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Exome sequencing from a child with neurofibromatosis and relapsed refractory acute lymphoblastic leukaemia

Dataset contains 5 exome BAM files from a child with neurofibromatosis and relapsed refractory acute lymphoblastic leukaemia. The samples are CD19 positive and CD19 negative bone marrow mononuclear cells at both diagnosis and relapse as well as mesenchymal stem cells as the germline control. Libraries were prepared using the SureSelect Clinical Research Exome v2 kit (Agilent Technologies, Santa Clara, CA, USA) and run on the Illumina NextSeq 500 platform.

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SAHMRI data transfer agreement to access exam data files.

DATA TRANSFER AGREEMENT [XXX] (Recipient) South Australian Health and Medical Research Institute Limited (SAHMRI)   Party and Notice details Date 2022 Parties Name ABN Short form name Recipient Notice details Name SOUTH AUSTRALIAN HEALTH AND MEDICAL RESEARCH INSTITUTE LIMITED ABN 54 141 228 346 Short form name SAHMRI Notice details SAHMRI Building, North Terrace, Adelaide SA 5000 Australia Attention : Professor Steve Wesselingh Executive Director with a copy to Ms Heather Croucher SAHMRI’s General Counsel Steve.wesselingh@sahmri.com cc: heather.croucher@sahmri.com BACKGROUND A. SAHMRI owns the Data. B. The Recipient has requested SAHMRI to provide the Recipient with the Data for the purposes of the Research Project. C. SAHMRI has agreed to provide the Data to the Recipient for the purposes of the Research Project, on the terms and conditions of this Agreement. OPERATIVE PROVISIONS 1 DEFINITIONS 1.1 In this Agreement unless expressed or implied to the contrary, the following definitions shall apply: Agreement means this Data Transfer Agreement and includes all its schedules, attachments and annexures and any replacement of them. Business Day means a day that is not a Saturday or Sunday or a public holiday in Adelaide, South Australia. Commencement Date means the date described at item 1 of the Schedule. Confidential Information of a party (‘Disclosing Party’) means all information (whether or not in material form) which: a) by its nature is confidential, is treated by the Disclosing Party as confidential or which the other party (‘Receiving Party’) knows, or ought reasonably to be expected to know, is confidential to the Disclosing Party; or b) is disclosed by the Disclosing Party to the Receiving Party pursuant to this Agreement, or of which the Receiving Party becomes aware pursuant to or during the term of this Agreement, but excluding any information which: c) is publicly known; d) is disclosed to the Receiving Party by a third party without breach of confidentiality by the third party; e) is developed independently by the Receiving Party without reliance on any of the Disclosing Party’s Confidential Information; or f) is already known to the Receiving Party at the time of the disclosure (unless such knowledge arose from a breach of confidentiality). For the avoidance of doubt, the Data is deemed to be the Confidential Information of SAHMRI. Data means the data described at item 3 of the Schedule and any other data provided by SAHMRI to the Recipient under this Agreement. Intellectual Property means a) statutory and other proprietary rights in respect of copyright, future copyright, all rights in relation to inventions, patents, plant varieties, plant breeders’ rights, registered and unregistered trade marks, registered and unregistered designs, circuit layouts, trade secrets, rights to require information be kept confidential, any other form of intellectual property recognised by the Agreement on Trade-Related Aspects of Intellectual Property Rights and other rights arising out of intellectual activity in the industrial, scientific, literary or artistic fields, and includes all intellectual property owned by or licensed to a party whether before or after the date of this agreement and all Intellectual Property in the Confidential Information, but does not include Moral Rights; and b) includes any application or right to apply for registration of any of the rights referred to in paragraph (a) of this definition. Research Project means the application of machine learning methods to assess whether these identify predictors of mortality and morbidity in preterm infants, as described in the application for the Grant. Privacy Act means the Privacy Act 1988 (Cth) including the Australian Privacy Principles. Results means all data and results arising from performing the Research Project. Schedule means the Schedule attached to this Agreement. 2 PROVISION OF DATA 2.1 The Recipient acknowledges that the Data is provided to the Recipient, and will be stored, handled and used the Recipient, at the Recipient’s own risk. Without limiting the foregoing, SAHMRI gives no warranties of any nature in relation to the Data and in particular (but without limitation) SAHMRI gives no warranty or guarantee that the Data will be accurate, be merchantable or useful for any particular purpose. 3 USE OF DATA 3.1 The Recipient must: a) only use the Data for the academic purposes as described in the Research Project; b) ensure that the Data is stored, handled and used in compliance with all applicable legislation, regulations, codes and guidelines; and c) comply with its obligations under this Agreement. 3.2 The Recipient agrees that they must not: a) transfer, distribute or disclose the Data to any third party; b) carry out any procedures with the Data (linking, comparison, processing) with the intention of identifying the individual to whom any item of Data relates; or c) use the Data for commercial, diagnostic or therapeutic purposes. 3.3 The Recipient must notify SAHMRI immediately if either of them becomes aware of any unauthorised access to or use of the Data and comply with all reasonable directions of SAHMRI. 4 OWNERSHIP AND INTELLECTUAL PROPERTY RIGHTS 4.1 The Recipient acknowledges and agrees that the Data is and remains the property of SAHMRI. 4.2 The Recipient will ensure that their respective Recipient’ scientists will keep SAHMRI informed of the Results. 4.3 The Recipient agrees to notify SAHMRI (promptly and in writing) of any Intellectual Property created, discovered or reduced to practice in the course of conducting the Research Project. 4.4 The Recipient acknowledges and agrees that all new Intellectual Property discovered or arising in the course of conducting the Research Project will vest in accordance with the parties contributions. 5 PUBLICATION 5.1 If the Recipient wants to publish the Results of the Research Project, the Recipient will provide a copy of any proposed Publication to SAHMRI at least 45 calendar days prior to any proposed submission for publication of any Publication. 5.2 SAHMRI agrees to respond in writing to a request for approval of a proposed Publication or presentation within 30 calendar days of the request being made. If SAHMRI does not reject the request for approval, or fails to respond, within the 30 calendar day period, SAHMRI will be deemed to have consented to publication. 5.3 If SAHMRI does not consent to publication, the Recipient agrees to delete all Confidential Information relating to the Data and to make such other changes as SAHMRI may reasonably require. 5.4 The Recipient agrees to acknowledge the source of the Data in any publications reporting use of such Data. 5.5 In any publications based on the 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., EGAS00000000029), and acknowledge its use in a form agreed by the Recipient with SAHMRI. 6 PRIVACY 6.1 The Recipient agrees to comply with the Privacy Act 1988 (Cth) and the Australian Privacy Principles under that Act in the use, collection, storage and disclosure of the Data or otherwise in connection with this Agreement; 6.2 The Recipient must notify SAHMRI immediately if it becomes aware of any breach or possible breach of that party’s obligations under this clause 6. 7 CONFIDENTIALITY 7.1 Each Receiving Party must keep confidential any Confidential Information received from a Disclosing Party and must not, without the prior written consent of the Disclosing Party, disclose or permit the same to be disclosed to any third party. 7.2 Each Receiving Party may disclose Confidential Information to such of its employees and agents as have a need to know the same for the purposes of the Research Project, provided that each such employee or agent is under a duty of confidentiality to the Receiving Party no less onerous than the confidentiality obligation owed by the Receiving Party under this Agreement. 7.3 This obligation of confidentiality shall not apply to any disclosure required by law, provided that the Receiving Party shall notify the Disclosing Party of any disclosure required by law in sufficient time so that the Disclosing Party may contest such requirement, if the Disclosing Party so chooses. 8 LIABILITY 8.1 The Recipient acknowledges and agrees that SAHMRI will not be liable for, and the Recipient hereby expressly releases SAHMRI from, any loss or damage suffered by a Recipient, in connection with or as a result of use of the Data. 8.2 The Recipient hereby indemnifies SAHMRI, its affiliates and their respective officers, directors, employees and agents against any and all claims, actions, demands, suits or causes of action for damages (including those made by a third party) arising out of or relating to the Recipient’s use, storage, disposal or destruction of the Data. 9 TERMINATION 9.1 SAHMRI may terminate this Agreement immediately by giving notice to the Recipient if a Recipient breaches any provision of this Agreement and such breach not capable of remedy. 9.2 Any termination of the Agreement under this clause 9 shall be without prejudice to the rights of any party accrued under the Agreement before termination. 9.3 Upon termination of this Agreement, the Recipient will immediately, at SAHMRI’s option: a) return to SAHMRI all of the Data and (subject to clause 9.4) all other Confidential Information of SAHMRI; or b) destroy all of the Data and (subject to clause 9.4) all other Confidential Information of SAHMRI in whatever form recorded and certify its destruction to SAHMRI. 9.4 The Recipient may retain one copy of Confidential Information received from SAHMRI (other than Data) solely for record keeping purposes to the extent required by law provided that each Recipient continues to comply with its obligations under clauses 3 and 6. 10 GENERAL 10.1 Notices: All notices to be served under this Agreement: a) may be served personally, via email, or sent by express post to the address of the Party as set out in this Agreement (or to such alternative address which has been notified by the recipient to the sender); and b) will be deemed to have been given: (i) if served personally, on the date upon which it is served; (ii) if sent by email, upon receipt by the sender of confirmation that the notice has been sent in its entirety to the recipient; and (iii) if sent by express post, two Business Days after the date of posting. 10.2 Entire Agreement: This Agreement together with the Collaborative Research Agreement will constitute the entire agreement between the parties in relation to its subject matter. To the maximum extent permitted by law, all previous agreements, representations, warranties, explanations and commitments, express or implied, are superseded and have no effect. 10.3 Relationship between parties: This Agreement shall not be construed as creating any partnership, joint venture or agency between the Parties. No Party shall, by virtue of this Agreement be deemed to have any power or authority to bind or represent any other Party. 10.4 Variation: This Agreement may only be varied in writing signed by the Parties. 10.5 Reading down and severance a) Where a part of this agreement would otherwise be unenforceable, illegal or void, the effect of that provision will so far as possible, be limited and read down so that it is not unenforceable, illegal or void, provided that the effect of such limitation or reading down does not defeat the material objectives of this agreement. b) If despite the operation of paragraph a): (i) a court of competent jurisdiction finds any part of this agreement to be unenforceable, illegal or void, that finding will not invalidate other parts of this agreement; or (ii) if it is not possible to limit or read down a part of this agreement without defeating the material objectives of this agreement, the parties will negotiate in good faith a replacement for the relevant part of this agreement. 10.6 Waiver: A Party’s failure or delay to exercise a power or right does not operate as a waiver of that power or right and does not preclude the Party from exercising that, or any other, power or right in the future. 10.7 Survival of terms: Clauses 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10.7 survive the expiry or earlier termination of this Agreement. 10.8 Governing Law: This Agreement is governed by and must be construed in accordance with the laws of South Australia. The parties submit to the non-exclusive jurisdiction of the courts of South Australia and the courts competent to determine appeals from those courts with respect to any proceedings which may be brought at any time relating in any way to this Agreement. 10.9 Assignment: A party must not assign its rights or obligations under this Agreement without the prior written consent of all of the other parties. 10.10 Electronic Signing & Counterparts: Each Party agrees that this Agreement may be executed by electronic signature (regardless of the form of electronic signature utilised) and that this method of signature is conclusive of the Parties’ intention to be bound by this Agreement as if physical signing had occurred. This Agreement may be executed in any number of counterparts and by the Parties on separate counterparts. Each counterpart constitutes the agreement of each Party who has executed and delivered that counterpart. Each Party may communicate its execution of this Agreement by successfully transmitting an executed copy of the Agreement by an electronic method to each other Party. EXECUTED AS AN AGREEMENT SIGNED for and on behalf of ) [XXX] by ) its authorised officer: ) ) ................................................ ) ................................................ Print Name ) Signature ) ................................................ ) ................................................ Title ) Date SIGNED for and on behalf of ) SOUTH AUSTRALIAN HEALTH AND ) MEDICAL RESEARCH INSTITUTE LIMITED) by its authorised officer: ) ) ................................................ ) ................................................ Print Name ) Signature ) ................................................ ) ................................................ Title ) Date 

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
EGAS00001006187 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
EGAF00006141350 bam 2.5 GB
EGAF00006141351 bam 2.4 GB
EGAF00006141352 bam 2.3 GB
EGAF00006141353 bam 2.1 GB
EGAF00006141354 bam 2.3 GB
5 Files (11.5 GB)