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Whole-genome sequencing data for 449 Nigerian individuals

Whole-genome sequencing data in the form of multi-sample, per-chromosome VCFs for n=449 individuals across 47 unique ethnolinguistic groups.

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NCD-GHS Data Access Policy

Terms and Conditions 1. The User agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for non-commercial research purposes. The User further agrees that theywill only use these Data for research purposes which are within the limitations (if any) set out in Appendix I and any Joint Controller Arrangement. 2. The process for accessing these Data in accordance with this DAA is as set forth below: • The process of the application review by the Data Access Committee (DAC) is being managed by 54gene GDS team in coordination with its Data Protection Officer (DPO) where appropriate; but the authority for final approval to grant access and to oversee data usage is under the responsibility and control of 54gene. The organization or individual entering into this Agreement with 54gene is referred to as the “User.” User’s agreement with 54gene through the DAA is to obtain access to the 54gene Data stored in The European Genome-phenome Archive at the European Bioinformatics Institute Database for the stated purpose of conducting the Research Purposes as detailed in the Project and this DAA. • User Institution will apply for EGA Database access via email to the main contact, Colm O’Dushlaine (colm@54gene.com), which will see that applications are reviewed by the DAC. Final responsibility for access to Data will be governed by 54gene; however, oversight of its usage and compliance with applicable laws and this DAA will be the responsibility of User. • In order to access the Data, the User and User Institution must apply for and receive approval from both the DAC and the Data Producer for access to the Data in the EGA Database in accordance with the terms and conditions hereunder. • Once the application and DAA are received, the DAC will review the application to confirm the following: the application is complete and the DAA has been properly completed and signed; the User or User Institution is not on any type of debarment list; the User is from a recognized institution that has the appropriate research, legal and financial means to support the project; the Project is feasible given the resources in the EGA Database; and the Project aims to advance scientific exploration and principles of openness in research. • The DAC will have the discretion to approve or decline an application or DAA based on ethical, scientific, programmatic or other relevant considerations. Among other things, the DAC may consider the following criteria: the User is qualified to conduct the Project and undertake the proposed analysis; the User Institution has confirmed that the minimum data security safeguards described at Section 6, below, have been implemented; the User has confirmed that IRB approval has been obtained, or, if no confirmation of IRB approval is provided, documentation explaining why the Institutional Review Board is not requiring approval. • The DAC will submit to the User its decision as to whether a User’s application and/or DAA is approved, declined or conditionally approved. If the DAC has approved the User application, the DAC will then determine if access is appropriate and sign the DAA. An Access Authorization Letter with directions for accessing the EGA database and Data will be emailed to the address provided by the User in the application. Even though the Data is provided by the Data Producer at no cost to the User, access to the Data will require the User to establish an account on the EGA Website and cover all costs associated with access, storage, egress charges, compute costs, and/or maintenance to service the User’s account. This account will be owned by the User requesting Data and all costs associated with work undertaken in that account will be the responsibility of the User. • The Access Authorization Letter will also be accompanied with a copy of the DAA executed by the Data Producer and User. This DAA will govern the User’s access to the EGA Database and Data. The terms of this DAA will prevail over any inconsistent terms of the EGA Website or elsewhere, and over any oral or written statement made by the staff of the DAC. • If the DAC has conditionally approved a User’s application, the Access Authorization Letter will set forth the additional information required to be submitted to the DAC, which may include additional data access and use terms to which User and User Institution must assent. Upon receipt of such additional information, the DAC will review User’s revised application, should one be submitted, together with the additional required information in accordance with the above steps and a notification of the decision of the DAC will be provided in accordance with this step. • Each DAA will have a term of one (1) year from the date of last signature (“Effective Date”) of the DAA. To renew a DAA and continue access to the EGA Database after expiration of the then-existing DAA, the User will be required to submit a renewal request. The Renewal Request will require User to provide: an updated User application or confirmation that the content of the User application originally submitted remains correct and complete; an updated list of and contact information for the Authorized Personnel, or confirmation that the list of and contact information for the original Authorized Personnel remains correct and complete; and all Publications prepared using the results of the Project in accordance with the Publication Policy at Appendix III. 3. Data may be used only for an IRB-approved Project as mutually agreed upon by both the DAC and the User Institution and only for the purposes of advancing science, deriving outcomes, and generating research results. The User acknowledges and understands that the Data is/are valuable and that except as expressly permitted only User, Authorized Personnel, and External Collaborators agreeing to abide by the protections set forth herein are the only persons permitted to use the Data under this Agreement. Confirmation that an Institutional Review Board (IRB) and ethics committee has approved the User’s use of these Data, including the name of the approved protocol, the date of approval and the name, address and email address of the IRB, and a letter from the IRB approving the Project subject to annual oversight and approval or stating that approval is not required due to the type of data being accessed, must be received by the DAC prior to approval. 4. The User will notify the DAC prior to any significant changes to the protocol for the Project or the Project itself. 5. The User will notify the DAC within thirty (30) days of any changes or departures of Authorized Personnel. The User agrees to distribute a copy of these terms to the Authorized Personnel. The User shall ensure that the Authorized Personnel comply with the terms of this agreement. 6. User and User Institution agree to use the Data only in connection with this Agreement and to hold the Data in strict confidence. The User agrees not to disclose, share, sell or allow access to any of the Data except as expressly permitted by this Agreement. Furthermore, with regard to PII/PHI received in connection with the Data, the User represents and warrants that it shall comply with all Applicable Law and ensure that all computer systems and devices used to access or process these Data meet Data Producers’ minimum security standards for high risk data in order to protect these Data. 7. If requested, the User will allow data security and management documentation to be inspected to verify that it is complying with the terms of this agreement. 8. The User agrees only to transfer or disclose these Data, in whole or part, or any material derived from these Data, only to the Authorized Personnel. Should the User Institution wish to share these Data with an External Collaborator, the External Collaborator must complete a separate Data Access Agreement for access to these Data. 9. The User agrees not to link, attempt to link, combine, or attempt to combine these Data to any other information or archived data available in a way that could reasonably be used to re-identify the Research Participants, even if access to that data has been formally granted to the User or is freely available without restriction. Should User inadvertently receive identifiable information or otherwise identify a subject, Recipient shall immediately notify the Data Producers and follow Data Producers’ reasonable written instructions, which may include return or destruction of the identifiable information. 10. The User agrees to protect the confidentiality of Research Participants in any research papers or Publications that they prepare by taking all reasonable care to limit the possibility of identification. 11. The User will notify the DAC immediately upon becoming aware of a breach of the terms or conditions of this agreement or upon User’s discovery of any unauthorized use or disclosure of these Data. 12. The parties will promptly confer and agree on legally required steps the User shall take to minimize the harm (if any) resulting from such breach. The User Institution will cooperate with the Data Producer in complying with such steps. In the event of actual or suspected unauthorized disclosure of, access to, or other breach of these Data, the User will comply with all Applicable Law and regulations related to such breach, and will cooperate with the Data Producer in assisting it to fulfill its legal obligations. 13. The User agrees that the Data Producers, and all other parties involved in the creation, funding or protection of these Data: a) make no warranty or representation, express or implied, of any kind as to the accuracy, quality, or comprehensiveness of these Data; b) exclude to the fullest extent permitted by law all liability for actions, claims, proceedings, demands, losses (including but not limited to loss of profit), costs, awards damages and payments made by the User that may arise (whether directly or indirectly) in any way whatsoever from the User’s use of these Data or from the unavailability of, or break in access to, these Data for whatever reason and; c) bear no responsibility for the further analysis or interpretation of these Data. 14. The User shall defend, indemnify and hold the Data Producer and its directors, officers, employees, students, agents, successors and assigns harmless, to the full extent permitted in law or equity, from and against any and all losses, claims, actions, damages, regulatory actions or investigations, liabilities, costs and expenses (including reasonable attorneys' fees and expenses), fines, penalties, judgments, and costs (including but not limited to the costs of providing appropriate notice to all parties and credit monitoring, credit rehabilitation, or other credit support services to individuals with information impacted by the actual or suspected breach, to the extent procured by the User (each a “Claim” or, collectively, “Claims”) to the extent that a Claim or Claims: (i) arise out of a breach of the User’s obligations hereunder; (ii) arise out of the User’s use, handling or storage of these Data in a manner not permitted by this Agreement or Protocol; or (iii) relate to User’s gross negligence or intentional acts under this Agreement, except to the extent a Claim or Claims is/are caused by the Data Producer’s own gross negligence or intentional misconduct. 15. THE DATA PRODUCER WILL NOT BE LIABLE FOR ANY INDIRECT, INCIDENTAL, PUNITIVE, SPECIAL OR CONSEQUENTIAL DAMAGES OF THE OTHER ARISING OUT OF OR IN CONNECTION TO ANY PERFORMANCE OF THIS AGREEMENT OR IN FURTHERANCE OF THE PROVISIONS OR OBJECTIVES OF THIS AGREEMENT, REGARDLESS OF WHETHER SUCH DAMAGES ARE BASED ON TORT, WARRANTY, CONTRACT OR ANY OTHER LEGAL THEORY, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. 16. The User agrees to follow the Publication Policy in Appendix I. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analyzing these Data. 17. The User agrees that all Data shall be owned exclusively by the Data Producer. To the extent the User has or acquires any rights in or to the Data, the User and User Institution each hereby irrevocably assigns, transfers and conveys to the Data Producer all of its right, title and interest in and to the Data, excluding any modifications, enhancements or derivative works developed by the User using the Data. For clarity, summaries, analyses and interpretations of the Data generated by the User pursuant to this Agreement shall not be considered "Data" and rights with respect to such summaries, analyses and interpretations shall be the property of the User or User Institution, as the case may be. Furthermore, and notwithstanding anything to the contrary herein, to the extent Data cannot be segregated from the User’s research results generated under the Project, the User and User Institution hereby grants to the Data Producer perpetual unrestricted right and license in and to that subset of Data necessary to fully exploit its rights in the Data and research results generated therefrom. 18. The User can elect to perform further research that would add intellectual and resource capital to these Data and decide to obtain intellectual property rights on these downstream discoveries. In this case, the User Institution agrees to implement licensing policies that will not obstruct further research and to follow the U.S. National Institutes of Health Best Practices for the Licensing of Genomic Inventions (2005) (https://www.icgc.org/files/daco/NIH_BestPracticesLicensingGenomicInventions_2005_en.pdf) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) (http://www.oecd.org/science/biotech/36198812.pdf ). The User hereby grants to the Data Producer a perpetual unrestricted right and license to use these intellectual property rights on these downstream discoveries. 19. The User agrees to certify the destruction or, if destruction is not feasible, the return of the Data held once it is no longer used for the Project, unless obliged to retain the Data for archival purposes in conformity with audit or legal requirements. 20. The Data Producer may terminate this agreement at any time and at its sole discretion by written notice to the User. If this agreement terminates for any reason, the User will be required to destroy any Data held, including copies and backup copies. This clause does not prevent the User from retaining these data for archival purposes in conformity with audit or legal requirements. 21. The User accepts that it may be necessary for the Data Producers to alter the terms of this agreement from time to time. As an example, this may include specific provisions relating to the Data required by Data Producers other than the DAC. In the event that changes are required, the Data Producers or their appointed agent will contact the User to inform it of the changes and the User may elect to accept the changes by written amendment to this Agreement, or terminate the agreement. 22. The validity, construction and performance of this Agreement and the legal relations among the parties hereto shall be governed by and construed in accordance with the laws of the Federal Republic of Nigeria, excluding that body of law applicable to choice of law and the parties consent to the jurisdiction of the Nigerian courts in connection with the resolution of any dispute among them arising from the validity, construction or performance hereof. If any provision of this Agreement or the application of any such provision shall be held by a tribunal of competent jurisdiction to be unenforceable or contrary to law, the remaining provisions of this Agreement shall continue in full force and effect. 23. In the event of a dispute arising out of or relating to this Agreement, the parties shall first attempt in good faith to resolve such dispute by negotiation and consultation between themselves. Either party may, by written notice to the other party, refer the dispute to the other party for attempted resolution by formal good faith negotiation within thirty (30) days after such notice is received. If the dispute remains unresolved after the good faith negotiation period provided in the previous sentence, either party by written notice to the other party may have such issue referred for resolution to the parties’ respective executive officers or senior legal counsel. The executive officers or senior legal counsel shall meet promptly to discuss the matter submitted and to determine a resolution. If the executive officers or senior legal counsel fail to resolve the dispute within thirty (30) days after it is referred to them, each party shall have the right to pursue any other remedies legally available to resolve the dispute and the matter may be brought by a party as a suit in a court of competent jurisdiction in accordance with Section 22, above. 24. The User shall not use the name, symbol, logo, likeness, service mark or trademark of the Data Producer without the prior written consent of the Data Producer.

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
EGAS00001007036 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
EGAF00007954647 tsv 12.4 kB
EGAF00007954648 vcf.gz 213.6 MB
EGAF00007954649 tbi 180.9 kB
EGAF00007954650 vcf.gz 132.2 MB
EGAF00007954651 tbi 105.5 kB
EGAF00007954652 vcf.gz 130.0 MB
EGAF00007954653 tbi 106.6 kB
EGAF00007954654 vcf.gz 128.8 MB
EGAF00007954655 tbi 107.2 kB
EGAF00007954656 vcf.gz 96.9 MB
EGAF00007954657 tbi 79.6 kB
EGAF00007954658 vcf.gz 89.3 MB
EGAF00007954659 tbi 73.8 kB
EGAF00007954660 vcf.gz 78.5 MB
EGAF00007954661 tbi 62.9 kB
EGAF00007954662 vcf.gz 85.7 MB
EGAF00007954663 tbi 60.9 kB
EGAF00007954664 vcf.gz 76.4 MB
EGAF00007954665 tbi 62.6 kB
EGAF00007954666 vcf.gz 77.3 MB
EGAF00007954667 tbi 62.6 kB
EGAF00007954668 vcf.gz 63.2 MB
EGAF00007954669 tbi 44.6 kB
EGAF00007954670 vcf.gz 230.6 MB
EGAF00007954671 tbi 191.9 kB
EGAF00007954672 vcf.gz 62.1 MB
EGAF00007954673 tbi 49.1 kB
EGAF00007954674 vcf.gz 37.1 MB
EGAF00007954675 tbi 26.7 kB
EGAF00007954676 vcf.gz 35.9 MB
EGAF00007954677 tbi 27.4 kB
EGAF00007954678 vcf.gz 195.4 MB
EGAF00007954679 tbi 161.4 kB
EGAF00007954680 vcf.gz 193.8 MB
EGAF00007954681 tbi 154.3 kB
EGAF00007954682 vcf.gz 177.5 MB
EGAF00007954683 tbi 144.8 kB
EGAF00007954684 vcf.gz 174.9 MB
EGAF00007954685 tbi 138.8 kB
EGAF00007954686 vcf.gz 152.1 MB
EGAF00007954687 tbi 122.4 kB
EGAF00007954688 vcf.gz 154.1 MB
EGAF00007954689 tbi 117.9 kB
EGAF00007954690 vcf.gz 117.0 MB
EGAF00007954691 vcf.gz 127.0 MB
EGAF00007954692 tbi 119.4 kB
EGAF00007955660 tbi 90.4 kB
47 Files (2.8 GB)