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Whole exome sequencing of long-term, never relapse exceptional responders of trastuzumab-treated HER2+ metastatic breast cancer

The dataset contains Whole Exome Sequencing data (BAM files) of 22 samples from HER2+ metastatic breast patients. For 9 of the 13 tumours samples there are paired controls available from normal tissue. There are 8 tumours samples that are from treatment-responder patients and 5 tumours samples from non responder patients.

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The Data Access Committee must approve the purposes of the study that requires the dataset and the Data Access Agreement must be signed by both parties.

DATA ACCESS AGREEMENT This Data Access Agreement (the “Agreement”) is made on the [ ] day of [ ] 20.. BETWEEN (1) Cancer Clinical Research Trust (“CCRT” or the “Data Custodian”) having its place of business at St. Vincent’s University Hospital, Elm Park, Dublin 4, Ireland; AND (2) [Other party] (the “Data recipient”) having its place of business at [ ]. (each a “Party” and together, the “Parties”) WHEREAS (A) WHEREAS CCRT wishes to provide such Data directly to Recipient and Investigator, or by way of the European Genome-phenome Archive (“EGA”) which maintains a copy of portions of such Data, and (B) WHEREAS Recipient wishes to receive such Data for the purposes of the Study as further described in Appendix B. 1. DEFINITIONS In this Agreement, and the recitals hereto, the following expressions bear the following meanings unless the context otherwise requires: 1.1 “Data” means coded Genomic Sequence Data and/or clinical data that cannot, alone, reasonably be used to identify an individual. 1.2 “Genomic Sequence Data” means whole exome sequencing of DNA. 1.3 “Confidential Information” means, subject to Clause 7, any and all information provided to Recipient by CCRT and/or EGA relating to the Data. 1.4 “Investigator” means XXXXX, the Recipient investigator who will receive the Data and oversee the research. 1.5 “Licensed Use” means use of the Data only by Recipient, and solely for the Study. “Study” means the XXXXX as further described in Appendix B and updated from time to time (the “Study”). Where there is disagreement between the details of the Study described in Appendix B and this Agreement, this Agreement dominates. 2. GRANT 2.1 CCRT hereby grants, and Recipient accepts, a nonexclusive, non-transferable (except as provided in Section 11), limited right and license to use the Data described in Appendix A only for the Licensed Use. Except as otherwise permitted herein, in no event shall Recipient transfer Data to any third parties or allow any third parties to view or use the Data. CCRT retains title to all Data. 2.2 Recipient acknowledges and agrees that the Data is comprised of whole exome sequence data and may include data such as risk factors, gene-sample identifier links and germline DNA information associated with a unique, but not directly identified, person, and as such, for the purposes of this Agreement, the Data contained therein must be treated as personally identifiable information. 2.3 Recipient agrees that it shall not attempt, by any means, to establish the identity of, or make contact with, either directly or indirectly, any donor of Data and agrees only to publish or to disclose data that has been categorized or otherwise grouped into a format that precludes determination of individual records, such as data in an aggregate form. 2.4 Recipient represents, warrants and covenants that it has in place reasonable and effective administrative, technological and physical safeguards to stop theft, loss and unauthorized access, copying, modification, use, disclosure or disposal of personally identifiable information and that these safeguards are consistent with industry practice. 2.5 Investigator and Recipient shall treat the Data as though it were personally identifiable information and shall maintain the Data in a secure manner and take all reasonable steps to ensure that the Data is protected against theft, loss, modification and unauthorized copying, use, or disclosure and that safeguards employed are consistent with industry best practice. 2.6 Recipient and Investigator shall: (a) immediately notify CCRT in writing if either becomes aware of any breach or suspected breach of this Agreement or if Data has been (or is believed to have been) stolen, lost or accessed by unauthorized persons; (b) take reasonable steps to contain the breach, theft, loss or unauthorized access; and (c) co-operate with CCRT in a commercially reasonable manner to deal with such unauthorized access. 2.7 Recipient will maintain the confidentiality of the Data and ensure that only persons with a need to know and who are aware of and have agreed to comply with the terms and conditions of this Agreement will have access to the Data. 2.8 Recipient shall ensure that its use of the Data, complies with all applicable laws and regulations. 2.9 Upon request of CCRT, Recipient shall permit all privacy and data security and management documents to be inspected to verify that it is complying with the terms of this Agreement. 3. FINANCIAL ARRANGEMENTS Recipient shall bear its own cost of implementing this Agreement. 4. NO WARRANTIES CCRT MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF THE DATA WILL NOT INFRINGE ANY PATENT, COPYRIGHT, OR TRADEMARK, OR OTHER RIGHTS OR ANY OTHER EXPRESS OR IMPLIED WARRANTIES. CCRT DOES NOT WARRANT THAT THE DATA WILL MEET THE RECIPIENT’S REQUIREMENTS OR EXPECTATIONS. ALL DATA IS PROVIDED ON AN “AS IS” AND “AS AVAILABLE” BASIS. RECIPIENT’S USE OF THE MATERIAL IS AT ITS OWN RISK. 5. INDEMNIFICATION Recipient agree to indemnify, hold harmless and defend CCRT, its members, officers, employees, contractors, subcontractors, students and agents against any and all third party claims, suits, proceedings, costs, or expenses resulting from any negligence or from any injury (including death), damage, or loss or the alleged infringement of any copyright, patent, trademark, trade secret or other intellectual property or proprietary right arising out of Recipient’s use of the Data or any products or services derived from the Data. 6. LIMIT OF LIABILITY The Recipient acknowledges and agrees that CCRT and its officers, employees, contractors, subcontractors students and agents, shall not be liable for any direct, indirect, consequential, exemplary, special, or punitive damages arising from breach of this Agreement or from any cause of action relating to its provision of the Data to Recipient or Recipient’s use or inability to use the Data. CCRT shall not be liable for any lost profits or other economic loss of Recipient. 7. CONFIDENTIALITY Subject to Section 8 hereof Recipient will treat CCRT's Confidential Information with at least the same degree of care that Recipient uses for its own confidential information and will not reveal CCRT’s Confidential Information to third parties without the written consent of CCRT and will not use such Confidential Information except for the purpose of this Agreement. These restrictions will not apply to information which: (a) Was demonstrably in the possession of Recipient prior to the date of disclosure of the Confidential Information by CCRT to Recipient; or (b) Is publicly known at the time of the disclosure; or (c) Is required to be disclosed under applicable laws, regulations or orders of any governmental authority; or (d) Is furnished by CCRT to others without restrictions on its use or disclosure. 8. NAMES AND PUBLICATION Investigator and Recipient agree to acknowledge the contributions of the CCRT in all publications and presentations of studies utilizing Data received from CCRT and to provide a copy of all publications and/or abstracts of presentations to CCRT thirty (30) days in advance of publication or presentation. Recipient will ensure that the following wording accompanies any publication and/or abstracts of presentations: This study was conducted with the support of the Cancer Clinical Research Trust, Ireland. 9. TERMINATION 9.1 Recipient may terminate this Agreement by giving CCRT ninety (90) days notice in writing. 9.2 CCRT may terminate this Agreement if Recipient is in breach of any provision hereof; and Recipient fails to remedy such breach within thirty (30) days written notice from CCRT. 9.3 CCRT may terminate this Agreement upon the bankruptcy, or insolvency of Recipient or if Recipient becomes party to any bankruptcy proceeding. 9.4 This Agreement terminates upon the completion or termination of the Study. 9.5 Upon termination of this Agreement, Recipient shall: (a) cease all use of the Data; (b) Promptly destroy any remaining Data in a secure manner. Notwithstanding any such termination, any provisions of these terms that by their nature are intended to survive, will survive termination. 10. ASSIGNMENT. This agreement may not be assigned. 11. NOTICES 11.1 All general notices to Recipient shall be sent to: Name: Address Email: Telephone: 11.2 All general notices to CCRT shall be sent to: CCRT: Cancer Clinical Research Trust c/o Department of Medical Oncology St. Vincent’s University Hospital Elm Park, Dublin 4 Ireland Phone: +353 1 2213445 Fax: +353 1 2837719 12. MISCELLANEOUS 12.1 Entire Agreement. This document is the entire agreement between the parties in relation to its subject matter, and supersedes all prior and collateral representations, warranties, covenants, negotiations or discussions. This Agreement may only by modified by a written document, signed by authorized representatives of the Parties. 12.2 Choice of Law. This Agreement shall be governed and interpreted according the laws of Ireland and the parties attorn to the jurisdiction of Irish courts. 12.3 Counterparts. This Agreement may be executed electronically or by facsimile in any number of counterparts, each of which will be deemed an original and all of which together will constitute one and the same instrument. 12.4 Relationship. Recipient and CCRT are independent contractors. Nothing in this Agreement constitutes Recipient and CCRT as partners or joint venturers. Recipient does not have the authority to bind CCRT. 12.5 Severability. Each of the provisions contained in this Agreement is distinct and severable. Any declaration by a court of competent jurisdiction of the invalidity or unenforceability of any provision or part of a provision will not affect the validity or enforceability of any other provision of this Agreement. 12.6 Waiver. The failure of either party to insist upon strict performance of any terms and conditions or to exercise any of its rights set out in this Agreement shall not constitute a waiver of these rights, and these rights shall continue in full force and effect. IN WITNESS WHEREOF the undersigned Parties hereto agree to all the terms and conditions herein. CANCER CLINICAL RESEARCH TRUST (Date and signature) Name: Prof John Crown Title: Director and Head, CCRT (I have authority to bind the Corporation) Recipient Inc. (Date and signature) Name: Title: (I have authority to bind the Corporation) ACKNOWLEDGEMENT OF INVESTIGATOR: In signing below I, as an Investigator in this research project, hereby agree to act in accordance with all the terms and conditions of this agreement and further agree to ensure that all research project participants are informed of their obligations under such terms and conditions. (Date and signature) Name of Investigator: APPENDIX A : THE DATA Whole exome sequencing of long-term, never relapse exceptional responders of trastuzumab-treated HER2+ metastatic breast cancer; APPENDIX B : DESCRIPTION OF THE STUDY TO BE CONDUCTED

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
EGAS00001004486 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
EGAF00004042729 bam 17.8 GB
EGAF00004042730 bam 19.1 GB
EGAF00004042731 bam 4.1 GB
EGAF00004042732 bam 10.4 GB
EGAF00004042733 bam 9.6 GB
EGAF00004042734 bam 13.0 GB
EGAF00004042735 bam 19.0 GB
EGAF00004042736 bam 14.9 GB
EGAF00004042737 bam 19.5 GB
EGAF00004042738 bam 15.5 GB
EGAF00004042739 bam 6.0 GB
EGAF00004042740 bam 10.9 GB
EGAF00004042741 bam 15.7 GB
EGAF00004042742 bam 13.9 GB
EGAF00004042743 bam 10.4 GB
EGAF00004042744 bam 11.5 GB
EGAF00004042745 bam 18.4 GB
EGAF00004042746 bam 11.9 GB
EGAF00004042747 bam 7.1 GB
EGAF00004042748 bam 14.8 GB
EGAF00004042749 bam 15.9 GB
EGAF00004042750 bam 11.5 GB
22 Files (291.0 GB)