing this agreement, You are agreeing to be bound by the terms and conditions of access set out in this agreement. For the sake of clarity, the terms of access set out in this agreement apply both to the User and the User’s Institution (as defined below). User Institution and User are referred to within the agreement as “You” and “Your” shall be construed accordingly. Definitions: Data means all and any human genetic data obtained from the Project. Data Subject means a person, who has been informed of the purpose for which the Data are held and has given his/her informed consent thereto. User means a researcher whose User Institution has previously completed this Data Access Agreement and has received acknowledgement of its acceptance. Publications means, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. User Institution means the organization at which the User is employed, affiliated or enrolled. Terms and Conditions: In signing this Agreement: 1. You agree to use the Data only for the advancement of medical research, according to the consent obtained from sample donors. 2. You agree to use the Data for the study of type 2 diabetes and related traits (limited to hypertension, cardiovascular disease, obesity, diabetes, and kidney disease) and non-commercial use only. 3. You acknowledge and agree that the Data may only be used by non-for-profit organizations. 4. Please note that due to the consents of the cohorts involved in this project, applicants are required to submit local IRB approval along with this application to view the data. We note that cohort specific individual level data is also available under less restrictive terms for specific cohorts, and query of all this data is available on the T2D Knowledge Portal 5. You agree that the Data will not be used to investigate individual pedigree structures or individual participant genotypes for the purpose of identifying individuals or families; assess variables or proxies that could be considered as stigmatizing an individual or a group; perform phenotype-only analyses; or explore issues such as false maternity and false paternity. 6. You agree to preserve, at all times, the confidentiality of information and Data pertaining to Data Subjects. In particular, You undertake not to use, or attempt to use the Data to compromise or otherwise infringe the confidentiality of information on Data Subjects and their right to privacy. 7. You agree not to attempt to link the data provided under this agreement to other information or archive data available for the data sets provided, even if access to that data has been formally granted to you, or it is freely available without restriction, without specific permission being sought from the relevant access committees. 8. You agree not to transfer or disclose the Data, in whole or part, or any identifiable material derived from the Data, to others, except as necessary for data/safety monitoring or program management. Should You wish to share the Data with a collaborator within the same Institution, the collaborator must make a separate application for access to the Data. 9. You agree to use the data for the approved purpose and project described in your application; use of the data for a new purpose or project will require a new application and approval. 10. You accept that Data will be reissued from time to time, with suitable versioning. If the reissue is at the request of sample donors and/or other ethical scrutiny, You will destroy earlier versions of the Data. 11. You agree to abide by the terms outlined in the 'Publications Policy' as set out in Schedule 1. 12. You agree to acknowledge in any work based in whole or part on the Data, the published paper from which the Data derives, the version of the data, and the role of the GoT2D/GENES Consortium and the relevant primary collectors and their funders. Suitable wording is provided in the Publications Policy given in Schedule 1. 13. You accept that the GoT2D/T2D-GENES consortium, the original data creators, depositors or copyright holders, or the funders of the Data or any part of the Data supplied: a) bear no legal responsibility for the accuracy or comprehensiveness of the Data; and b) accept no liability for indirect, consequential, or incidental, damages or losses arising from use of the Data, or from the unavailability of, or break in access to, the Data for whatever reason. 14. You understand and acknowledge that the Data are protected by copyright and other intellectual property rights, and that duplication, except as reasonably required to carry out Your research with the Data, or sale of all or part of the Data on any media is not permitted. 15. You recognize that nothing in this agreement shall operate to transfer to the User Institution any intellectual property rights relating to the Data. The User Institution has the right to develop intellectual property based on comparisons with their own data. 16. You accept that this agreement will terminate immediately upon any breach of this agreement by You and You will be required to destroy any Data held. 17. You accept that it may be necessary for the GoT2D/T2D-GENES Consortium or its appointed agent to alter the terms of this agreement from time to time in order to address new concerns. In this event, the GoT2D/T2D-GENES Consortium or its appointed agent will contact You to inform You of any changes and You agree that Your continued use of the Data shall be dependent on the parties entering into a new version of the Agreement. 18. You agree that you will submit a report to the GoT2D/T2D-GENES Data Access Committee, if requested, on completion of the agreed purpose. The GoT2D/T2D-GENES Data Access Committee agrees to treat the report and all information, data, results, and conclusions contained within such report as confidential information belonging to the User Institution. 19. You agree to comply with all applicable laws, rules, and regulations related to the use, storage, access, processing or other use of the Data, including but not limited to the Federal Health Insurance Portability and Accountability Act (HIPAA, 45 C.F.R. 164) (“HIPAA”). 20. This agreement shall be governed by, construed and enforced in accordance with the laws of the Commonwealth of Massachusetts, without giving effect to the principles of conflicts of law thereof. SCHEDULE 1 Publications Policy The GoT2D/T2D-GENES Data Access Committee anticipates that data generated from the Project will be used by others, such as required for developing new analytical methods, in understanding patterns of polymorphism and in guiding selection of markers to map genes involved in specific diseases. Authors who use data from this project must acknowledge the Genetics of Type 2 Diabetes (GoT2D) and Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Ethnic Samples (T2D-GENES) consortia using the following wording: “This study makes use of data generated by the GoT2D and T2D-GENES consortia. A full list of the investigators who contributed to the generation of data is available from and Funding for data generation was provided by NHGRI, NIDDK, the Wellcome Trust, and Helmholtz Zentrum München. For a full list of award numbers, please see the primary publication (Fuchsberger et al., Nature, 2016). Users should note that the GoT2D and T2D-GENES consortia and Broad Institute bear no responsibility for the further analysis or interpretation of these data, over and above that published by the Broad.

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001001459 Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00001227468 vcf.gz 30.6 GB
EGAF00001227469 vcf.gz 27.3 GB
EGAF00001227470 vcf.gz 26.5 GB
EGAF00001227471 vcf.gz 20.6 GB
EGAF00001227472 vcf.gz 23.7 GB
EGAF00001227473 vcf.gz 24.0 GB
EGAF00001227474 vcf.gz 26.9 GB
EGAF00001227475 vcf.gz 16.9 GB
EGAF00001227476 vcf.gz 15.8 GB
EGAF00001227477 vcf.gz 14.1 GB
EGAF00001227478 vcf.gz 15.6 GB
EGAF00001227479 vcf.gz 13.9 GB
EGAF00001227480 vcf.gz 13.4 GB
EGAF00001227482 vcf.gz 12.7 GB
EGAF00001227483 vcf.gz 6.4 GB
EGAF00001227484 vcf.gz 6.6 GB
EGAF00001227485 vcf.gz 13.5 GB
EGAF00001227486 vcf.gz 38.3 GB
EGAF00001227487 vcf.gz 40.9 GB
EGAF00001227488 vcf.gz 34.4 GB
EGAF00001227489 vcf.gz 33.3 GB
EGAF00001227490 vcf.gz 30.8 GB
EGAF00001235044 txt 361.4 kB
EGAF00001709844 vcf.gz 11.2 GB
24 Files (497.6 GB)