Exome sequencing of matching primary tumor and venous tumor thrombus (VTT) renal cell carcinoma (RCC) samples
We performed multiregion whole exome sequencing of a total of 37 samples from five consecutive patients (normal tissue, n=5; primary tumors, n=16; tumor thrombi, n=16) to >35-fold target coverage. Matching primary tumor and venous tumor thrombus samples were analyzed. Four patients had a clear cell RCC, one patient had a poorly differentiated type II papillary RCC (RCC-VTT-04). The latter patient had a friable thrombus, the others were of solid consistency.
- 37 samples
- DAC: EGAC00001000470
- Technology: Illumina HiSeq 2500
- GRU-CC DUO:0000005 (version: 2019-01-07)general research use and clinical careThis data use limitation indicates that use is allowed for health/medical/biomedical purposes and other biological research, including the study of population origins or ancestry.
- RU DUO:0000014 (version: 2019-01-07)research use onlyThis data use limitation indicates that use is limited to research purposes (e.g., does not include its use in clinical care).
- NPUNCU DUO:0000018 (version: 2019-01-07)not for profit, non commercial use onlyThis data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use.
- PUB DUO:0000019 (version: 2019-01-07)publication requiredThis data use modifier indicates that requestor agrees to make results of studies using the data available to the larger scientific community.
- COL DUO:0000020 (version: 2019-01-07)collaboration requiredThis data use modifier indicates that the requestor must agree to collaboration with the primary study investigator(s).
- US DUO:0000026 (version: 2019-01-07)user specific restrictionThis data use modifier indicates that use is limited to use by approved users.
- PS DUO:0000027 (version: 2019-01-07)project specific restrictionThis data use modifier indicates that use is limited to use within an approved project.
- IS DUO:0000028 (version: 2019-01-07)institution specific restrictionThis data use modifier indicates that use is limited to use within an approved institution.
- RTN DUO:0000029 (version: 2019-01-07)return to database or resourceThis data use modifier indicates that the requestor must return derived/enriched data to the database/resource.
Data Access Agreement MUO
Human genetic data access agreement for institutionsBetween:(1) The Section of Molecular Urooncology ("MUO") of the Department of Urology of the University of Heidelberg School of Medicine and(2) [INSERT INSTITUTION DETAILS] (the “Recipient”).In response to the Recipient's request for access to the Data (as defined below), MUOand the Recipient agree as follows:1 Definitions1.1 “Analysis of tumor periphery and center-specific mutations in renal cell carcinoma” shall mean the project undertakenat the MUO to identify genetic sequencevariants and mutations relevant to the development of intratumoral heterogeneity;1.2 “Data” shall mean all and any human genetic data obtained from theMUO including the Data Subjects’ age, sex and tumour pathology. Explicitly,Data does not include samples or biological materials;1.3 “Data Subject” shall mean the person (irrespective of state of health) towhom Data refers and who has been informed of the purpose for which the Datais held and has given his/her informed consent thereto;1.4 “Intellectual Property” means (i) patents, designs, trade marks and tradenames (whether registered or unregistered), copyright and related rights,database rights, know-how and confidential information; (ii) all other intellectualproperty rights and similar or equivalent rights anywhere in the world whichcurrently exist or are recognised in the future; and (iii) applications, extensionsand renewals in relation to any such rights;1.5 “Registered User” shall mean a Researcher (or an individual conductingResearch under the supervision of a Researcher) that is employed by theRecipient and is bound by confidentiality and non-use obligations in respect ofData and who has signed this Agreement and has received acknowledgement ofits acceptance. 1.6 “Research” shall mean research that is seeking to advance theunderstanding and treatment of cancer and closely related diseases, and work onstatistical methods that may be applied to such research;1.7 “Researcher(s)” shall mean an individual or individuals carrying outResearch who:(a) in the case of an individual seeking access to Data heldsolely under the control of MUO, has authored a relevant peer-reviewed article that MUO can locate on PubMed and who is stillworking in the field; or(b) in the case of an individual seeking access to Data held aspart of a wider consortium, is a successful applicant to the consortiumdata access committee.2 Purpose2.1 The Recipient agrees to use Data only for the Research.3 Confidentiality3.1 The Recipient agrees to preserve, at all times, the confidentiality of Datapertaining to identifiable Data Subjects. In particular, the Recipient undertakesnot to use, or attempt to use the Data to deliberately compromise or otherwiseinfringe the confidentiality of information on Data Subjects and their right toprivacy.4 Data Protection4.1 The Recipient agrees that it, and its Registered Users, are covered byand shall comply with the obligations contained in the Data Protection Act 1998as amended from time to time, or equivalent national provisions no less onerousthen those contained in the Data Protection Act. In particular, the Recipient andits Registered Users understand their duties under such legislation in relation tothe handling of Data and the rights of Data Subjects.4.2 The Recipient agrees that it, and its Registered Users, shall not analyseor make any use of the Data in such a way that has the potential to:(a) lead to the identification of any Data Subject; or(b) compromise the anonymity of any Data Subject in anyway.5 Access and Governance5.1 The Recipient agrees that it shall take all reasonable security precautionsto keep the Data confidential, such precautions to be no less onerous than thoseapplied in respect of the Recipient’s own confidential information.5.2 The Recipient agrees to only give access to Data, in whole or part, or anyidentifiable material derived from the Data, to a Registered User. The Recipientagrees that before it gives any Registered User access to Data, it shall first showthe Registered User a copy of this Agreement and shall inform the RegisteredUser that he or she must comply with the obligations contained in this Agreementand sign up to the provisions of this Agreement in the form set out at the end ofthis Agreement. The Recipient shall provide MUO with a copy of the RegisteredUser’s acceptance form within thirty (30) days of the date of acceptance by theRegistered User.5.3 The Recipient agrees that it shall only give Registered Users that are notResearchers (including but not limited to students or new researchers to the field) access to the Data if they are supervised by a Researcher who will takeresponsibility for such Registered Users’ use of the Data.5.4 MUO reserves the right to request and inspect data security andmanagement documentation to ensure the adequacy of data protectionmeasures in countries that have no national laws comparable to that pertaining inthe European Economic Area (EEA).6 Errors6.1 The Recipient agrees to notify the MUO of any errors detected in theData.7 Data reissue7.1 The Recipient accepts that Data will be reissued from time to time, withsuitable versioning. If Data is reissued at the request of sample donors and/or asthe result of other ethical scrutiny, the Recipient agrees to destroy all earlierversions of the Data.8 Intellectual Property8.1 The Recipient recognises that nothing in this Agreement shall operate totransfer to the Recipient or its Registered Users any Intellectual Property rights inor relating to the Data.8.2 The Recipient and its Registered Users shall have the right to developIntellectual Property based on comparisons with their own data.9 Publications9.1 The Recipient agrees to acknowledge in any work based in whole or parton the Data, the published paper from which the Data derives, the version of theData, and the role of the MUO and its funders in its distribution. The Recipientagrees to use the acknowledgement wording provided for the relevant Data in itspublication. The Recipient will also declare in any such work that those whocarried out the original analysis and collection of the Data bear no responsibilityfor the further analysis or interpretation of it by the Recipient.10 Termination of Agreement10.1 This Agreement will terminate immediately upon any breach of theprovisions of this Agreement by the Recipient or by the Recipient’s RegisteredUsers.10.2 The Recipient accepts that the changing ethical framework of humangenetic research may lead to: (i) alteration to the provisions of this Agreement, inwhich case the Recipient may accept such alterations or terminate thisAgreement; or (ii) the withdrawal of this Agreement in extreme circumstances.10.3 Either party shall have the right to terminate this Agreement withimmediate effect upon giving written notice of termination to the other party.10.4 In the event that this Agreement is terminated in accordance with thisClause 10 the Recipient shall return or destroy all Data at the direction of MUO.11 Costs11.1 The Recipient acknowledges that MUO shall incur costs in providing theData to the Recipient, including but not limited to administrative costs and thecost of obtaining appropriate data storage devices. The Recipient agrees to pay,on the request of MUO, such reasonable costs as MUO may incur in providing theData, within thirty (30) days of MUO making such a request for payment.12 Legal statement12.1 The Recipient acknowledges that MUO and all other parties involved inthe creation, funding or protection of the Data:(a) make no warranty or representation, express or implied asto the accuracy, quality or comprehensiveness of the Data; and(b) exclude to the fullest extent permitted by law all liability foractions, claims, proceedings, demands, losses (including but not limited toloss of profit), costs, awards damages and payments made by theRecipient that may arise (whether directly or indirectly) in any waywhatsoever from the Recipient’s use of the Data, or from the unavailabilityof, or break in access to the Data for whatever reason.12.2 The Recipient understands that all the Data is protected by copyright andother intellectual property rights, such that duplication or sale of all of or part ofthe Data on any media is not permitted under any circumstances, except with theprior written consent of MUO.13 Governing Law13.1 This Agreement (and any dispute, controversy, proceedings or claim ofwhatever nature arising out of this Agreement or its formation) shall beconstrued, interpreted and governed by the laws of Germany and shallbe subject to the exclusive jurisdiction of the German courts.AGREED by the parties through their authorised signatoriesMUOAuthorised Signature:Name:Title:Date:Recipient:Recipient Name:Address:Telephone No:Email:Authorised Signature:Name:Title:Date:Registered Users:The Registered Users acknowledge the contents of this Agreement and agree tocomply with the obligations herein. For the avoidance of doubt the RegisteredUsers are not a party to this Agreement.Signature:Name:Title:Date:Email:Signature:Name:Title:Date:Email:Please send completed forms to:Stefan DuensingSection of Molecular UrooncologyUniversity of HeidelbergIm Neuenheimer Feld 517D-69120 Heidelberg, GermanyMUO complies with the requirements of the Data Protection Act 1998 with regard to thecollection, storage, processing and disclosure of personal information and is committedto upholding the Act's core Data Protection Principles.Information collected under the Agreement will be used for the purposes of maintainingthe Agreement, and may be used for statistical reporting.
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 |
---|---|---|
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 | |
---|---|---|---|---|
EGAF00001301542 | fastq.bz2 | 1.3 GB | ||
EGAF00001301543 | fastq.bz2 | 1.3 GB | ||
EGAF00001301544 | fastq.bz2 | 912.3 MB | ||
EGAF00001301545 | fastq.bz2 | 1.1 GB | ||
EGAF00001301546 | fastq.bz2 | 957.3 MB | ||
EGAF00001301547 | fastq.bz2 | 1.1 GB | ||
EGAF00001301548 | fastq.bz2 | 2.0 GB | ||
EGAF00001301549 | fastq.bz2 | 2.1 GB | ||
EGAF00001301550 | fastq.bz2 | 956.0 MB | ||
EGAF00001301551 | fastq.bz2 | 1.1 GB | ||
EGAF00001301552 | fastq.bz2 | 899.5 MB | ||
EGAF00001301553 | fastq.bz2 | 1.0 GB | ||
EGAF00001301554 | fastq.bz2 | 853.5 MB | ||
EGAF00001301555 | fastq.bz2 | 965.2 MB | ||
EGAF00001301556 | fastq.bz2 | 998.8 MB | ||
EGAF00001301557 | fastq.bz2 | 1.2 GB | ||
EGAF00001301558 | fastq.bz2 | 773.5 MB | ||
EGAF00001301559 | fastq.bz2 | 846.0 MB | ||
EGAF00001301560 | fastq.bz2 | 957.4 MB | ||
EGAF00001301561 | fastq.bz2 | 1.1 GB | ||
EGAF00001301562 | fastq.bz2 | 754.4 MB | ||
EGAF00001301563 | fastq.bz2 | 884.8 MB | ||
EGAF00001301564 | fastq.bz2 | 807.3 MB | ||
EGAF00001301565 | fastq.bz2 | 923.7 MB | ||
EGAF00001301566 | fastq.bz2 | 822.4 MB | ||
EGAF00001301567 | fastq.bz2 | 946.0 MB | ||
EGAF00001301568 | fastq.bz2 | 846.2 MB | ||
EGAF00001301569 | fastq.bz2 | 947.1 MB | ||
EGAF00001301570 | fastq.bz2 | 1.1 GB | ||
EGAF00001301571 | fastq.bz2 | 1.2 GB | ||
EGAF00001301572 | fastq.bz2 | 921.8 MB | ||
EGAF00001301573 | fastq.bz2 | 1.0 GB | ||
EGAF00001301574 | fastq.bz2 | 771.7 MB | ||
EGAF00001301575 | fastq.bz2 | 878.0 MB | ||
EGAF00001301576 | fastq.bz2 | 937.5 MB | ||
EGAF00001301577 | fastq.bz2 | 1.1 GB | ||
EGAF00001301578 | fastq.bz2 | 717.9 MB | ||
EGAF00001301579 | fastq.bz2 | 824.6 MB | ||
EGAF00001301580 | fastq.bz2 | 858.8 MB | ||
EGAF00001301581 | fastq.bz2 | 947.8 MB | ||
EGAF00001301582 | fastq.bz2 | 819.2 MB | ||
EGAF00001301583 | fastq.bz2 | 937.7 MB | ||
EGAF00001301584 | fastq.bz2 | 734.0 MB | ||
EGAF00001301585 | fastq.bz2 | 808.4 MB | ||
EGAF00001301586 | fastq.bz2 | 897.8 MB | ||
EGAF00001301587 | fastq.bz2 | 1.0 GB | ||
EGAF00001301588 | fastq.bz2 | 946.1 MB | ||
EGAF00001301589 | fastq.bz2 | 1.0 GB | ||
EGAF00001301590 | fastq.bz2 | 149.7 MB | ||
EGAF00001301591 | fastq.bz2 | 162.6 MB | ||
EGAF00001301592 | fastq.bz2 | 878.3 MB | ||
EGAF00001301593 | fastq.bz2 | 999.8 MB | ||
EGAF00001301594 | fastq.bz2 | 804.7 MB | ||
EGAF00001301595 | fastq.bz2 | 904.8 MB | ||
EGAF00001301596 | fastq.bz2 | 1.1 GB | ||
EGAF00001301597 | fastq.bz2 | 1.2 GB | ||
EGAF00001301598 | fastq.bz2 | 994.6 MB | ||
EGAF00001301599 | fastq.bz2 | 1.1 GB | ||
EGAF00001301600 | fastq.bz2 | 1.0 GB | ||
EGAF00001301601 | fastq.bz2 | 1.1 GB | ||
EGAF00001301602 | fastq.bz2 | 738.1 MB | ||
EGAF00001301603 | fastq.bz2 | 873.0 MB | ||
EGAF00001302956 | fastq.bz2 | 153.0 MB | ||
EGAF00001302957 | fastq.bz2 | 167.7 MB | ||
EGAF00001302958 | fastq.bz2 | 854.1 MB | ||
EGAF00001302959 | fastq.bz2 | 934.9 MB | ||
EGAF00001302960 | fastq.bz2 | 989.2 MB | ||
EGAF00001302961 | fastq.bz2 | 1.1 GB | ||
EGAF00001302962 | fastq.bz2 | 995.5 MB | ||
EGAF00001302963 | fastq.bz2 | 1.1 GB | ||
EGAF00001302964 | fastq.bz2 | 1.0 GB | ||
EGAF00001302965 | fastq.bz2 | 1.1 GB | ||
EGAF00001302966 | fastq.bz2 | 667.5 MB | ||
EGAF00001302967 | fastq.bz2 | 725.3 MB | ||
74 Files (69.7 GB) |