RNA-seq data for 67 patient cohort
This dataset includes RNA-seq data of samples from our paper titled "Dynamic phenotypic heterogeneity and the evolution of multiple RNA subtypes in Hepatocellular Carcinoma: The PLANET study." (National Science Review, nwab192. https://doi.org/10.1093/nsr/nwab192)
- DAC: EGAC00001001784
- Technology: Illumina HiSeq 4000
Data access agreement (PLANET)
DATA ACCESS AGREEMENT Data of genomic variant calls and/or raw sequencing data generated by Next Generation Sequencing European Genome-phenome Archive THIS AGREEMENT is made the ______ day of __________ . Between: 1. GenomeInstituteofSingapore, Biomedical Sciences Institutes (Co. Reg. No. 199702109N), having its principal office at 60 Biopolis Street, Genome #02-01, Singapore 138672 (“GIS”); 2. ___________________________________ [Name of Company/Institution] (Co. Reg. No. ___________________), of __________________________________ [Insert address] (“Recipient”); and 3. ____________________________________ [Name of Registered User], of ____________________________________ [Insert address] (“Registered User”) RECITALS (A) GIS is a national research institution based in Singapore and funded by the Agency for Science, Technology And Research (“A*STAR”). (B) The European Genome-phenome Archive (EGA) is designed to be a repository for all types of sequence and genotype experiments, including case-control, population, and family studies. EGA is managed by European Bioinformatics Institute (EBI). (C) The Recipient is a ___________________________________ [Insert description of Recipient] (D) Anonymous data which is stripped of all personal identifiers is collected by GIS and disclosed to the Recipient, for the sole purpose of facilitating academic research conducted solely by the Recipient by providing a means for the Recipient to validate information relevant to its academic, non-commercial research. (E) GIS owns the Data (as defined below) and reserves the absolute discretion to decide whether or not to grant access to the Data. In response to the Recipient’s request for access to the Data, GIS hereby agrees to provide the Data to the Recipient for the sole purpose of the Research upon the terms and conditions hereinafter appearing: 1. DEFINITIONS In this Agreement, unless the context otherwise requires, the following definitions shall apply. ‘Data’ means the data as described in Schedule 1. ‘Data Subject’ means the individual to whom the Data refers to. ‘Intellectual Property’ means (i) patents, designs, trade marks and trade names (whether registered or unregistered), copyright and related rights, database rights; (ii) all other intellectual property rights and similar or equivalent rights anywhere in the world which currently exist or are recognised in the future; and (iii) applications, extensions and renewals in relation to any such rights. ‘PDPA’ means the Republic of Singapore Personal Data Protection Act 2012. ‘Registered User’ means a Researcher (or an individual conducting research under the supervision of a Researcher) that is employed by, or enrolled in, the Recipient and is bound by confidentiality and non-use obligations in respect of the Data and who has signed this Agreement and has received acknowledgement of its acceptance. For the avoidance of doubt, “Registered User” may also include students, visiting academics, or independent academic consultants provided that any such individual is bound by confidentiality and non-use obligations no less onerous than those binding the Recipient’s employees. ‘Research’ means the academic, non-commercial research to be undertaken by the Registered User at the Recipient’s laboratory, as described in Schedule 2, and as approved by GIS. ‘Researcher’ means an individual or individuals who carry out the Research. 2. OWNERSHIP OF DATA The Recipient and its Registered Users agree that the Data is the property of GIS and that GIS retains ownership of the Data at all times, and shall not do anything to question or challenge GIS’s rights in the Data. 3. INTELLECTUAL PROPERTY RIGHTS 3.1 Nothing in this Agreement shall operate to transfer to the Recipient or its Registered Users any Intellectual Property Rights in the Data. 3.2 The Recipient and its Registered Users acknowledge that the Data is or may be subject of a patent application. Nothing in this Agreement grants any implied or express licence or right under any patents or in any know-how or trade secrets or other proprietary rights of GIS nor any rights to use the Data or any product or process related thereto for profit-making or commercial purposes such as, but not limited to, production, sale, screening or drug design. The Recipient shall negotiate in good faith a licence with GIS before making any such profit-making or commercial use. GIS shall have no obligation to grant such any licence to the Recipient, and may grant exclusive or non-exclusive licences to others. 3.3 The Recipient and its Registered Users shall not file any patent or other application claiming any rights over the Data. 3.4 If any new Intellectual Property Rights are created through, arising from, or as a result of the Recipient’s and/or its Registered Users’ use of the Data, ownership of these Intellectual Property Rights shall be determined in good faith depending on each party’s relative contribution (including contribution of the Data) to the creation of the relevant Intellectual Property Rights, and any applicable laws and regulations relating to inventorship. Further, where the Recipient and its Registered Users own any such new Intellectual Property Rights, each of them agree to grant to GIS a non-exclusive, royalty-free licence to use such new Intellectual Property Rights for GIS’ internal research and development activities. 3.5 The Recipient and its Registered Users acknowledge that the Data may be protected by copyright and other intellectual property rights, such that any duplication, sale, hire of or other dealing in all or part of the Data on any media is not permitted under any circumstances, except with the prior written consent of GIS. 4. USE OF DATA 4.1 The Recipient and its Registered Users undertake to use the Data: - 4.1.1 solely for the Research and no other purposes; and 4.1.2 in accordance with the terms of this Agreement and all applicable laws, statutes, regulations, and policies. 5. ACCESS AND GOVERNANCE 5.1 GIS has absolute discretion to determine whether or not to grant access to the Data. 5.2 The Data shall only be used for academic, non-commercial research by the Registered User at the Recipient and/or individuals working under the direct supervision of the Registered User and who shall be bound by terms no less stringent than those of this Agreement. 5.3 The Recipient agrees that it shall, and shall ensure that its Registered User shall, take all reasonable security and confidentiality precautions to keep any information relating to the Data confidential. 5.4 Save as provided herein, the Recipient will not transfer or permit anyone else, including any other laboratory within the Recipient, access to the Data. 5.5 Recipient and its Registered Users agree that GIS shall have the right to request and forthwith be allowed to inspect the Recipient’s and its Registered Users’ data security and management documentation to ensure the adequacy of data protection measures in countries that have no national laws comparable to the PDPA. 6. PERSONAL DATA PROTECTION 6.1 The Recipient agrees that it, and its Registered Users, are covered by, and shall comply with the obligations contained in the PDPA and the relevant subsidiary legislation, as amended from time to time, or equivalent national laws which are no less onerous than those contained in the PDPA. 6.2 The Recipient and its Registered Users agree to protect the confidentiality of the Data Subjects in any research papers or publications that they may prepare, by taking all reasonable care to limit the possibility of identification. In particular, the Recipient and its Registered Users undertake not to use, or attempt to use, the Data to deliberately compromise or otherwise infringe the confidentiality of information on Data Subjects and their right to privacy. 6.3 The Recipient and its Registered Users shall not analyse, make any use of or otherwise subject the Data to any process in such a way that has the potential to lead to the identification of any Data Subject or compromise the anonymity of any Data Subject in any way. In particular, the Recipient and its Registered Users shall not pursue any research with the goal of identifying the Data Subjects or link or combine the Data with other information or archived data available in any way that could re-identify the Data Subjects, even if access to that data has been formally granted to the Recipient or its Registered Users, or is freely available without restriction. 7. PUBLICATION 7.1 The Recipient and/or its Registered User may publish or otherwise disclose research results with respect to the Data in scientific communications only. If any publication results from research using the Data, the Recipient and its Registered User agree to acknowledge the contributions of GIS. Appropriate wording is provided in the Publications Policy given in Schedule 3. 7.2 Notwithstanding the generality of sub-clause 7.1 above, the Recipient and/or its Registered User as the case may be, shall provide GIS with a copy of the intended publication at least thirty (30) days before submitting the same for publication, for GIS’ evaluation. If GIS deems that the publication will prejudice a patent application or contains information which may compromise personal data, GIS shall within thirty (30) days of the intended publication give notice in writing of any objections they may have to the Recipient and/or the Registered User and the Recipient and/or Registered User shall delay any such publication for a further thirty (30) days from the date of the aforesaid notice from GIS to permit GIS to file the appropriate patent application. 7.3 The Recipient and/or its Registered Users shall also declare in any such work that those who carried out the original analysis and collection of the Data shall bear no responsibility for the further analysis or interpretation of it by the Recipient and/or its Registered User. 8. DATA REISSUE The Recipient and its Registered Users accept that Data will be reissued from time to time, with suitable versioning. If Data is reissued at the request of sample donors and/or as the result of other ethical scrutiny, the Recipient and its Registered Users agree to destroy all earlier versions of the Data. 9. DISCLAIMER OF WARRANTY 9.1 GIS makes no representations, conditions or warranties, either express or implied with respect to any of the Data. Without limiting the generality of the foregoing, GIS expressly disclaims any implied warranty, condition or representation that the Data corresponds with a particular description, is of merchantable quality or fit for a particular purpose. 9.2 GIS shall not be liable for any loss, whether direct, consequential, incidental or special (and whether arising out of contract or tort), including pure economic loss, which the Recipient and/or its Registered User may suffer arising from any defect, error, fault or failure to perform with respect to the Data. 9.3 Nothing in this Agreement shall be construed as a warranty or representation by GIS that the Data is or will be free from infringement of patents, copyrights, trademarks, industrial designs or other intellectual property rights of any third party. 10. INDEMNITY 10.1 The Recipient and its Registered Users hereby jointly and severally agree and undertake to indemnify, hold harmless and defend GIS against any and all claims, actions, damages, liabilities, loss whatsoever (including all legal costs and expenses on a full indemnity basis) arising out of or resulting from directly or indirectly, the possession, use and/or storage of any of the Data or by reason of any breach of the terms herein by the Recipient and/or Registered User including, without limiting the generality of the foregoing, any consequential losses suffered by GIS by reason of the foregoing howsoever the same may arise. 10.2 In no event shall GIS be liable for consequential or incidental damages, including any pure economic loss, arising from breach or breaches of this Agreement. 10.3 No action, whether in contract or tort (including negligence) or otherwise arising out of or in connection with this Agreement may be brought by the Recipient or the Registered User more than six (6) months after the cause of action has occurred. 11 TERMINATION 11.1 This Agreement will terminate on the earliest of the following dates:- 11.1.1 on completion of the Research, or 11.1.2 on thirty (30) days written notice by one party to the other party. 11.2 In addition, GIS may terminate this Agreement immediately if it is of the view that the Recipient and/or its Registered Users are in breach of any of the terms hereof. 11.3 Upon termination of this Agreement as provided above, the Recipient and its Registered Users will discontinue its use of the Data and will, upon direction from GIS, return or destroy any remaining Data. The Recipient must provide written confirmation of the destruction of the Data received from GIS in accordance with any applicable laws and/or procedures. 11.4 Clauses 6, 7, 9 to 12, 13.1, and 13.2 shall survive the termination of this Agreement howsoever caused. 12. GOVERNING LAW AND JURISDICTION This Agreement shall be construed, governed, interpreted and applied in accordance with the laws of the Republic of Singapore in all respects. 13. GENERAL 13.1 No exercise or failure to exercise or delay in exercising any right, power, or remedy vested in any party under or pursuant to this Agreement shall constitute a waiver by that party of that or any right, power or remedy. 13.2 The parties agree that no person who is not a party to this Agreement shall have any right to enforce any term of this Agreement by virtue of the Contracts (Rights of Third Parties) Act or otherwise. 13.3 The Recipient and its Registered Users accept that it may be necessary for GIS to alter the terms of this Agreement from time to time in order to address new concerns. In this event, GIS will contact the Recipient to inform it of any changes and the Recipient and/or its Registered Users agree that its continued use of the Data shall be dependent on the parties entering into a variation of the Agreement. Amendments to this Agreement must be made in writing and agreed to by both parties. 14. ASSIGNMENT 14.1 If, at any time after the date of this Agreement the functions and operations of GIS are assigned, merged, transferred into or otherwise forms part of another organisation ("the New Entity"), such that the New Entity takes over the whole or substantially the whole of GIS’ operations, then it is agreed that this Agreement may, at the option of GIS, be novated to the New Entity which will then assume all of GIS’ rights and obligations hereunder. It is further agreed that GIS may assign all or any part of its rights hereunder to the New Entity or to any A*STAR Affiliate at nominal consideration. “A*STAR Affiliate” shall mean a national research institute or company within the purview of or funded by the Agency for Science, Technology and Research (or its assign or successor). 14.2 Save as aforesaid, this Agreement is not assignable by either party, whether by operation of law or otherwise, without the prior written consent of the other party. 15. FORCE MAJEURE 15.1 Neither party shall be liable for delays in delivery or performance when caused by any of the following which are beyond the actual control of the delayed party: (i) acts of God, (ii) acts of the public enemy, (iii) acts or failure to act by the other party or by any third party, (iv) acts of civil or military authority, (v) governmental priorities, (vi) hurricanes, (vii) earthquakes, (viii) fires, (ix) floods, (x) epidemics or pandemics, (xi) embargoes, (xii) war, and (xiii) riots (hereinafter referred to as the “Force Majeure Event”). 15.2 The respective obligations of either party hereunder shall be suspended during the time and to the extent that such party is prevented from complying therewith by a Force Majeure Event, provided that such party shall have given written notice thereof, specifying the nature and details of such event and the probable extent of the delay to the other party. 15.3 In case of a Force Majeure Event, the time for performance required by either party under this Agreement shall be extended for any period during which the performance is prevented by the event. However, the other party may terminate this Agreement by notice if such an event prevents performance continuously for more than thirty (30) days. AS WITNESS the hands of the parties hereto the day and year first above written. SIGNED by ) ) for and on behalf of GENOME INSTITUTE OF ) ) SINGAPORE ) ______________________ ) Name: in the presence of: ) Designation: Date: ___________________________ Name of Witness: Designation of Witness: Date: For and on behalf of Recipient _________________________________ Name: Designation: Date: Registered User _________________________________ Name: Designation: Date: SCHEDULE 1 Data The data comprises of genomic variant calls and/or raw sequencing data generated by Next Generation Sequencing (NGS) technologies. SCHEDULE 2 Research SCHEDULE 3 Publications Policy The primary purpose of GIS granting access to the Data to the Recipient and its Registered Users is to facilitate academic research conducted by the Recipient and to provide a means for the Recipient to validate information relevant to its academic, non-commercial research. GIS anticipates that the Data will be used by others. Persons who use the Data must acknowledge GIS using the following wording “This study makes use of data generated by the Genome Institute of Singapore” and cite the relevant primary GIS publication from which the Data was taken. All users of the Data must take note that GIS bears no responsibility for the further analysis or interpretation of the Data.
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.
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