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Whole exome sequencing (WES) of 95 previously untreated AML samples

MNC were isolated from bone of 95 AML patients at initial diagnosis via Ficoll gradient. WES has been performed on all 95 samples. Paired exome sequencing was done on a NovaSeq 6000 sequencer with Twist human core exome plus kit.

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Transfer agreement of DKFZ for the data "Whole exome sequencing (WES) of previously untreated AML samples"

Data Transfer Agreement of Human Genomic Data for Research Purposes Between: (1) Deutsches Krebsforschungszentrum (DKFZ), Stiftung des öffentlichen Rechts, legally represented by its Management Board , Prof. Dr. med. Michael Baumann and Ursula Weyrich Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany (“PROVIDER“) and (2) [INSERT INSTITUTION DETAILS] (“RECIPIENT”). 1 Preamble Public genetic sequence databases are a critical part of our academic biomedical research infrastructure. However, human genetic data should only be made public if we can adequately protect the privacy of research subjects. Individual genomic sequence data are sensitive patient data and any attempt to re-identify such data is forbidden under any circumstances. Our efforts to understand disease susceptibility or therapeutic opportunity require access to large genomic data sets. Therefore, the special privacy challenges posed by genomic data are addressed by PROVIDER with this Agreement. In response to the RECIPIENT's request for access to the DATA (as defined below), PROVIDER and the RECIPIENT agree as follows: 2 Definitions “DATA” shall mean all and any human genetic data obtained by the RECIPIENT from the PROVIDER including the Data Subjects’ e.g. age, sex and tumor pathology (as listed in Annex 2). For the avoidance of doubt, Data does not include samples or biological materials; “DATA SUBJECT” shall mean the person (irrespective of the state of health) to whom Data refers and who has been informed of the purpose for which the Data is held and has given his/her informed consent thereto; “COMMERCIAL PURPOSES” shall mean the sale, lease, license, or other transfer and/or the use of the DATA to and/or by a for-profit organization. However, industrially sponsored academic research shall not be considered a use of the DATA for Commercial Purposes per se. “INTELLECTUAL PROPERTY” shall mean (i) patents, designs, trademarks and trade names (whether registered or unregistered), copyright and related rights, database rights, know-how and confidential information; (ii) all other intellectual property rights and similar or equivalent rights (whether registered or unregistered and whether registrable or unregistrable) anywhere in the world which currently exist or are recognized in the future; and (iii) applications, extensions and renewals in relation to any such rights; “RECIPIENT SCIENTIST” shall mean a researcher (or an individual conducting Research under the supervision of a researcher) that is employed by the RECIPIENT and is bound by confidentiality and non-use obligations in respect of DATA and who has accepted the terms of this Agreement in writing (however, for the avoidance of doubt, without being a party to this Agreement) and has received acknowledgement of its acceptance. For the avoidance of doubt and without having explicitly accepted the terms of this Agreement in writing, “RECIPIENT SCIENTIST” may also include any other RECIPIENT’s employees, students, visiting academics, contractors, sub-contractors or independent consultants provided that any of such latter individuals is bound by confidentiality and non- use obligations no less onerous than those binding the RECIPIENT’s employees; “RESEARCH” shall mean research that is seeking to advance the understanding and treatment of cancer and closely related diseases, and work on statistical methods that may be applied to such research; “PROJECT” shall mean a detailed description as in Annex 3; 3 Purpose of the Project The RECIPIENT agrees to use DATA only for RESEARCH as described in the purpose of the PROJECT (Annex 3). 4 Confidentiality The RECIPIENT agrees to preserve, at all times, the confidentiality of DATA pertaining to DATA SUBJECTs. In particular, the RECIPIENT undertakes not to use, or attempt to use the DATA to deliberately compromise or otherwise infringe the confidentiality of information on DATA SUBJECTs and their respective rights to privacy. 5 DATA Protection The Recipient and its RECIPIENT SCIENTIST are covered by and the RECIPIENT shall, and shall procure that its RECIPIENT SCIENTISTS shall, comply with the obligations contained in the applicable German and EU data protection laws and regulations as amended from time to time. In particular, the RECIPIENT and its RECIPIENT SCIENTISTs inter alia understands, and shall procure that its RECIPIENT SCIENTISTs understand, their duties under the German and EU legislation in relation to the handling of DATA and the rights of DATA SUBJECTs. The RECIPIENT agrees that it, and its RECIPIENT SCIENTISTs, shall not analyze or make any use of the DATA in such a way that has the potential to: a) lead to the re-identification of any DATA SUBJECT; or b) compromise the anonymity of any DATA SUBJECT in any way. The RECIPIENT shall, and it shall procure that its RECIPIENT SCIENTISTS shall, adhere to the principles of IT-Security as set forth in Annex 1 hereto. 6 Access and Governance The RECIPIENT agrees that it shall take all (commercially) reasonable security precautions to keep the DATA confidential, such precautions to be no less onerous than in the applicable German and EU data protection laws and regulations. The RECIPIENT agrees to use the DATA solely for RESEARCH in the frame of the purpose of the PROJECT. The RECIPIENT agrees that the DATA shall not be distributed or released to any other location and/or to any other person other than RECIPIENT SCIENTISTs or laboratory personnel under the RECIPIENT SCIENTISTs direct supervision. RECIPIENT does not have the right to sublicense the DATA. RECIPIENT shall inform PROVIDER about any third party requests for the DATA. PROVIDER reserves the right to request and inspect DATA security and management documentation at the RECIPIENT’s premises to ensure the adequacy of DATA protection measures with prior notice during the RECIPIENT’s ordinary working hours. DATA shall not be used for COMMERCIAL PURPOSES (e.g. diagnostic services). In case of intended commercial use of DATA, the RECIPIENT shall start negotiations in good faith leading to a fair market compensation of PROVIDER. Such a disclosure of DATA shall require a binding declaration of consent in writing from the person concerned. 7 Errors The RECIPIENT agrees to notify the PROVIDER of any errors detected in the DATA without undue delay. 8 DATA reissue The RECIPIENT accepts that PROVIDER will reissue DATA from time to time, with suitable versioning. If DATA is reissued at the request of the DATA SUBJECT and/or as the result of other ethical scrutiny, the RECIPIENT agrees to destroy all earlier versions of the DATA without undue delay once he has received such information. This shall not apply to the extent that DATA is saved in automatic back-up systems for which destruction shall follow the regular process of such back-up system, however, such DATA shall be eliminated within a period of four (4) weeks after reception of the respective request to do so or within a period of four (4) weeks upon termination in accordance with this Agreement. 9 INTELLECTUAL PROPERTY The RECIPIENT recognizes that nothing in this Agreement shall operate to transfer to the RECIPIENT or its RECIPIENT SCIENTISTs any INTELLECTUAL PROPERTY rights in or relating to the DATA, i.e. ownership of DATA remains unchanged. The RECIPIENT does not have the right to sublicense the DATA. The RECIPIENT shall inform PROVIDER about any third party requests for the DATA. In case the RECIPIENT and its RECIPIENT SCIENTISTs develops INTELLECTUAL PROPERTY based on or related to DATA as set forth in this Agreement the RECIPIENT shall become owner of such results. The RECIPIENT will inform PROVIDER about all developed INTELLECTUAL PROPERTY based on or related to DATA as set forth in this Agreement without undue delay in writing. The RECIPIENT grants PROVIDER a non-exclusive, non-transferable, royalty-free, perpetual, non-sublicensable right to use such developed INTELLECTUAL PROPERTY for internal research purposes including collaborations with any third parties excluding any COMMERCIAL PURPOSES. 10 Publications The RECIPIENT agrees to acknowledge in any RECIPIENT’s work based in whole or part on the DATA, any PROVIDER publications which encompass and from which DATA derive, the respective version of the DATA obtained, and the role of PROVIDER. The RECIPIENT is also entitled to release publications and, in doing so, agrees to acknowledge any of PROVIDER’s work based in whole or part on the DATA in its publication. The RECIPIENT will also declare in any such work that PROVIDER and its employees bear no responsibility for the further analysis or interpretation of the DATA by the RECIPIENT. 11 Violation/Termination of Agreement This Agreement shall expire automatically three (3) years after its signature by both parties. This Agreement will terminate immediately upon any material breach of a provision of this Agreement. The RECIPIENT accepts that the changing ethical framework of human genetic research may lead to: (i) alteration to the provisions of this Agreement, in which case the RECIPIENT may accept such alterations or terminate this Agreement; or (ii) the withdrawal of this Agreement in extreme circumstances. Either party shall have the right to terminate this Agreement with immediate effect upon giving written notice of termination to the other party. In the event that this Agreement is expired the RECIPIENT is required to destroy/discard any Data held, including but not limited to copies and backup copies. This shall not apply to the extent that DATA is saved in automatic back-up systems for which destruction shall follow the regular process of such back-up system, however, such DATA shall be eliminated within a period of four (4) weeks after the date of termination. Upon request of PROVIDER, the RECIPIENT will certify the destruction of the DATA. Sections 4, 5, 9 and 10 of this Agreement remain in full force and effect in case of termination. Notwithstanding the aforementioned, any provision of this Agreement related to confidentiality and/or DATA protection shall survive the expiration of this Agreement to the extent applicable statutory law provides for a deviating period of validity and effectiveness. Nothing contained in this paragraph shall restrict the right of the PROVIDER to seek injunctive relief to prevent any breach or threatened breach of this agreement, furthermore nothing contained in this paragraph shall prohibit the PROVIDER from pursuing any other remedies available to it for such breach or threatened breach, including the recovery of damages from RECIPIENT. 12 Costs The RECIPIENT acknowledges that PROVIDER shall incur costs in providing the DATA to the RECIPIENT, including but not limited to administrative costs and the cost of obtaining appropriate data storage devices. The RECIPIENT agrees to pay, at the request of PROVIDER, such reasonable costs as PROVIDER may incur in providing the DATA, within thirty (30) days after having received an invoice by PROVIDER consistent with the current provisions of the German VAT Act (Umsatzsteuergesetz - UStG) as amended from time to time. 13 Legal statement The RECIPIENT acknowledges that PROVIDER and all other parties involved in the creation, funding or protection of the DATA: a) make no warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of the DATA; and b) Except to the extent prohibited by law, the RECIPIENT assumes all liability for damages which may arise from its use, storage or disposal of the DATA. PROVIDER will not be liable to the RECIPIENT for any loss, claim or demand made by the RECIPIENT, or made against the RECIPIENT by any other party, due to or arising from the use of the data by the RECIPIENT, except to the extent permitted by law when caused by the gross negligence or willful misconduct of PROVIDER. The RECIPIENT understands that all the DATA are protected by INTELLECTUAL PROPERTY rights, such that duplication or sale of all of or part of the DATA on any media is not permitted under any circumstances, except with the prior written consent of PROVIDER. In no event shall PROVIDER be liable for any use by RECIPIENT of the PROVIDER DATA or any loss, claim, damage or liability, of whatsoever kind of nature, which may arise from or in connection with this agreement or the use, handling or storage of the PROVIDER DATA or derived from PROVIDER DATA by the RECIPIENT. 14 Governing Law This Agreement (and any dispute, controversy, proceedings or claim of whatever nature arising out of this Agreement or its formation) shall be construed, interpreted and governed by the laws of Germany excluding its conflict of law rules and shall be subject to the exclusive jurisdiction of the competent courts in Mannheim. PROVIDER complies with the requirements of the applicable German (LDSG) and EU data protection laws and regulations with regard to the collection, storage, processing and disclosure of personal information and is committed to upholding the Act's core data protection principles.

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
EGAS00001007223 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
EGAF00008065647 fastq.gz 4.7 GB
EGAF00008065648 fastq.gz 4.9 GB
EGAF00008065649 fastq.gz 4.8 GB
EGAF00008065650 fastq.gz 5.2 GB
EGAF00008065651 fastq.gz 4.5 GB
EGAF00008065652 fastq.gz 4.8 GB
EGAF00008065653 fastq.gz 3.6 GB
EGAF00008065654 fastq.gz 3.9 GB
EGAF00008065655 fastq.gz 3.4 GB
EGAF00008065656 fastq.gz 3.7 GB
EGAF00008065657 fastq.gz 2.1 GB
EGAF00008065658 fastq.gz 2.3 GB
EGAF00008065659 fastq.gz 2.7 GB
EGAF00008065660 fastq.gz 2.9 GB
EGAF00008065661 fastq.gz 2.7 GB
EGAF00008065662 fastq.gz 3.0 GB
EGAF00008065663 fastq.gz 7.3 GB
EGAF00008065664 fastq.gz 7.7 GB
EGAF00008065665 fastq.gz 2.5 GB
EGAF00008065666 fastq.gz 2.6 GB
EGAF00008065667 fastq.gz 3.8 GB
EGAF00008065668 fastq.gz 4.1 GB
EGAF00008065669 fastq.gz 3.2 GB
EGAF00008065670 fastq.gz 3.4 GB
EGAF00008065671 fastq.gz 3.0 GB
EGAF00008065672 fastq.gz 3.2 GB
EGAF00008065673 fastq.gz 4.3 GB
EGAF00008065674 fastq.gz 4.5 GB
EGAF00008065675 fastq.gz 4.0 GB
EGAF00008065676 fastq.gz 4.2 GB
EGAF00008065677 fastq.gz 4.5 GB
EGAF00008065678 fastq.gz 4.7 GB
EGAF00008065679 fastq.gz 3.7 GB
EGAF00008065680 fastq.gz 3.9 GB
EGAF00008065681 fastq.gz 3.3 GB
EGAF00008065682 fastq.gz 3.5 GB
EGAF00008065683 fastq.gz 2.4 GB
EGAF00008065684 fastq.gz 2.6 GB
EGAF00008065685 fastq.gz 6.8 GB
EGAF00008065686 fastq.gz 7.3 GB
EGAF00008065687 fastq.gz 4.5 GB
EGAF00008065688 fastq.gz 4.8 GB
EGAF00008065689 fastq.gz 2.6 GB
EGAF00008065690 fastq.gz 2.8 GB
EGAF00008065691 fastq.gz 2.3 GB
EGAF00008065692 fastq.gz 2.5 GB
EGAF00008065693 fastq.gz 6.2 GB
EGAF00008065694 fastq.gz 6.5 GB
EGAF00008065695 fastq.gz 2.3 GB
EGAF00008065696 fastq.gz 2.4 GB
EGAF00008065697 fastq.gz 2.4 GB
EGAF00008065698 fastq.gz 2.5 GB
EGAF00008065699 fastq.gz 3.3 GB
EGAF00008065700 fastq.gz 3.5 GB
EGAF00008065701 fastq.gz 4.2 GB
EGAF00008065702 fastq.gz 4.4 GB
EGAF00008065703 fastq.gz 3.3 GB
EGAF00008065704 fastq.gz 3.5 GB
EGAF00008065705 fastq.gz 3.8 GB
EGAF00008065706 fastq.gz 4.1 GB
EGAF00008065707 fastq.gz 5.6 GB
EGAF00008065708 fastq.gz 6.0 GB
EGAF00008065709 fastq.gz 3.4 GB
EGAF00008065710 fastq.gz 3.7 GB
EGAF00008065711 fastq.gz 2.9 GB
EGAF00008065712 fastq.gz 3.0 GB
EGAF00008065713 fastq.gz 2.5 GB
EGAF00008065714 fastq.gz 2.7 GB
EGAF00008065715 fastq.gz 3.1 GB
EGAF00008065716 fastq.gz 3.2 GB
EGAF00008065717 fastq.gz 3.5 GB
EGAF00008065718 fastq.gz 3.7 GB
EGAF00008065719 fastq.gz 2.8 GB
EGAF00008065720 fastq.gz 2.9 GB
EGAF00008065721 fastq.gz 5.0 GB
EGAF00008065722 fastq.gz 5.5 GB
EGAF00008065723 fastq.gz 3.0 GB
EGAF00008065724 fastq.gz 3.1 GB
EGAF00008065725 fastq.gz 3.6 GB
EGAF00008065726 fastq.gz 3.8 GB
EGAF00008065727 fastq.gz 3.0 GB
EGAF00008065728 fastq.gz 3.3 GB
EGAF00008065729 fastq.gz 2.5 GB
EGAF00008065730 fastq.gz 2.7 GB
EGAF00008065731 fastq.gz 3.6 GB
EGAF00008065732 fastq.gz 3.9 GB
EGAF00008065733 fastq.gz 3.6 GB
EGAF00008065734 fastq.gz 3.9 GB
EGAF00008065735 fastq.gz 2.5 GB
EGAF00008065736 fastq.gz 2.7 GB
EGAF00008065737 fastq.gz 4.1 GB
EGAF00008065738 fastq.gz 4.3 GB
EGAF00008065739 fastq.gz 3.0 GB
EGAF00008065740 fastq.gz 3.2 GB
EGAF00008065741 fastq.gz 3.4 GB
EGAF00008065742 fastq.gz 3.7 GB
EGAF00008065743 fastq.gz 3.9 GB
EGAF00008065744 fastq.gz 4.2 GB
EGAF00008065745 fastq.gz 3.4 GB
EGAF00008065746 fastq.gz 3.6 GB
EGAF00008065747 fastq.gz 2.2 GB
EGAF00008065748 fastq.gz 2.4 GB
EGAF00008065749 fastq.gz 2.6 GB
EGAF00008065750 fastq.gz 2.8 GB
EGAF00008065751 fastq.gz 4.5 GB
EGAF00008065752 fastq.gz 4.8 GB
EGAF00008065753 fastq.gz 5.6 GB
EGAF00008065754 fastq.gz 6.0 GB
EGAF00008065755 fastq.gz 3.3 GB
EGAF00008065756 fastq.gz 3.5 GB
EGAF00008065757 fastq.gz 3.0 GB
EGAF00008065758 fastq.gz 3.1 GB
EGAF00008065759 fastq.gz 2.7 GB
EGAF00008065760 fastq.gz 2.8 GB
EGAF00008065761 fastq.gz 3.1 GB
EGAF00008065762 fastq.gz 3.3 GB
EGAF00008065763 fastq.gz 2.4 GB
EGAF00008065764 fastq.gz 2.6 GB
EGAF00008065765 fastq.gz 2.5 GB
EGAF00008065766 fastq.gz 2.7 GB
EGAF00008065767 fastq.gz 4.6 GB
EGAF00008065768 fastq.gz 4.9 GB
EGAF00008065769 fastq.gz 3.6 GB
EGAF00008065770 fastq.gz 3.9 GB
EGAF00008065771 fastq.gz 2.6 GB
EGAF00008065772 fastq.gz 2.9 GB
EGAF00008065773 fastq.gz 4.8 GB
EGAF00008065774 fastq.gz 5.2 GB
EGAF00008065775 fastq.gz 3.9 GB
EGAF00008065776 fastq.gz 4.1 GB
EGAF00008065777 fastq.gz 3.6 GB
EGAF00008065778 fastq.gz 3.8 GB
EGAF00008065779 fastq.gz 4.0 GB
EGAF00008065780 fastq.gz 4.3 GB
EGAF00008065781 fastq.gz 2.8 GB
EGAF00008065782 fastq.gz 3.0 GB
EGAF00008065783 fastq.gz 3.2 GB
EGAF00008065784 fastq.gz 3.4 GB
EGAF00008065785 fastq.gz 4.0 GB
EGAF00008065786 fastq.gz 4.3 GB
EGAF00008065787 fastq.gz 4.9 GB
EGAF00008065788 fastq.gz 5.2 GB
EGAF00008065789 fastq.gz 2.8 GB
EGAF00008065790 fastq.gz 3.1 GB
EGAF00008065791 fastq.gz 2.3 GB
EGAF00008065792 fastq.gz 2.4 GB
EGAF00008065793 fastq.gz 2.4 GB
EGAF00008065794 fastq.gz 2.5 GB
EGAF00008065795 fastq.gz 5.8 GB
EGAF00008065796 fastq.gz 6.2 GB
EGAF00008065797 fastq.gz 2.5 GB
EGAF00008065798 fastq.gz 2.6 GB
EGAF00008065799 fastq.gz 2.9 GB
EGAF00008065800 fastq.gz 3.0 GB
EGAF00008065801 fastq.gz 4.3 GB
EGAF00008065802 fastq.gz 4.7 GB
EGAF00008065803 fastq.gz 2.7 GB
EGAF00008065804 fastq.gz 2.8 GB
EGAF00008065805 fastq.gz 3.8 GB
EGAF00008065806 fastq.gz 4.0 GB
EGAF00008065807 fastq.gz 3.0 GB
EGAF00008065808 fastq.gz 3.2 GB
EGAF00008065809 fastq.gz 4.8 GB
EGAF00008065810 fastq.gz 5.2 GB
EGAF00008065811 fastq.gz 4.3 GB
EGAF00008065812 fastq.gz 4.7 GB
EGAF00008065813 fastq.gz 2.9 GB
EGAF00008065814 fastq.gz 3.1 GB
EGAF00008065815 fastq.gz 4.1 GB
EGAF00008065816 fastq.gz 4.3 GB
EGAF00008065817 fastq.gz 2.7 GB
EGAF00008065818 fastq.gz 2.9 GB
EGAF00008065819 fastq.gz 3.2 GB
EGAF00008065820 fastq.gz 3.5 GB
EGAF00008065821 fastq.gz 3.0 GB
EGAF00008065822 fastq.gz 3.3 GB
EGAF00008065823 fastq.gz 2.4 GB
EGAF00008065824 fastq.gz 2.6 GB
EGAF00008065825 fastq.gz 2.9 GB
EGAF00008065826 fastq.gz 3.0 GB
EGAF00008065827 fastq.gz 2.5 GB
EGAF00008065828 fastq.gz 2.7 GB
EGAF00008065829 fastq.gz 2.5 GB
EGAF00008065830 fastq.gz 2.7 GB
EGAF00008065831 fastq.gz 2.4 GB
EGAF00008065832 fastq.gz 2.5 GB
EGAF00008065833 fastq.gz 2.7 GB
EGAF00008065834 fastq.gz 2.8 GB
EGAF00008065835 fastq.gz 2.5 GB
EGAF00008065836 fastq.gz 2.6 GB
190 Files (681.7 GB)