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RRBS - MBD4-deficient AML

Reduced Representation Bisulfite Sequencing for WEHI-AML-1 and WEHI-AML-2. RRBS libraries were made with the NuGEN Ovation RRBS Methyl-Seq System. Bisulfite conversion was performed with the Qiagen Epitect kit. Sequencing was performed on an Illumina HiSeq2500.

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Data Transfer Agreement - WEHI

DATA TRANSFER AGREEMENT This agreement (hereinafter referred to as “Agreement”) is made and entered by and between: The Walter and Eliza Hall Institute of Medical Research having its principle office at 1G Royal Parade, Parkville, Victoria, Australia 3052, hereinafter referred to as “WEHI”; and xxxxxxxxxxxxxxxxxxxx having its principle office at xxxxxxxxxxxxxxxxxxxx, represented by its legal representative, xxxxxxxxxxxxxxxxxxxx, hereinafter referred to as “Recipient”. Hereinafter jointly referred to as “Parties” and individually as “Party”; WHEREAS * WEHI is the exclusive owner of the coded patient data set (EGAS00001002581) (“Data”) specified in Annex I to this Agreement; * Recipient, has requested WEHI, through The European Genome-phenome Archive (EGA) to provide Recipient with the Data for use by Recipient for the specific purpose as described in the Research Plan as specified in Annex II; * WEHI is willing, subject to the terms and conditions of this Agreement, to provide the Data to Recipient; I. Definitions Completion Date means the date as specified in Annex II to this Agreement. Confidential Information means all information, know-how, data and experience of WEHI regarding the Data, its characteristics, WEHI’s research concerning the Data, whether of a scientific, technical, engineering, operational, or economic nature, supplied to or obtained by Recipient in written form, in the form of drawings or in the recording of oral conversation, or samples, which is reasonably required by Recipient for performance of Research. Data means the data being transferred under this Agreement as specified in Annex I to this Agreement. Effective Date means the date of last signing of this Agreement. Research Plan means the research plan specified in Annex II to this Agreement for which the Data will be used. Results means all research activities, analyses, tests or studies performed using the Data. II. Terms and Conditions of this Agreement: 1. The Data and any other information provided is and remains the property of WEHI and is made available for use in ethically approved research into haematological malignancy as a service. 2. The Recipient agrees that the Data: (a) is to be used only for the purposes as described in the Research Plan not for any other purpose; (b) will not be used for any commercial purposes and (c) will not be transferred to any third party. Recipient shall not carry out the Research Plan with any third party or entity without prior written approval of WEHI. 3. The Data will be transferred with a code. Under no circumstances will the identity of the patient or any means to derive such identity be provided to Recipient. Recipient shall not carry out any procedures with the Data (linking, comparison, processing) through which the identity of the patient could be derived. No disclosure of Data containing germline variants is permitted in any circumstances.
 4. The Data is collected in accordance with the informed consent form (ICF) and/or the applicable Australian rules and legislation including but not limited to protection of privacy aspects of the medical and personal data of the patients. Recipient acknowledges that the patients shall at all times have the right to request WEHI to destroy their data. In the event a patient files such a request with WEHI, Recipient shall – upon first request by WEHI - promptly destroy the Data in an approved manner. Any Results (defined in article 5) already obtained through the use of the Data prior to such request shall remain at the disposal of Recipient. 5. The Results shall be owned by WEHI and the Recipient, and Recipient shall keep WEHI’s Scientist informed of the Results arising from the Research Plan and when requested shall provide an update of such Results. Within thirty (30) days after the completion of the Research Plan or the expiration or earlier termination of this Agreement, whichever occurs earlier, Recipient shall provide WEHI with a written description of all Results. Within two (2) days after the Completion Date of the Research Plan or the expiration or earlier termination of this Agreement, whichever occurs earlier, Recipient shall destroy all Data received and will send WEHI a written confirmation hereof. 6. Except as provided in this agreement, no express or implied licenses or other rights are provided to the Recipient under any Intellectual Property (IP) rights of WEHI. 7. All Data and Confidential Information are made available “as is” and parties understand and agree that all Data and Confidential Information are experimental in nature and are made available without any representation or warranty, express or implied, including any implied warranty of merchantability, satisfactory quality or fitness for any particular purpose or any warranty that the use of the Data and/or Confidential Information will not infringe or violate any patent or other proprietary rights of any third party. Recipient accepts all liability for any loss, claims and damages which may arise from the use, storage or disposal of the Data, Confidential Information or the use of the Results by Recipient. Recipient shall hold harmless, defend and indemnify and its employees, directors, agents and representatives against any and all loss, damage, liability, costs and expenses arising out of or in connection with third party claims relating to use, handling, storage or disposal of the Data. Confidential Information and the Results by Recipient, except to the extent that such loss or damage are attributable to any gross negligent or willful misconduct on the part of WEHI. 8. Recipient agrees in its use of the Data to comply with all applicable international and national laws, statutes, regulations and guidelines. 9. Recipient shall treat all Confidential Information confidential for the duration of this Agreement including any extension thereof and thereafter following termination or expiry of this Agreement. Excluded from this obligation of confidentiality shall be any Confidential Information of which the Recipient can reasonably demonstrate that it (a) was previously known to the Recipient, or (b) is, and/or becomes, publicly available through no fault of Recipient, or (c) is independently and lawfully developed by the Recipient. This obligation of confidentiality shall not apply to any disclosure required by law, provided that receiving Party shall notify WEHI of any disclosure required by law in sufficient time so that WEHI may contest such requirement, if WEHI so chooses. Recipient agrees to use the same level of care in safeguarding Confidential Information that is used with Recipient’s own confidential information of a similar nature, but in no event less than reasonable care. Should Recipient become aware of any unauthorised disclosure of confidential Information, Recipient shall notify WEHI within 5 (five) days of becoming aware of such disclosure. At any time upon the request of WEHI all tangible expressions, in any media, of Confidential Information shall be delivered to WEHI, or at WEHI's option, destroyed. 10. Recipient shall indemnify and hold harmless WEHI, its affiliates, and each of their respective officers, director and employees (collectively, the “WEHI Indemnitees") from and against any and all costs, charges, damages, expenses, fees (including, without limitation reasonable attorneys’ fees) and losses (including, without limitation fees and costs incurred in recovering the same) incurred by any WEHI Indemnitee that arises from Supplier's negligence or willful misconduct related to WEHI Confidential Information or a breach by Recipient. 11. Subject to clause 9 and the prior publication of WEHI’s first paper disclosing use of the Data, Recipient will be free to publish and disclose the Results and will acknowledge WEHI in any publication, including citing the original publication of the dataset. Recipient agrees to submit the proposed disclosure to WEHI for review at least thirty (30) days prior to the scheduled submission for publication or disclosure. If WEHI believes that the publication or disclosure contains Confidential Information, WEHI has the right to request to postpone the publication for up to sixty (60) days from the date of submission of the documents to WEHI. Any such Confidential Information will be removed from the publication or disclosure. WEHI also has the right to provide comments on the manuscript and both Parties shall discuss in good faith to incorporate such comments in the publication or disclosure.
 11. This Agreement will become effective on the Effective Date and will terminate one (1) year after the Effective Date. Parties can terminate this Agreement by giving a one (1) month prior written notice. Any clauses that will be expected or intended by its nature to survive the termination or the expiration of this Agreement, shall survive the termination or the expiration of this Agreement. Upon expiration or termination of this Agreement, the right to use the Data and Confidential Information will automatically end and Recipient will return or, at WEHI’s option, destroy all data received from WEHI. Upon request from WEHI, Recipient shall confirm in writing the complete deletion of such Data and Confidential Information. 12. This Agreement will be construed, governed, interpreted and enforced according to the laws of Victoria. All disputes arising out of or in relation to this agreement will be brought before the competent court in Victoria. 13. This Agreement will be binding upon and inure to the benefit of the respective successors and assignees of the parties hereto. However, Recipient may not assign this Agreement in whole or in part without the prior written consent of WEHI. 14. This Agreement represents this entire Agreement among the Parties with respect to the subject matter hereof, and may only be altered or amended by an instrument in writing signed by all of the Parties. 15. If any portion of this Agreement is in violation of any applicable regulation, or is unenforceable or void for any reason whatsoever, such portion will be inoperative and the remainder of this Agreement will be binding upon the parties. Recipient represents that there are no agreements with any third party that might affect its ability to meet any of Recipient’s obligations under this Agreement. 16. Both Parties acknowledge that the signatories to this Agreement are authorised representatives of each of the Parties and legally authorised to sign this Agreement. 17. If the lawful performance of any part of this Agreement by a Party is rendered impossible by or as a result of any cause beyond such Party's reasonable control, such Party will not be considered in breach hereof as a result of failing so to perform. 18. In case of disputes where this Agreement does not provide a decisive answer, the Parties will consult each other before taking legal action. Agreed, executed and effective as of this [●] day of [●] Month, [●]Year, by: Organisation: Address: Authorised Official: Title: Signature: Date: Please return an executed copy of this Agreement to the Business Development Office of WEHI per busdev@wehi.edu.au with a copy to diggle@wehi.edu.au. The WEHI will be maintaining signed originals and the list of signatory organisations. ** ANNEX I Description of the DATA Sequencing data derived from samples taken from two individuals with MBD4-deficient AML., designated WEHI-AML-1 and WEHI-AML-2 deposited at EGA [EGAS00001002581]. In total samples were taken at 7 time points for WEHI-AML-1, and at 3 time points for WEHI-AML-2. These samples were analysed by whole genome sequencing (4), whole exome sequencing (9), reduced representation bisulphite sequencing (7) and RNA sequencing (9). ** ANNEX II Title project: Primary location project: Completion Date of the Project: xx/xx/xxxx Research plan (a brief description, confirming the research is focused on haematological malignancy): Evidence of ethical approval: Information Technolgy: The recipient confirms that they have the necessary research and information technology (IT) infrastructure in place to ensure appropriate data security policies and procedures are in place. …………………………………………………………………… Head of IT - Signature …………………………………………………………………. Head of IT - Name and Title References:

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
EGAS00001002581 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
EGAF00001726266 bam 3.7 GB
EGAF00001726267 bai 4.4 MB
EGAF00001726268 bam 3.9 GB
EGAF00001726269 bai 4.4 MB
EGAF00001726274 bam 2.9 GB
EGAF00001726275 bai 4.3 MB
EGAF00001726284 bam 3.7 GB
EGAF00001726285 bai 4.4 MB
EGAF00001726296 bam 3.5 GB
EGAF00001726297 bai 4.4 MB
EGAF00001726306 bam 4.6 GB
EGAF00001726307 bai 4.5 MB
EGAF00001726314 bam 4.4 GB
EGAF00001726315 bai 4.6 MB
14 Files (26.9 GB)