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Low-coverage Whole Genome Sequencing, Colorectal adenomas, NKI-AvL TGO series Stool-Proteomics

For this tissue dataset, we applied low-pass whole genome sequencing to 98 non-advanced and advanced adenomas. As small number of lesions was sequenced multiple times, this dataset consists of 103 fastq files. These adenomas were classified as lesions with low-risk or high-risk of progression, according to the presence of specific DNA copy number changes (Carvalho et al, CancerPrevRes, 2018).

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DATA TRANSFER AGREEMENT NKI-AvL TGO DAC

DATA TRANSFER AGREEMENT This agreement (hereinafter referred to as “Agreement”) is made and entered by and between: Stichting Het Nederlands Kanker Instituut – Antoni van Leeuwenhoek Ziekenhuis having its principle office at Plesmanlaan 121, 1066 CX Amsterdam represented by its legal representative, Dr. Koen Verhoef, hereinafter referred to as “NKI-AVL”; and XXXXXXXXXXXXXX having its principle office at xxxxxxxxxxxxxxxxxxxxxx, represented by its legal representative, xxxxxxxxxxxxx, hereinafter referred to as “Recipient”. Hereinafter jointly referred to as “Parties” and individually as “Party”; WHEREAS a) NKI-AVL is the custodian of the (xxxxxxxxxxxxxxxxxxxx) coded patient data set (“Data”) specified in Annex I to this Agreement; b) Recipient, has requested NKI-AVL, through Dr. xxxxxxxxxxxxx, hereinafter referred to as “NKI-AVL’s Scientist”, 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; c) NKI-AVL 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 I to this Agreement. Confidential Information means all information, know-how, data and experience of NKI-AVL regarding the Data, its characteristics, NKI-AVL’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 under the custodianship of the of NKI-AVL and is made available 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 NKI-AVL. 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. As the Data is coded, this will be regarded as personal data and Recipient shall safeguard the Data received with a degree of care which is no less than NKI-AVL uses to protect such Data, but always in compliance with the applicable data privacy laws and regulations. Any accidental or unauthorised access to the Data or loss of Data must be reported to NKI-AVL immediately, and Parties agree that NKI-AVL will be the party to contact the supervisory authority and the patients concerned in accordance with the applicable data privacy law and regulations. 4. The Data is collected in accordance with the informed consent form (ICF) and/or the applicable (Dutch and international) 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 NKI-AVL to destroy their data. In the event a patient files such a request with NKI-AVL, Recipient shall – upon first request by NKI-AVL - promptly destroy the Data in an approved manner. Any Results (defined in article 5) already obtained through the use of the Data shall remain at the disposal of Recipient. 5. The Results shall be owned by the NKI-AVL and the Recipient, and Recipient shall keep NKI-AVL’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 NKI-AVL 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 NKI-AVL 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 NKI-AVL. 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 NKI-AVL. 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 for a period of five (5) years 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 during said five (5) year period 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 the NKI-AVL of any disclosure required by law in sufficient time so that the NKI-AVL may contest such requirement, if NKI-AVL so chooses. 10. Recipient will be free to publish and disclose the Results but agrees to submit the proposed disclosure to NKI-AVL for review at least thirty (30) days prior to the scheduled submission for publication or disclosure. If NKI-AVL believes that the publication or disclosure contains information of NKI-AVL, NKI-AVL has the right to request to postpone the publication for up to sixty (60) days from the date of submission of the documents to NKI-AVL. After sixty (60) days the publication is permitted. All publications will acknowledge the NKI-AVL and the NKI-AVL Scientist. 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 destroy all data received from NKI-AVL. Upon request from NKI-AVL, 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 The Netherlands. All disputes arising out of or in relation to this agreement will be brought before the competent court in Amsterdam, The Netherlands. 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 the NKI-AVL. 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 authorized representatives of each of the Parties and legally authorized 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. IN WITNESS WHEREOF, the parties have executed this Agreement, in duplicate originals, as of the Effective Date. For RECIPIENT, By:______________________________________ Xxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxx Date:__________________ For NKI-AVL, By:______________________________________ Dr. Koen Verhoef Manager Technology Transfer Office NKI-AVL Date:__________________ For NKI-AVL's Scientist By:______________________________________ Date:__________________ ANNEX I Description of the DATA (EGA study and dataset accession numbers) ANNEX II Title project: Completion Date of the Project: Xx/xx/xxxx Summary: Description: Primary location project: 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
EGAS00001002953 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
EGAF00001993546 fastq.gz 646.4 MB
EGAF00001993547 fastq.gz 349.6 MB
EGAF00001993548 fastq.gz 467.8 MB
EGAF00001993549 fastq.gz 642.5 MB
EGAF00001993550 fastq.gz 342.6 MB
EGAF00001993551 fastq.gz 490.8 MB
EGAF00001993552 fastq.gz 472.0 MB
EGAF00001993553 fastq.gz 591.5 MB
EGAF00001993554 fastq.gz 296.0 MB
EGAF00001993555 fastq.gz 281.5 MB
EGAF00001993556 fastq.gz 244.1 MB
EGAF00001993557 fastq.gz 339.5 MB
EGAF00001993558 fastq.gz 531.6 MB
EGAF00001993559 fastq.gz 155.8 MB
EGAF00001993560 fastq.gz 345.7 MB
EGAF00001993561 fastq.gz 117.8 MB
EGAF00001993562 fastq.gz 430.8 MB
EGAF00001993563 fastq.gz 260.9 MB
EGAF00001993564 fastq.gz 524.5 MB
EGAF00001993565 fastq.gz 422.1 MB
EGAF00001993566 fastq.gz 471.7 MB
EGAF00001993567 fastq.gz 212.3 MB
EGAF00001993568 fastq.gz 346.7 MB
EGAF00001993569 fastq.gz 451.3 MB
EGAF00001993570 fastq.gz 310.1 MB
EGAF00001993571 fastq.gz 286.8 MB
EGAF00001993572 fastq.gz 344.2 MB
EGAF00001993573 fastq.gz 360.7 MB
EGAF00001993574 fastq.gz 302.4 MB
EGAF00001993575 fastq.gz 385.2 MB
EGAF00001993576 fastq.gz 524.4 MB
EGAF00001993577 fastq.gz 305.6 MB
EGAF00001993578 fastq.gz 502.1 MB
EGAF00001993579 fastq.gz 257.1 MB
EGAF00001993580 fastq.gz 532.4 MB
EGAF00001993581 fastq.gz 592.8 MB
EGAF00001993582 fastq.gz 328.2 MB
EGAF00001993583 fastq.gz 326.7 MB
EGAF00001993584 fastq.gz 195.3 MB
EGAF00001993585 fastq.gz 335.7 MB
EGAF00001993586 fastq.gz 208.1 MB
EGAF00001993587 fastq.gz 394.5 MB
EGAF00001993588 fastq.gz 607.0 MB
EGAF00001993589 fastq.gz 249.0 MB
EGAF00001993590 fastq.gz 307.8 MB
EGAF00001993591 fastq.gz 255.5 MB
EGAF00001993592 fastq.gz 520.2 MB
EGAF00001993593 fastq.gz 206.0 MB
EGAF00001993594 fastq.gz 557.8 MB
EGAF00001993595 fastq.gz 193.5 MB
EGAF00001993596 fastq.gz 243.3 MB
EGAF00001993597 fastq.gz 280.8 MB
EGAF00001993598 fastq.gz 257.4 MB
EGAF00001993599 fastq.gz 441.0 MB
EGAF00001993600 fastq.gz 156.2 MB
EGAF00001993601 fastq.gz 337.2 MB
EGAF00001993602 fastq.gz 218.3 MB
EGAF00001993603 fastq.gz 273.4 MB
EGAF00001993604 fastq.gz 139.7 MB
EGAF00001993605 fastq.gz 410.2 MB
EGAF00001993606 fastq.gz 323.2 MB
EGAF00001993607 fastq.gz 392.6 MB
EGAF00001993608 fastq.gz 207.6 MB
EGAF00001993609 fastq.gz 235.4 MB
EGAF00001993610 fastq.gz 560.1 MB
EGAF00001993611 fastq.gz 637.5 MB
EGAF00001993612 fastq.gz 285.9 MB
EGAF00001993613 fastq.gz 269.6 MB
EGAF00001993614 fastq.gz 528.0 MB
EGAF00001993615 fastq.gz 281.8 MB
EGAF00001993616 fastq.gz 235.5 MB
EGAF00001993617 fastq.gz 264.8 MB
EGAF00001993618 fastq.gz 250.2 MB
EGAF00001993619 fastq.gz 486.2 MB
EGAF00001993620 fastq.gz 335.9 MB
EGAF00001993621 fastq.gz 352.9 MB
EGAF00001993622 fastq.gz 362.7 MB
EGAF00001993623 fastq.gz 295.5 MB
EGAF00001993624 fastq.gz 372.1 MB
EGAF00001993625 fastq.gz 427.6 MB
EGAF00001993626 fastq.gz 449.6 MB
EGAF00001993627 fastq.gz 176.9 MB
EGAF00001993628 fastq.gz 535.1 MB
EGAF00001993629 fastq.gz 294.5 MB
EGAF00001993630 fastq.gz 370.2 MB
EGAF00001993631 fastq.gz 307.3 MB
EGAF00001993632 fastq.gz 336.7 MB
EGAF00001993633 fastq.gz 292.7 MB
EGAF00001993634 fastq.gz 461.5 MB
EGAF00001993635 fastq.gz 262.3 MB
EGAF00001993636 fastq.gz 443.7 MB
EGAF00001993637 fastq.gz 410.5 MB
EGAF00001993638 fastq.gz 258.1 MB
EGAF00001993639 fastq.gz 591.6 MB
EGAF00001993640 fastq.gz 635.4 MB
EGAF00001993641 fastq.gz 542.1 MB
EGAF00001993642 fastq.gz 506.3 MB
EGAF00001993643 fastq.gz 584.6 MB
EGAF00001993644 fastq.gz 361.8 MB
EGAF00001993645 fastq.gz 489.9 MB
EGAF00001993646 fastq.gz 330.2 MB
EGAF00001993647 fastq.gz 155.1 MB
EGAF00001993648 fastq.gz 400.8 MB
103 Files (37.9 GB)