Need Help?

Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer

The dataset for the study Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer includes 207 bam files from hybrid capture targeted error-correction next-generation sequencing (TEC-Seq) from plasma cell-free DNA and matched white blood cell DNA from 30 individuals with non-small cell lung cancer, alongside 46 bam files from whole exome sequencing of tumor and matched normal DNA for 21 individuals with non-small cell lung cancer who received immunotherapy-containing regimens.

Request Access

Data access agreement for EGA study EGAS00001007291.

DATA ACCESS AGREEMENT 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 EGA study accession EGAS00001007291, Sequence Data from “Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer”, EGA DAC EGAC00001003261. Authorized 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 Authorized Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access and for which the DAC has agreed to grant such access. Data Producers: The DAC and the collaborators listed in Appendix I responsible for the development, organization, 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 individual at User Institution who will serve as 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. 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 Authorized 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 including a proper acknowledgement in all reports or publications resulting from the use of these Data. 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. Copies of all Publications arising from the Project must be sent to DAC at least 30 days prior to submission. If requested in writing by DAC, User Institution shall withhold material from submission for publication or presentation for an additional 60 days from the date of DAC’s request to allow for the filing of a patent application or the taking of such measures as DAC deems appropriate to establish and preserve proprietary rights in the information and the material being submitted for publication or presentation. 9. The DAC shall own and retain all right, title and interest in and to the Data and any derivatives, modifications, replications or compositions made or discovered by or on behalf of User Institution in relation to the Data. 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 Authorized 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. This Agreement shall commence upon the date last signed below and shall continue until the Project is completed, unless earlier terminated by the DAC. 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 confidentially 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 Authorized Personnel. The User Institution will procure that the Authorized Personnel comply with the terms of this agreement. 19. If the Data Producer is a HIPAA Covered Entity, and if 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 of University Official: 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 EGAS00001007291: Sequence data from “Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer”. EGA dataset for study EGAS00001007291: The dataset for the study “Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer” includes 207 bam files from targeted error-correction next-generation sequencing (TEC-Seq) from plasma cell-free DNA and matched white blood cell DNA from 30 individuals with non-small cell lung cancer, alongside 46 bam files from whole exome sequencing of tumor and matched normal DNA for 21 individuals with non-small cell lung cancer receiving immunotherapy-containing regimens. Name of project that created the dataset EGA study accession EGAS00001007291: Sequence data from “Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer”. Names of other data producers/collaborators Joseph C. Murray, Lavanya Sivapalan, Karlijn Hummelink, Archana Balan, James R. White, Noushin Niknafs, Lamia Rhymee, Gavin Pereira, Nisha Rao, Benny Weksler, Nathan Bahary, Jillian Phallen, Alessandro Leal, David L. Bartlett, Kristen A. Marrone, Jarushka Naidoo, Akul Goel, Benjamin Levy, Samuel Rosner, Christine L. Hann, Susan C. Scott, Josephine Feliciano, Vincent K. Lam, David S. Ettinger, Qing Kay Li1, Peter B. Illei, Kim Monkhorst, Robert B. Scharpf, Julie R. Brahmer, Victor E. Velculescu, Ali H. Zaidi, Patrick M. Forde and Valsamo Anagnostou. Specific limitations on areas of research The User Institution agrees that it will only use these Data for Research Purposes. Use of this data by for-profit organizations is not allowed. Minimum protection measures required File access: Data can be held in unencrypted files on an institutional computer 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 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 anticipate 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 2 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
EGAS00001007291 Cancer Genomics

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
EGAF00008262662 bam 8.9 GB
EGAF00008262663 bam 15.7 GB
EGAF00008262664 bam 7.6 GB
EGAF00008262665 bam 13.6 GB
EGAF00008262666 bam 7.6 GB
EGAF00008262667 bam 14.5 GB
EGAF00008262668 bam 8.5 GB
EGAF00008262669 bam 17.0 GB
EGAF00008262670 bam 7.7 GB
EGAF00008262671 bam 2.5 GB
EGAF00008262672 bam 2.5 GB
EGAF00008262673 bam 4.8 GB
EGAF00008262674 bam 3.3 GB
EGAF00008262675 bam 5.3 GB
EGAF00008262676 bam 4.7 GB
EGAF00008262677 bam 3.5 GB
EGAF00008262678 bam 13.7 GB
EGAF00008262679 bam 13.8 GB
EGAF00008262680 bam 4.3 GB
EGAF00008262681 bam 3.0 GB
EGAF00008262682 bam 3.5 GB
EGAF00008262683 bam 3.3 GB
EGAF00008262684 bam 4.2 GB
EGAF00008262685 bam 3.5 GB
EGAF00008262686 bam 3.5 GB
EGAF00008262687 bam 3.3 GB
EGAF00008262688 bam 3.5 GB
EGAF00008262689 bam 3.9 GB
EGAF00008262690 bam 4.4 GB
EGAF00008262691 bam 2.7 GB
EGAF00008262692 bam 2.0 GB
EGAF00008262693 bam 2.1 GB
EGAF00008262694 bam 2.2 GB
EGAF00008262695 bam 2.3 GB
EGAF00008262696 bam 3.6 GB
EGAF00008262697 bam 4.0 GB
EGAF00008262698 bam 4.2 GB
EGAF00008262699 bam 4.0 GB
EGAF00008262700 bam 2.5 GB
EGAF00008262701 bam 2.6 GB
EGAF00008262702 bam 3.7 GB
EGAF00008262703 bam 4.4 GB
EGAF00008262704 bam 8.5 GB
EGAF00008262705 bam 4.9 GB
EGAF00008262706 bam 4.3 GB
EGAF00008262707 bam 16.7 GB
EGAF00008262708 bam 3.9 GB
EGAF00008262709 bam 3.4 GB
EGAF00008262710 bam 3.6 GB
EGAF00008262711 bam 3.9 GB
EGAF00008262712 bam 3.9 GB
EGAF00008262713 bam 4.7 GB
EGAF00008262714 bam 8.2 GB
EGAF00008262715 bam 4.2 GB
EGAF00008262716 bam 4.1 GB
EGAF00008262717 bam 5.6 GB
EGAF00008262718 bam 13.9 GB
EGAF00008262719 bam 2.3 GB
EGAF00008262720 bam 8.5 GB
EGAF00008262721 bam 4.4 GB
EGAF00008262722 bam 4.6 GB
EGAF00008262723 bam 3.9 GB
EGAF00008262724 bam 3.6 GB
EGAF00008262725 bam 4.0 GB
EGAF00008262726 bam 4.2 GB
EGAF00008262727 bam 4.3 GB
EGAF00008262728 bam 18.5 GB
EGAF00008262729 bam 3.4 GB
EGAF00008262730 bam 4.1 GB
EGAF00008262731 bam 3.0 GB
EGAF00008262732 bam 4.0 GB
EGAF00008262733 bam 4.5 GB
EGAF00008262734 bam 3.5 GB
EGAF00008262735 bam 3.5 GB
EGAF00008262736 bam 3.9 GB
EGAF00008262737 bam 4.4 GB
EGAF00008262738 bam 4.7 GB
EGAF00008262739 bam 4.8 GB
EGAF00008262740 bam 5.7 GB
EGAF00008262741 bam 2.8 GB
EGAF00008262742 bam 3.5 GB
EGAF00008262743 bam 4.3 GB
EGAF00008262744 bam 4.0 GB
EGAF00008262745 bam 3.2 GB
EGAF00008262746 bam 3.4 GB
EGAF00008262747 bam 3.6 GB
EGAF00008262748 bam 3.1 GB
EGAF00008262749 bam 8.5 GB
EGAF00008262750 bam 4.3 GB
EGAF00008262751 bam 3.2 GB
EGAF00008262752 bam 13.6 GB
EGAF00008262753 bam 3.1 GB
EGAF00008262754 bam 3.3 GB
EGAF00008262755 bam 3.3 GB
EGAF00008262756 bam 6.4 GB
EGAF00008262757 bam 3.4 GB
EGAF00008262758 bam 3.7 GB
EGAF00008262759 bam 3.8 GB
EGAF00008262760 bam 4.3 GB
EGAF00008262761 bam 4.1 GB
EGAF00008262762 bam 4.3 GB
EGAF00008262763 bam 4.7 GB
EGAF00008262764 bam 4.3 GB
EGAF00008262765 bam 3.7 GB
EGAF00008262766 bam 13.4 GB
EGAF00008262767 bam 4.0 GB
EGAF00008262768 bam 3.6 GB
EGAF00008262769 bam 3.9 GB
EGAF00008262770 bam 3.6 GB
EGAF00008262771 bam 3.4 GB
EGAF00008262772 bam 3.5 GB
EGAF00008262773 bam 3.5 GB
EGAF00008262774 bam 3.4 GB
EGAF00008262775 bam 3.5 GB
EGAF00008262776 bam 4.1 GB
EGAF00008262777 bam 3.6 GB
EGAF00008262778 bam 3.9 GB
EGAF00008262779 bam 14.9 GB
EGAF00008262780 bam 15.4 GB
EGAF00008262781 bam 3.7 GB
EGAF00008262782 bam 5.1 GB
EGAF00008262783 bam 4.4 GB
EGAF00008262784 bam 4.6 GB
EGAF00008262785 bam 6.5 GB
EGAF00008262786 bam 6.4 GB
EGAF00008262787 bam 3.9 GB
EGAF00008262788 bam 4.1 GB
EGAF00008262789 bam 6.1 GB
EGAF00008262790 bam 6.0 GB
EGAF00008262791 bam 6.7 GB
EGAF00008262792 bam 4.5 GB
EGAF00008262793 bam 4.5 GB
EGAF00008262794 bam 3.9 GB
EGAF00008262795 bam 4.6 GB
EGAF00008262796 bam 10.9 GB
EGAF00008262797 bam 5.6 GB
EGAF00008262798 bam 4.6 GB
EGAF00008262799 bam 4.1 GB
EGAF00008262800 bam 5.0 GB
EGAF00008262801 bam 4.7 GB
EGAF00008262802 bam 4.9 GB
EGAF00008262803 bam 4.6 GB
EGAF00008262804 bam 3.9 GB
EGAF00008262805 bam 4.9 GB
EGAF00008262806 bam 4.0 GB
EGAF00008262807 bam 4.3 GB
EGAF00008262808 bam 4.1 GB
EGAF00008262809 bam 4.1 GB
EGAF00008262810 bam 4.7 GB
EGAF00008262811 bam 3.9 GB
EGAF00008262812 bam 4.0 GB
EGAF00008262813 bam 4.5 GB
EGAF00008262814 bam 10.4 GB
EGAF00008262815 bam 13.9 GB
EGAF00008262816 bam 4.2 GB
EGAF00008262817 bam 5.2 GB
EGAF00008262818 bam 5.8 GB
EGAF00008262819 bam 4.9 GB
EGAF00008262820 bam 14.2 GB
EGAF00008262821 bam 5.6 GB
EGAF00008262822 bam 4.3 GB
EGAF00008262823 bam 5.8 GB
EGAF00008262824 bam 5.9 GB
EGAF00008262825 bam 4.2 GB
EGAF00008262826 bam 5.5 GB
EGAF00008262827 bam 6.9 GB
EGAF00008262828 bam 4.2 GB
EGAF00008262829 bam 4.4 GB
EGAF00008262830 bam 15.4 GB
EGAF00008262831 bam 4.7 GB
EGAF00008262832 bam 7.8 GB
EGAF00008262833 bam 3.1 GB
EGAF00008262834 bam 3.2 GB
EGAF00008262835 bam 16.2 GB
EGAF00008262836 bam 3.3 GB
EGAF00008262837 bam 3.8 GB
EGAF00008262838 bam 6.8 GB
EGAF00008262839 bam 3.9 GB
EGAF00008262840 bam 3.9 GB
EGAF00008262841 bam 4.1 GB
EGAF00008262842 bam 3.8 GB
EGAF00008262843 bam 3.9 GB
EGAF00008262844 bam 13.1 GB
EGAF00008262845 bam 3.9 GB
EGAF00008262846 bam 4.2 GB
EGAF00008262847 bam 3.9 GB
EGAF00008262848 bam 3.4 GB
EGAF00008262849 bam 2.5 GB
EGAF00008262850 bam 3.0 GB
EGAF00008262851 bam 2.8 GB
EGAF00008262852 bam 3.6 GB
EGAF00008262853 bam 2.9 GB
EGAF00008262854 bam 6.9 GB
EGAF00008262855 bam 3.6 GB
EGAF00008262856 bam 4.7 GB
EGAF00008262857 bam 3.5 GB
EGAF00008262858 bam 3.9 GB
EGAF00008262859 bam 3.4 GB
EGAF00008262860 bam 4.2 GB
EGAF00008262861 bam 15.8 GB
EGAF00008262862 bam 4.0 GB
EGAF00008262863 bam 4.1 GB
EGAF00008262864 bam 4.1 GB
EGAF00008262865 bam 6.0 GB
EGAF00008262866 bam 4.2 GB
EGAF00008262867 bam 3.9 GB
EGAF00008262868 bam 4.2 GB
EGAF00008262869 bam 3.4 GB
EGAF00008262870 bam 3.8 GB
EGAF00008262871 bam 3.8 GB
EGAF00008262872 bam 4.7 GB
EGAF00008262873 bam 2.8 GB
EGAF00008262874 bam 5.6 GB
EGAF00008262875 bam 3.8 GB
EGAF00008262876 bam 4.0 GB
EGAF00008262877 bam 4.3 GB
EGAF00008262878 bam 3.8 GB
EGAF00008262879 bam 10.7 GB
EGAF00008262880 bam 3.6 GB
EGAF00008262881 bam 3.6 GB
EGAF00008262882 bam 4.0 GB
EGAF00008262883 bam 4.4 GB
EGAF00008262884 bam 3.7 GB
EGAF00008262885 bam 4.1 GB
EGAF00008262886 bam 4.0 GB
EGAF00008262887 bam 3.6 GB
EGAF00008262888 bam 4.1 GB
EGAF00008262889 bam 4.3 GB
EGAF00008262890 bam 3.9 GB
EGAF00008262891 bam 2.9 GB
EGAF00008262892 bam 7.1 GB
EGAF00008262893 bam 5.0 GB
EGAF00008262894 bam 3.0 GB
EGAF00008262895 bam 3.6 GB
EGAF00008262896 bam 6.1 GB
EGAF00008262897 bam 15.9 GB
EGAF00008262898 bam 3.8 GB
EGAF00008262899 bam 6.5 GB
EGAF00008262900 bam 3.8 GB
EGAF00008262901 bam 4.3 GB
EGAF00008262902 bam 4.0 GB
EGAF00008262903 bam 3.8 GB
EGAF00008262904 bam 12.6 GB
EGAF00008262905 bam 3.8 GB
EGAF00008262906 bam 3.0 GB
EGAF00008262907 bam 3.7 GB
246 Files (1.3 TB)