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Multimodal Genomic Features Predict Outcome of Immune Checkpoint Blockade in Non-small Cell Lung Cancer

The dataset for Multimodal Genomic Features Predict Outcome of Immune Checkpoint Blockade in Non-small Cell Lung Cancer includes 106 bam files from whole exome next-generation sequencing on the Illumina HiSeq2500. The samples analyzed include matched tumor/normal samples from non-small cell lung cancer patients treated with immunotherapy.

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Data access agreement for Multimodal Genomic Features Predict Outcome of Immune Checkpoint Blockade in Non-small Cell Lung Cancer

DATA ACCESS AGREEMENT for EGA Study EGAS00001003892 These terms and conditions govern access to the managed access datasets (details of which are set out in Appendix I) to which the User Institution has requested access. The User Institution agrees to be bound by these terms and conditions. Definitions DAC: The data access committee for Multimodal Genomic Features Predict Outcome of Immune Checkpoint Blockade in Non-small Cell Lung Cancer, EGA DAC EGAC00001001331. Authorised Personnel: The individuals at the User Institution to whom the DAC grants access to the Data. This includes the User, the individuals listed in Appendix II and any other individuals for whom the User Institution subsequently requests access to the Data. Details of the initial Authorised Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: The DAC and the collaborators listed in Appendix I responsible for the development, organisation, and oversight of these Data. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. Project: The project for which the User Institution has requested access to these Data. A description of the Project is set out in Appendix II. Publications: Includes, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. Research Participant: An individual whose data form part of these Data. Research Purposes: Shall mean research that is seeking to advance the understanding of genetics and genomics, including the treatment of disorders, and work on statistical methods that may be applied to such research. User: The principal investigator for the Project. User Institution(s): The Institution that has requested access to the Data. Please include your Institution details here: 1. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for Research Purposes. The User Institution further agrees that it will only use these Data for Research Purposes which are within the limitations (if any) set out in Appendix I. 2. The User Institution agrees to preserve, at all times, the confidentiality of these Data. In particular, it undertakes not to use, or attempt to use these Data to compromise or otherwise infringe the confidentiality of information on Research Participants. Without prejudice to the generality of the foregoing, the User Institution agrees to use at least the measures set out in Appendix I to protect these Data. 3. The User Institution 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. 4. The User Institution agrees not to link or combine these Data to other information or archived data available in a way that could re-identify the Research Participants, even if access to that data has been formally granted to the User Institution or is freely available without restriction. Should User Institution inadvertently receive identifiable information or otherwise identify a subject, Recipient shall promptly notify Provider and follow Data Producer’s reasonable written instructions, which may include return or destruction of the identifiable information. 5. The User Institution agrees only to transfer or disclose these Data, in whole or part, or any material derived from these Data, to the Authorised Personnel. Should the User Institution wish to share these Data with an External Collaborator, the External Collaborator must complete a separate application for access to these Data. 6. The User Institution 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 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 Recipient that may arise (whether directly or indirectly) in any way whatsoever from the Recipient’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. 7. The User Institution agrees to follow the Fort Lauderdale Guidelines (http://www.wellcome.ac.uk/stellent/groups/corporatesite/@policy_communications/documents/web_document/wtd003207.pdf ) and the Toronto Statement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html). This includes but is not limited to recognising the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of these Data. Nothing herein shall authorize the User Institution to use or further disclose the Data in a manner that would violate the requirements of Data Producers under U.S. law, including 45 CFR 164.514. 8. The User Institution agrees to follow the Publication Policy in Appendix III. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing these Data. 9. The User Institution agrees not to make intellectual property claims on these Data and not to use intellectual property protection in ways that would prevent or block access to, or use of, any element of these Data, or conclusion drawn directly from these Data. 10. The User Institution 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 ). 11. The User Institution agrees to destroy/discard 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. 12. The User Institution will notify the DAC within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify the DAC prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the DAC as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The DAC may terminate this agreement by written notice to the User Institution. If this agreement terminates for any reason, the User Institution will be required to destroy any Data held, including copies and backup copies. This clause does not prevent the User Institution from retaining these data for archival purpose in conformity with audit or legal requirements. 16. The User Institution 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 Institution to inform it of the changes and the User Institution may elect to accept the changes or terminate the agreement. 17. If requested, the User Institution will allow data security and management documentation to be inspected to verify that it is complying with the terms of this agreement. 18. The User Institution agrees to distribute a copy of these terms to the Authorised Personnel. The User Institution will procure that the Authorised Personnel comply with the terms of this agreement. 19. If the Data Producer is a HIPAA Covered Entity, and if the the Data will be a Limited Data Set as defined by the Health Insurance Portability and Accountability Act of 1996 (“HIPAA”). In accordance with Section 164.514(e)(2) of the HIPAA Privacy Rule, the Data shall exclude the following direct identifiers of the individual or of relatives, employers, or household members of the individual: (i) Names; (ii) Postal address information, other than town or city, State, and zip code; (iii) Telephone numbers; (iv) Fax numbers; (v) Electronic mail addresses; (vi) Social security numbers; (vii) Medical record numbers; (viii) Health plan beneficiary numbers; (ix) Account numbers; (x) Certificate/license numbers; (xi) Vehicle identifiers and serial numbers, including license plate numbers; (xii) Device identifiers and serial numbers; (xiii) Web Universal Resource Locators (URLs); (xiv) Internet Protocol (IP) address numbers; (xv) Biometric identifiers, including finger and voice prints; and (xvi) Full face photographic images and any comparable images. If the Data being provided is coded, the Data Producer will not release, and the User Institution will not request, the key to the code.   Agreed for User Institution Signature: Name: Title: Date: Principal Investigator I confirm that I have read and understood this Agreement. Signature: Name: Title: Date: Agreed for the DAC Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY APPENDIX I – DATASET DETAILS Dataset reference (EGA Study ID and Dataset Details) EGA study accession EGAS00001003892: Multimodal Genomic Features Predict Outcome of Immune Checkpoint Blockade in Non-small Cell Lung Cancer EGA dataset for study EGAS00001003892: The dataset for Multimodal Genomic Features Predict Outcome of Immune Checkpoint Blockade in Non-small Cell Lung Cancer includes 12 bam files from whole exome next-generation sequencing on the Illumina HiSeq2500. The samples analyzed include matched tumor/normal samples from non-small cell lung cancer patients treated with immunotherapy. Name of project that created the dataset EGA study accession EGAS00001003892: Multimodal Genomic Features Predict Outcome of Immune Checkpoint Blockade in Non-small Cell Lung Cancer Names of other data producers/collaborators Valsamo Anagnostou, Noushin Niknafs, Kristen Marrone, Daniel C. Bruhm, James R. White, Jarushka Naidoo, Karlijn Hummelink, Kim Monkhorst, Ferry Lalezari, Mara Lanis, Samuel Rosner, Joshua E. Reuss, Kellie N. Smith, Vilmos Adleff, Kristen Rodgers, Zineb Belcaid, Lamia Rhymee, Benjamin Levy, Josephine Feliciano, Christine L. Hann, David S. Ettinger, Christos Georgiades, Franco Verde, Peter Illei, Qing Kay Li, Alexander S. Baras, Edward Gabrielson, Malcolm V. Brock, Rachel Karchin, Drew M. Pardoll, Stephen B. Baylin, Julie R. Brahmer, Robert B. Scharpf, Patrick M. Forde and Victor E. Velculescu Specific limitations on areas of research The User Institution agrees that it will only use these Data for Research Purposes. Minimum protection measures required File access: Data can be held in unencrypted files on an institutional compute system, with Unix user group read/write access for one or more appropriate groups but not Unix world read/write access behind a secure firewall. Laptops holding these data should have password protected logins and screenlocks (set to lock after 5 min of inactivity). If held on USB keys or other portable hard drives, the data must be encrypted. APPENDIX II – PROJECT DETAILS (to be completed by the Requestor) Details of dataset requested i.e., EGA Study and Dataset Accession Number Brief abstract of the Project in which the Data will be used (500 words max) All Individuals who the User Institution to be named as registered users Name of Registered User Email Job Title Supervisor* All Individuals that should have an account created at the EGA Name of Registered User Email Job Title APPENDIX III – PUBLICATION POLICY The DAC intend to publish the results of their analysis of this dataset and do not consider its deposition into public databases to be the equivalent of such publications. The DAC anticipates that the dataset could be useful to other qualified researchers for a variety of purposes. However, some areas of work are subject to a publication moratorium. The publication moratorium covers any publications (including oral communications) that describe the use of the dataset. For research papers, submission for publication should not occur until 0 months after these data were first made available on the relevant hosting database, unless the DAC has provided written consent to earlier submission. In any publications based on these data, please describe how the data can be accessed, including the name of the hosting database (e.g., The European Genome-phenome Archive at the European Bioinformatics Institute) and its accession numbers (e.g., EGAS000000000XX), and acknowledge its use in a form agreed by the User Institution with the DAC.

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
EGAS00001003892 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
EGAF00003249566 bam 18.0 GB
EGAF00003249567 bam 5.9 GB
EGAF00003249568 bam 16.6 GB
EGAF00003249569 bam 8.3 GB
EGAF00003249570 bam 15.0 GB
EGAF00003249571 bam 8.9 GB
EGAF00003249572 bam 18.3 GB
EGAF00003249573 bam 7.9 GB
EGAF00003249574 bam 15.9 GB
EGAF00003249575 bam 6.0 GB
EGAF00003249576 bam 14.2 GB
EGAF00003249577 bam 7.4 GB
EGAF00003249578 bam 15.5 GB
EGAF00003249579 bam 7.5 GB
EGAF00003249580 bam 16.3 GB
EGAF00003249581 bam 8.3 GB
EGAF00003249582 bam 14.7 GB
EGAF00003249583 bam 9.2 GB
EGAF00003249584 bam 21.7 GB
EGAF00003249585 bam 6.2 GB
EGAF00003249586 bam 11.9 GB
EGAF00003249587 bam 10.1 GB
EGAF00003249588 bam 27.1 GB
EGAF00003249589 bam 6.0 GB
EGAF00003249590 bam 10.9 GB
EGAF00003249591 bam 7.2 GB
EGAF00003249592 bam 13.2 GB
EGAF00003249593 bam 6.8 GB
EGAF00003249594 bam 16.1 GB
EGAF00003249595 bam 8.1 GB
EGAF00003249596 bam 16.9 GB
EGAF00003249597 bam 6.7 GB
EGAF00003249598 bam 15.6 GB
EGAF00003249599 bam 5.4 GB
EGAF00003249600 bam 11.2 GB
EGAF00003249601 bam 16.7 GB
EGAF00003249602 bam 8.1 GB
EGAF00003249603 bam 17.8 GB
EGAF00003249604 bam 9.3 GB
EGAF00003249605 bam 18.5 GB
EGAF00003249606 bam 4.5 GB
EGAF00003249607 bam 9.8 GB
EGAF00003249608 bam 8.2 GB
EGAF00003249609 bam 15.5 GB
EGAF00003249610 bam 7.3 GB
EGAF00003249611 bam 9.2 GB
EGAF00003249612 bam 7.3 GB
EGAF00003249613 bam 18.6 GB
EGAF00003249614 bam 5.7 GB
EGAF00003249615 bam 11.1 GB
EGAF00003249616 bam 7.8 GB
EGAF00003249617 bam 16.7 GB
EGAF00003249618 bam 6.0 GB
EGAF00003249619 bam 13.5 GB
EGAF00003249620 bam 5.2 GB
EGAF00003249621 bam 9.5 GB
EGAF00003249622 bam 6.3 GB
EGAF00003249624 bam 14.2 GB
EGAF00003249627 bam 13.7 GB
EGAF00003249628 bam 6.9 GB
EGAF00003249629 bam 11.7 GB
EGAF00003249630 bam 7.2 GB
EGAF00003249631 bam 11.4 GB
EGAF00003249632 bam 7.2 GB
EGAF00003249633 bam 20.7 GB
EGAF00003249634 bam 7.2 GB
EGAF00003249635 bam 12.4 GB
EGAF00003249636 bam 7.2 GB
EGAF00003249637 bam 14.7 GB
EGAF00003249638 bam 9.0 GB
EGAF00003249639 bam 14.1 GB
EGAF00003249640 bam 7.7 GB
EGAF00003249641 bam 14.3 GB
EGAF00003249643 bam 13.4 GB
EGAF00003249645 bam 15.5 GB
EGAF00003249647 bam 10.9 GB
EGAF00003249649 bam 13.9 GB
EGAF00003249650 bam 12.6 GB
EGAF00003249651 bam 6.2 GB
EGAF00003249652 bam 6.1 GB
EGAF00003249653 bam 12.3 GB
EGAF00003249654 bam 6.8 GB
EGAF00003249655 bam 19.2 GB
EGAF00003249656 bam 7.3 GB
EGAF00003249657 bam 15.5 GB
EGAF00003249658 bam 8.0 GB
EGAF00003249659 bam 11.3 GB
EGAF00003249660 bam 8.2 GB
EGAF00003249661 bam 19.4 GB
EGAF00003249662 bam 10.0 GB
EGAF00003249663 bam 5.8 GB
EGAF00003249664 bam 15.9 GB
EGAF00003249665 bam 6.5 GB
EGAF00003249666 bam 12.9 GB
EGAF00003249667 bam 6.5 GB
EGAF00003249668 bam 16.1 GB
EGAF00003249669 bam 3.9 GB
EGAF00003249670 bam 10.1 GB
EGAF00003249671 bam 9.6 GB
99 Files (1.1 TB)